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https://en.wikipedia.org/wiki/Transforming%20growth%20factor%2C%20beta%203 | Transforming growth factor beta-3 is a protein that in humans is encoded by the gene.
It is a type of protein, known as a cytokine, which is involved in cell differentiation, embryogenesis and development. It belongs to a large family of cytokines called the Transforming growth factor beta superfamily, which includes the TGF-β family, Bone morphogenetic proteins (BMPs), growth and differentiation factors (GDFs), inhibins and activins.
TGF-β3 is believed to regulate molecules involved in cellular adhesion and extracellular matrix (ECM) formation during the process of palate development. Without TGF-β3, mammals develop a deformity known as a cleft palate. This is caused by failure of epithelial cells in both sides of the developing palate to fuse. TGF-β3 also plays an essential role in controlling the development of lungs in mammals, by also regulating cell adhesion and ECM formation in this tissue, and controls wound healing by regulating the movements of epidermal and dermal cells in injured skin.
Interactions
Transforming growth factor, beta 3 has been shown to interact with TGF beta receptor 2.
Clinical research
After successful phase I/II trials, human recombinant TGF-β3 (Avotermin, planned trade name Juvista) failed in Phase III trials.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy, Autosomal Dominant
OMIM entries on Arrhythmogenic Right Ventricular Dysplasia/Cardiomyo |
https://en.wikipedia.org/wiki/NK2%20homeobox%201 | NK2 homeobox 1 (NKX2-1), also known as thyroid transcription factor 1 (TTF-1), is a protein which in humans is encoded by the NKX2-1 gene.
Function
Thyroid transcription factor-1 (TTF-1) is a protein that regulates transcription of genes specific for the thyroid, lung, and diencephalon. It is also known as thyroid specific enhancer binding protein. It is used in anatomic pathology as a marker to determine if a tumor arises from the lung or thyroid. NKX2.1 can be induced by activin A via SMAD2 signaling in a human embryonic stem cell differentiation model.
NKX2.1 is key to the fetal development of lung structures. The dorsal-ventral pattern of NKX2.1 expression forms the ventral boundary in the anterior foregut. NKX2.1 is expressed only in select cells in the ventral wall of the anterior foregut, and is not expressed in the dorsal wall, where the esophagus will emerge from. NKX2.1 knockout in mice results in the development of a shortened trachea which is fused to the esophagus, with the bronchi directly connecting this shared tube to the lungs. This resembles a complete tracheoesophageal fistula, which is a rare congenital condition in humans. Furthermore, distal lung structures do not develop in these knockout mice. Branching of the lungs in these mice did not occur past the main-stem bronchi, resulting in lungs that were smaller in size by about 50% compared to the wild-type mice. The epithelial lining of these distal structures did not show evidence of differentiatio |
https://en.wikipedia.org/wiki/Tropomyosin%203 | Tropomyosin alpha-3 chain is a protein that in humans is encoded by the TPM3 gene.
This gene encodes a member of the tropomyosin family of actin-binding proteins involved in the contractile system of striated and smooth muscles and the cytoskeleton of non-muscle cells. Tropomyosins are dimers of coiled-coil proteins that polymerize end-to-end along the major groove in most actin filaments. They provide stability to the filaments and regulate access of other actin-binding proteins. In muscle cells, they regulate muscle contraction by controlling the binding of myosin heads to the actin filament. Mutations in this gene result in autosomal dominant nemaline myopathy, and oncogenes formed by chromosomal translocations involving this locus are associated with cancer. Multiple transcript variants encoding different isoforms have been found for this gene.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Nemaline Myopathy |
https://en.wikipedia.org/wiki/YES1 | Proto-oncogene tyrosine-protein kinase Yes is a non-receptor tyrosine kinase that in humans is encoded by the YES1 gene.
This gene is the cellular homolog of the Yamaguchi sarcoma virus oncogene. The encoded protein has tyrosine kinase activity and belongs to the src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22.
Interactions
YES1 has been shown to interact with Janus kinase 2, CTNND1, RPL10 and Occludin.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Rad50 | DNA repair protein RAD50, also known as RAD50, is a protein that in humans is encoded by the RAD50 gene.
Function
The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Rad50, a protein involved in DNA double-strand break repair. This protein forms a complex with MRE11 and NBS1 (also known as Xrs2 in yeast). This MRN complex (MRX complex in yeast) binds to broken DNA ends and displays numerous enzymatic activities that are required for double-strand break repair by nonhomologous end-joining or homologous recombination. Gene knockout studies of the mouse homolog of Rad50 suggest it is essential for cell growth and viability. Two alternatively spliced transcript variants of Rad50, which encode distinct proteins, have been reported.
Structure
Rad50 is a member of the structural maintenance of chromosomes (SMC) family of proteins. Like other SMC proteins, Rad50 contains a long internal coiled-coil domain that folds back on itself, bringing the N- and C-termini together to form a globular ABC ATPase head domain. Rad50 can dimerize both through its head domain and through a zinc-binding dimerization motif at the opposite end of the coiled-coil known as the “zinc-hook”. Results from atomic force microscopy suggest that in free Mre11-Rad50-Nbs1 complexes, the zinc-hooks of a single Rad50 dimer associate to form a closed loop, while the zinc-hooks snap apart upon binding DNA, adopting a conformation that is thought to enable zinc-hook-mediated tethering |
https://en.wikipedia.org/wiki/ADAM10 | A Disintegrin and metalloproteinase domain-containing protein 10, also known as ADAM10 or CDw156 or CD156c is a protein that in humans is encoded by the ADAM10 gene.
Function
Members of the ADAM family are cell surface proteins with a unique structure, possessing both potential adhesion and protease domains. Sheddase, a generic name for the ADAM metallopeptidase, functions primarily to cleave membrane proteins at the cellular surface. Once cleaved, the sheddases release soluble ectodomains with an altered location and function.
Although a single sheddase may “shed” a variety of substances, multiple sheddases can cleave the same substrate resulting in different consequences. This gene encodes an ADAM family member that cleaves many proteins including TNF-alpha and E-cadherin.
ADAM10 (EC#: 3.4.24.81) is a sheddase, and has a broad specificity for peptide hydrolysis reactions.
ADAM10 cleaves ephrin, within the ephrin/eph complex, formed between two cell surfaces. When ephrin is freed from the opposing cell, the entire ephrin/eph complex is endocytosed. This shedding in trans had not been previously shown, but may well be involved in other shedding events.
In neurons, ADAM10 is the most important enzyme, with α-secretase activity for proteolytic processing of the amyloid precursor protein. ADAM10, along with ADAM17, cleaves the ectodomain of the triggering receptor expressed on myeloid cells 2 (TREM2), to produce soluble TREM2 (sTREM2), which has been proposed as a CSF and |
https://en.wikipedia.org/wiki/ADAR | The double-stranded RNA-specific adenosine deaminase enzyme family are encoded by the ADAR family genes. ADAR stands for adenosine deaminase acting on RNA. This article focuses on the ADAR proteins; This article details the evolutionary history, structure, function, mechanisms and importance of all proteins within this family.
ADAR enzymes bind to double-stranded RNA (dsRNA) and convert adenosine to inosine (hypoxanthine) by deamination. ADAR proteins act post-transcriptionally, changing the nucleotide content of RNA. The conversion from adenosine to inosine (A to I) in the RNA disrupts the normal A:U pairing, destabilizing the RNA. Inosine is structurally similar to guanine (G) which leads to inosine to cytosine (I:C) binding. Inosine typically mimics guanosine during translation but can also bind to uracil, cytosine, and adenosine, though it is not favored.
Codon changes may arise from RNA editing leading to changes in the coding sequences for proteins and their functions. Most editing sites are found in noncoding regions of RNA such as untranslated regions (UTRs), Alu elements, and long interspersed nuclear elements (LINEs). Codon changes can give rise to alternate transcriptional splice variants. ADAR impacts the transcriptome in editing-independent ways, likely by interfering with other RNA-binding proteins.
Mutations in this gene are associated with several diseases including HIV, measles, and melanoma. Recent research supports a linkage between RNA-editing and ner |
https://en.wikipedia.org/wiki/ADD1 | Alpha-adducin is a protein that in humans is encoded by the ADD1 gene.
Adducins are a family of cytoskeleton proteins encoded by three genes (alpha, beta, gamma). Adducin is a heterodimeric protein that consists of related subunits, which are produced from distinct genes but share a similar structure. Alpha- and beta-adducin include a protease-resistant N-terminal region and a protease-sensitive, hydrophilic C-terminal region. Alpha- and gamma-adducins are ubiquitously expressed. In contrast, beta-adducin is expressed at high levels in brain and hematopoietic tissues. Adducin binds with high affinity to Ca(2+)/calmodulin and is a substrate for protein kinases A and C. Alternative splicing results in multiple variants encoding distinct isoforms; however, not all variants have been fully described. Polymorphism in ADD1 is associated with hypertension.
References
External links
Further reading |
https://en.wikipedia.org/wiki/AKR1B1 | Aldo-keto reductase family 1, member B1 (AKR1B1), also known as aldose reductase, is an enzyme that is encoded by the AKR1B1 gene in humans. It is a reduced nicotinamide-adenine dinucleotide phosphate (NADPH)-dependent enzyme catalyzing the reduction of various aldehydes and ketones to the corresponding alcohol. The involvement of AKR1B1 in oxidative stress diseases, cell signal transduction, and cell proliferation process endows AKR1B1 with potential as a therapeutic target.
Structure
Gene
The AKR1B1 gene lies on the chromosome location of 7q33 and consists of 10 exons. There are a few putative pseudogenes for this gene, and one of them has been confirmed and mapped to chromosome 3.
Protein
AKR1B1 consists of 316 amino acid residues and weighs 35853Da. It does not possess the traditional dinucleotide binding fold. The way it binds NADPH differs from other nucleotide adenine dinucleotide-dependent enzymes. The active site pocket of human aldose reductase is relatively hydrophobic, lined by seven aromatic and four other non-polar residues.
Function
AR belongs to the aldehyde-keto reductase superfamily, with a widely expression in human organs including the kidney, lens, retina, nerve, heart, placenta, brain, skeletal muscle, testis, blood vessels, lung, and liver. It is a reduced nicotinamide-adenine dinucleotide phosphate (NADPH)-dependent enzyme catalyzing the reduction of various aldehydes and ketones to the corresponding alcohol. It also participates in glucose me |
https://en.wikipedia.org/wiki/ATRX | Transcriptional regulator ATRX also known as ATP-dependent helicase ATRX, X-linked helicase II, or X-linked nuclear protein (XNP) is a protein that in humans is encoded by the ATRX gene.
Function
Transcriptional regulator ATRX contains an ATPase / helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. ATRX is required for deposition of the histone variant H3.3 at telomeres and other genomic repeats. These interactions are important for maintaining silencing at these sites.
In addition, ATRX undergoes cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis.
Clinical significance
Inherited mutations
Inherited mutations of the ATRX gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATR-X) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. Female carriers may demonstrate skewed X chromosome inactivation.
Somatic mutations
Acquired mutations in ATRX have been reported in a number of human cancers including pancreatic neuroendocrine tumours, gliomas, osteo |
https://en.wikipedia.org/wiki/Carbonic%20anhydrase%209 | Carbonic anhydrase IX (CA9/CA IX) is an enzyme that in humans is encoded by the CA9 gene. It is one of the 14 carbonic anhydrase isoforms found in humans and is a transmembrane dimeric metalloenzyme with an extracellular active site that facilitates acid secretion in the gastrointestinal tract. CA IX is overexpressed in many types of cancer including clear cell renal cell carcinoma (RCC) as well as carcinomas of the cervix, breast and lung where it promotes tumor growth by enhancing tumor acidosis.
Function
Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva, and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization.
CA IX is mainly expressed in the gastrointestinal tract where it facilitates acid secretion. The CA IX enzyme, along with the CA II enzyme, binds to Anion Exchanger 2 (AE2) which increases bicarbonate transport and maximizes the rate of acid secretion by gastric parietal cells.
Structure
CA IX is a transmembrane glycoprotein with an extracellular active site. The cytoplasmic tail of the enzyme contains three residues that may be phosphorylated (Thr-443, Ser-448, and Tyr-449) and participate in signal transduction. Phosphorylated tyrosine 449 c |
https://en.wikipedia.org/wiki/Cyclin-dependent%20kinase%20inhibitor%201C | Cyclin-dependent kinase inhibitor 1C (p57, Kip2), also known as CDKN1C, is a protein which in humans is encoded by the CDKN1C imprinted gene.
Function
Cyclin-dependent kinase inhibitor 1C is a tight-binding inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations of CDKN1C are implicated in sporadic cancers and Beckwith-Wiedemann syndrome suggesting that it is a tumor suppressor candidate.
CDKN1C is a tumor suppressor human gene on chromosome 11 (11p15) and belongs to the cip/kip gene family. It encodes a cell cycle inhibitor that binds to G1 cyclin-CDK complexes. Thus p57KIP2 causes arrest of the cell cycle in G1 phase.
CDKN1C was found to lead to cancer cell dormancy; its gene expression is regulated through the activity of glucocorticoid receptors (GRs) through chromatin remodelling mediated by SWI/SNF.
Research Methods
Since it has been identified that mutation to this tumor suppressing gene can have dramatic effects in a newborn such as macroglossia there has been great research to determine the genetic significance. CDKN1C is prone to error during the process of gene imprinting. The process of gene imprinting is in concert with DNA methylation. This goes makes the gene become transcriptionally silent from the paternal side allowing the maternal gene to be active. If this gene fails to be properly methylated, or obtains a mutation, there will be a lack of cell cycle suppression leading to the pediatric tumor growth. |
https://en.wikipedia.org/wiki/Multidrug%20resistance-associated%20protein%202 | Multidrug resistance-associated protein 2 (MRP2) also called canalicular multispecific organic anion transporter 1 (cMOAT) or ATP-binding cassette sub-family C member 2 (ABCC2) is a protein that in humans is encoded by the ABCC2 gene.
Function
MRP2 is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). More specifically, this protein is a member of the MRP subfamily, which is involved in multi-drug resistance. This protein is expressed in the canalicular (apical) part of the hepatocyte and functions in biliary transport. Substrates include anticancer drugs such as vinblastine; therefore, this protein appears to contribute to drug resistance in mammalian cells.
MRP2 is also expressed in the apical membrane of proximal renal tubule endothelial cells where they are involved in the excretion of small organic anions.
MRP2 inhibitors
Clinical significance
Dubin–Johnson syndrome
Several different mutations in this gene have been observed in patients with Dubin–Johnson syndrome (DJS), an autosomal recessive disorder characterized by conjugated hyperbilirubinemia.
Iatrogenic Fanconi syndrome
Many negatively charged metabolic waste products are eliminated from the body by the kidneys. These organic anions are transported from the blood into the endothelial cells of the |
https://en.wikipedia.org/wiki/FGR%20%28gene%29 | Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog, also known as FGR, is a protein which in humans is encoded by the FGR gene.
Function
This gene is a member of the Src family of protein tyrosine kinases (PTKs). The encoded protein contains N-terminal sites for myristoylation and palmitoylation, a PTK domain, and SH2 and SH3 domains which are involved in mediating protein-protein interactions with phosphotyrosine-containing and proline-rich motifs, respectively. The protein localizes to plasma membrane ruffles, and functions as a negative regulator of cell migration and adhesion triggered by the beta-2 integrin signal transduction pathway. Infection with Epstein–Barr virus results in the overexpression of this gene. Multiple alternatively spliced variants, encoding the same protein, have been identified.
Discovery
The feline version of this gene was discovered by Suraiya Rasheed, Murray Gardner, and co-workers.
Interactions
FGR (gene) has been shown to interact with Wiskott–Aldrich syndrome protein.
References
Further reading
Tyrosine kinases |
https://en.wikipedia.org/wiki/GATA3 | GATA3 is a transcription factor that in humans is encoded by the GATA3 gene. Studies in animal models and humans indicate that it controls the expression of a wide range of biologically and clinically important genes.
The GATA3 transcription factor is critical for the embryonic development of various tissues as well as for inflammatory and humoral immune responses and the proper functioning of the endothelium of blood vessels. GATA3 plays central role in allergy and immunity against worm infections. GATA3 haploinsufficiency (i.e. loss of one or the two inherited GATA3 genes) results in a congenital disorder termed the Barakat syndrome.
Current clinical and laboratory research is focusing on determining the benefits of directly or indirectly blocking the action of GATA3 in inflammatory and allergic diseases such as asthma. It is also proposed to be a clinically important marker for various types of cancer, particularly those of the breast. However, the role, if any, of GATA3 in the development of these cancers is under study and remains unclear.
Gene
The GATA3 gene is located close to the end of the short arm of chromosome 10 at position p14. It consists of 8 exons, and codes for two variants viz., GATA3, variant 1, and GATA3, variant 2. Expression of GATA3 may be regulated in part or at times by the antisense RNA, GATA3-AS1, whose gene is located close to the GATA3 gene on the short arm of chromosome 10 at position p14. Various types of mutations including point mutation |
https://en.wikipedia.org/wiki/Granulin | Granulin is a protein that in humans is encoded by the GRN gene. Each granulin protein is cleaved from the precursor progranulin, a 593 amino-acid-long and 68.5 kDa protein. While the function of progranulin and granulin have yet to be determined, both forms of the protein have been implicated in development, inflammation, cell proliferation and protein homeostasis. The 2006 discovery of the GRN mutation in a population of patients with frontotemporal dementia has spurred much research in uncovering the function and involvement in disease of progranulin in the body. While there is a growing body of research on progranulin's role in the body, studies on specific granulin residues are still limited.
Progranulin
Progranulin is the precursor protein for granulin. Cleavage of progranulin produces a variety of active 6 kDa granulin peptides. These smaller cleavage products are named granulin A, granulin B, granulin C, etc. Epithelins 1 and 2 are synonymous with granulins A and B, respectively. Cleavage of progranulin into granulin occurs either in the extracellular matrix or the lysosome. Elastase, proteinase 3 and matrix metalloproteinase are proteases capable of cleaving progranulin into individual granulin peptides. Progranulin and granulin can be further differentiated by their hypothesized opposing roles in the cell. While progranulin is associated with anti-inflammation, cleaved granulin peptides have been implicated in pro-inflammatory behavior. A C. elegans study showed t |
https://en.wikipedia.org/wiki/MAP3K1 | Mitogen-activated protein kinase kinase kinase 1 (MAP3K1) is a signal transduction enzyme that in humans is encoded by the autosomal MAP3K1 gene.
Function
MAP3K1 (or MEKK1) is a serine/threonine kinase and ubiquitin ligase that performs a pivotal role in a network of enzymes integrating cellular receptor responses to a number of mitogenic and metabolic stimuli, including: TNF receptor superfamily (TNFRs), T-cell receptor (TCR), Epidermal growth factor receptor (EGFR), and TGF beta receptor (TGFβR). Mitogen-activated protein kinase kinases (MAP2Ks) are substrates for direct phosphorylation by the MAP3K1 protein kinase. The MAP3K1 kinase domain may also be a modest activator of IκB kinase activation. The MAP3K1 E3 ubiquitin ligase recruits a ubiquitin-conjugating enzyme (including UBE2D2, UBE2D3, and UBE2N:UBE2V1) that has been loaded with ubiquitin, interacts with its substrates, and facilitates the transfer of ubiquitin from the ubiquitin-conjugating enzyme onto its substrates. Genetics has revealed that MAP3K1 is important in: embryonic development, tumorigenesis, cell growth, cell migration, cytokine production, and humoral immunity. MAP3K1 mutants were identified in breast cancer by GWAS.
Structure
MAP3K1 contains a protein kinase domain, PHD finger (which has a RING finger domain-like structure) that serves as an E3 ubiquitin ligase, and scaffold protein regions that mediate protein–protein interactions.
Genetic analyses in murine and avian models
MAP3K1 is hig |
https://en.wikipedia.org/wiki/MED1 | Mediator of RNA polymerase II transcription subunit 1 also known as DRIP205 or Trap220 is a subunit of the Mediator complex and is a protein that in humans is encoded by the MED1 gene. MED1 functions as a nuclear receptor coactivator.
Function
The activation of gene transcription is a multistep process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators to direct transcriptional initiation by the RNA polymerase II apparatus. The mediator of RNA polymerase II transcription subunit 1 protein is a subunit of the CRSP (cofactor required for SP1 activation) complex, which, along with TFIID, is required for efficient activation by SP1. This protein is also a component of other multisubunit complexes [e.g., thyroid hormone receptor-(TR-) associated proteins that interact with TR and facilitate TR function on DNA templates in conjunction with initiation factors and cofactors]. It also regulates p53-dependent apoptosis and it is essential for adipogenesis. This protein is known to have the ability to self-oligomerize.
Interactions
MED1 has been shown to interact with:
Androgen receptor,
BRCA1,
Calcitriol receptor,
Cyclin-dependent kinase 8,
Estrogen receptor alpha,
Glucocorticoid receptor,
Hepatocyte nuclear factor 4 alpha,
P53,
PPARGC1A,
PPARG,
TGS1, and
Thyroid hormone receptor alpha.
Protein family
This entry represents subunit Med1 of the Mediator complex. The Med1 forms part of th |
https://en.wikipedia.org/wiki/SCN1A | Sodium channel protein type 1 subunit alpha (SCN1A), is a protein which in humans is encoded by the SCN1A gene.
Gene location
The SCN1A gene is located on chromosome 2 of humans, and is made up of 26 exons spanning a total length of 6030 nucleotide base pairs. Alternative splicing of exon 5 gives rise to two alternate exons. The promoter has been identified 2.5 kilobase pairs upstream of the transcription start site, and the 5'- untranslated exons may enhance expression of the SCN1A gene in SH-SY5Y cells, a human cell line derived from a neuroblastoma.
Function
The vertebrate sodium channel is a voltage-gated ion channel essential for the generation and propagation of action potentials, chiefly in nerve and muscle. Voltage-sensitive sodium channels are heteromeric complexes consisting of a large central pore-forming glycosylated alpha subunit and 2 smaller auxiliary beta subunits. Functional studies have indicated that the transmembrane alpha subunit of the brain sodium channels is sufficient for expression of functional sodium channels. Brain sodium channel alpha subunits form a gene subfamily with several structurally distinct isoforms clustering on chromosome 2q24, types I, II (Nav1.2), and III (Nav1.3). There are also several distinct sodium channel alpha subunit isoforms in skeletal and cardiac muscle (Nav1.4 and Nav1.5, respectively).
The SCN1A gene codes for the alpha subunit of the voltage-gated sodium ion channel making it a member of ten paralogous gene famili |
https://en.wikipedia.org/wiki/SLPI | Antileukoproteinase, also known as secretory leukocyte protease inhibitor (SLPI), is an enzyme that in humans is encoded by the SLPI gene. SLPI is a highly cationic single-chain protein with eight intramolecular disulfide bonds. It is found in large quantities in bronchial, cervical, and nasal mucosa, saliva, and seminal fluids. SLPI inhibits human leukocyte elastase, human cathepsin G, human trypsin, neutrophil elastase, and mast cell chymase. X-ray crystallography has shown that SLPI has two homologous domains of 53 and 54 amino acids, one of which exhibits anti-protease activity (C-terminal domain). The other domain (N-terminal domain) is not known to have any function.
Function
This gene encodes a secreted inhibitor which protects epithelial tissues from serine proteases. It is found in various secretions including seminal plasma, cervical mucus, and bronchial secretions, and has affinity for trypsin, leukocyte elastase, and cathepsin G. Its inhibitory effect contributes to the immune response by protecting epithelial surfaces from attack by endogenous proteolytic enzymes; the protein is also thought to have broad-spectrum antibiotic activity.
Clinical significance
The gene for SLPI is expressed by cells at many mucosal surfaces located in the tissues of the lungs, cervix, seminal vesicles, and parotid ducts. SLPI is also one of the dominantly present proteins in nasal epithelial lining fluid and other nasal secretions. Tissue SLPI expression reveals a clear compa |
https://en.wikipedia.org/wiki/Sj%C3%B6gren%20syndrome%20antigen%20B | Sjögren syndrome type B antigen (SS-B) also known as Lupus La protein is a protein that in humans is encoded by the SSB gene.
Function
La is involved in diverse aspects of RNA metabolism, including binding and protecting 3-prime UUU (OH) elements of newly RNA polymerase III-transcribed RNA, processing 5-prime and 3-prime ends of pre-tRNA precursors, acting as an RNA chaperone, and binding viral RNAs associated with hepatitis C virus. La protein was originally defined by its reactivity with autoantibodies from patients with Sjögren's syndrome and systemic lupus erythematosus.
Interactions
Sjögren syndrome antigen B has been shown to interact with nucleolin.
See also
La domain
References
Further reading |
https://en.wikipedia.org/wiki/SULT1A1 | Sulfotransferase 1A1 is an enzyme that in humans is encoded by the SULT1A1 gene.
Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene.
The SULT1A1 enzyme is expressed in outer roots sheath of hair follicles. Minoxidil, the only US FDA approved topical drug for re-growing hair in male and female pattern hair loss (androgenetic alopecia patients) is a pro-drug. Minoxidil is converted to its active form (minoxidil sulfate) by the hair sulfotransferase enzyme (SULT1A1). A large variability in sulfotransferase enzyme expression in hair is observed among people. Low sulfotransferase activity was found to be predictive to lack of response to topical minoxidil for hair re-growth. In a clinical study, a novel formula using a hypoxia mimetic pathway demonstrated to increase SULT1A1 activity in human subjects in-vivo.
See also
Steroid sulfotransferase
Steroidogenic enzyme
References
Further reading |
https://en.wikipedia.org/wiki/Uracil-DNA%20glycosylase | Uracil-DNA glycosylase (also known as UNG or UDG) is an enzyme. Its most important function is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway.
Function
The human gene encodes one of several uracil-DNA glycosylases. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway. Uracil bases occur from cytosine deamination or misincorporation of dUMP residues. After a mutation occurs, the mutagenic threat of uracil propagates through any subsequent DNA replication steps. Once unzipped, mismatched guanine and uracil pairs are separated, and DNA polymerase inserts complementary bases to form a guanine-cytosine (GC) pair in one daughter strand and an adenine-uracil (AU) pair in the other. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site. UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes. With high efficiency and specificity, this glycosylase repairs 100–500 bases damaged daily in the human cell. Human cells express five to six types of DNA glycosylases, all o |
https://en.wikipedia.org/wiki/USF1 | Upstream stimulatory factor 1 is a protein that in humans is encoded by the USF1 gene.
Function
This gene encodes a member of the basic helix-loop-helix leucine zipper family and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene.
A study of mice suggested reduced USF1 levels increases metabolism in brown fat.
Interactions
USF1 (human gene) has been shown to interact with USF2, FOSL1 and GTF2I.
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/Vasodilator-stimulated%20phosphoprotein | Vasodilator-stimulated phosphoprotein is a protein that in humans is encoded by the VASP gene.
Function
Vasodilator-stimulated phosphoprotein (VASP) is a member of the Ena-VASP protein family. Ena-VASP family members contain an N-terminal EVH1 domain that binds proteins containing E/DFPPPPXD/E motifs and targets Ena-VASP proteins to focal adhesions cell membranes. In the mid-region of the protein, family members have a proline-rich region that binds SH3 and WW domain-containing proteins. Their C-terminal EVH2 domain mediates tetramerization and binds both G and F actin. VASP is associated with filamentous actin formation and likely plays a widespread role in cell adhesion and motility. VASP may also be involved in the intracellular signaling pathways that regulate integrin-extracellular matrix interactions. VASP is regulated by the cyclic nucleotide-dependent kinases PKA and PKG.
Interactions
Vasodilator-stimulated phosphoprotein has been shown to interact with Zyxin, Profilin 1, and PFN2.
References
Further reading
EVH1 domain |
https://en.wikipedia.org/wiki/XPC%20%28gene%29 | Xeroderma pigmentosum, complementation group C, also known as XPC, is a protein which in humans is encoded by the XPC gene. XPC is involved in the recognition of bulky DNA adducts in nucleotide excision repair. It is located on chromosome 3.
Function
This gene encodes a component of the nucleotide excision repair (NER) pathway. There are multiple components involved in the NER pathway, including Xeroderma pigmentosum (XP) A-G and V, Cockayne syndrome (CS) A and B, and trichothiodystrophy (TTD) group A, etc. This component, XPC, plays an important role in the early steps of global genome NER, especially in damage recognition, open complex formation, and repair protein complex formation.
The complex of XPC-RAD23B is the initial damage recognition factor in global genomic nucleotide excision repair (GG-NER). XPC-RAD23B recognizes a wide variety of lesions that thermodynamically destabilize DNA duplexes, including UV-induced photoproducts (cyclopyrimidine dimers and 6-4 photoproducts ), adducts formed by environmental mutagens such as benzo[a]pyrene or various aromatic amines, certain oxidative endogenous lesions such as cyclopurines and adducts formed by cancer chemotherapeutic drugs such as cisplatin. The presence of XPC-RAD23B is required for assembly of the other core NER factors and progression through the NER pathway both in vitro and in vivo. Although most studies have been performed with XPC-RAD23B, it is part of a trimeric complex with centrin-2, a calcium-binding p |
https://en.wikipedia.org/wiki/PIAS1 | E3 SUMO-protein ligase PIAS1 is an enzyme that in humans is encoded by the PIAS1 gene.
Function
This gene encodes a member of the mammalian PIAS [protein inhibitor of activated STAT-1 (signal transducer and activator of transcription-1)] family. This member contains a putative zinc-binding motif and a highly acidic region. It inhibits STAT1-mediated gene activation and the DNA binding activity, binds to Gu protein/RNA helicase II/DEAD box polypeptide 21, and interacts with androgen receptor (AR). It functions in testis as a nuclear receptor transcriptional coregulator and may have a role in AR initiation and maintenance of spermatogenesis.
Interactions
PIAS1 has been shown to interact with:
DNMT3A,
P53,
STAT1,
Small ubiquitin-related modifier 1,
Sp3 transcription factor, and
UBE2I.
References
Further reading |
https://en.wikipedia.org/wiki/BCL10 | B-cell lymphoma/leukemia 10 is a protein that in humans is encoded by the BCL10 gene. Like BCL2, BCL3, BCL5, BCL6, BCL7A, and BCL9, it has clinical significance in lymphoma.
Function
Bcl10 was identified by its translocation in a case of mucosa-associated lymphoid tissue (MALT) lymphoma. The protein encoded by this gene contains a caspase recruitment domain (CARD), and has been shown to activate NF-κB. This protein is reported to interact with other CARD and coiled coil domain containing proteins including CARD9, -10, -11 and -14, which are thought to function as upstream regulators in NF-κB signaling. This protein is found to form a complex with the paracaspase MALT1, a protein encoded by another gene known to be translocated in MALT lymphoma. MALT1 and Bcl10 thought to synergize in the activation of NF-κB, and the deregulation of either of them may contribute to the same pathogenetic process that leads to the malignancy. Bcl10 is evolutionary conserved since cnidaria and has been shown to be functionally conserved all the way back to zebrafish. Notably, just like the upstream CARD-CC family, Bcl10 is absent in insects and nematodes, and the correlated phylogenetic distribution of Bcl10 and CARD-CC proteins indicate a conserved complex.
Interactions
BCL10 has been shown to interact with:
CARD10,
CARD11,
CARD14,
CARD9
CRADD,
IKBKG,
MALT1, and
TRAF2.
References
External links
Further reading
Proteins
Tumor_suppre |
https://en.wikipedia.org/wiki/HGS%20%28gene%29 | Hepatocyte growth factor-regulated tyrosine kinase substrate is an enzyme that in humans is encoded by the HGS gene.
Interactions
HGS has been shown to interact with:
CLTC
DLG4,
EPS15,
IL2RB,
Merlin,
STAM2,
Signal transducing adaptor molecule
TSG101.
References
External links
PDBe-KB provides an overview of all the structure information available in the PDB for Human Hepatocyte growth factor-regulated tyrosine kinase substrate (HGS)
Further reading |
https://en.wikipedia.org/wiki/PTTG1 | Securin is a protein that in humans is encoded by the PTTG1 gene.
Function
The encoded protein is a homolog of yeast securin proteins, which prevent separins from promoting sister chromatid separation. It is an anaphase-promoting complex (APC) substrate that associates with a separin until activation of the APC. The gene product has transforming activity in vitro and tumorigenic activity in vivo, and the gene is highly expressed in various tumors. The gene product contains 2 PXXP motifs, which are required for its transforming and tumorigenic activities, as well as for its stimulation of basic fibroblast growth factor expression. It also contains a destruction box (D box) that is required for its degradation by the APC. The acidic C-terminal region of the encoded protein can act as a transactivation domain. The gene product is mainly a cytosolic protein, although it partially localizes in the nucleus.
Interactions
PTTG1 has been shown to interact with:
DNAJA1,
Ku70
P53,
PTTG1IP, and
RPS10.
Regulation
During Mitosis CDK1 phosphorylate PTTG1 at Ser-165. PTTG1 is down-regulated in melanoma cells in response to the cyclin-dependent kinase inhibitor PHA-848125.
References
Further reading |
https://en.wikipedia.org/wiki/ATPase%2C%20Na%2B/K%2B%20transporting%2C%20alpha%201 | {{DISPLAYTITLE:ATPase, Na+/K+ transporting, alpha 1}}
Sodium/potassium-transporting ATPase subunit alpha-1 is an enzyme that in humans is encoded by the ATP1A1 gene.
The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+-ATPases. Na+/K+-ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+-ATPase is encoded by multiple genes. This gene encodes an alpha 1 subunit. Alternatively spliced transcript variants encoding different isoforms have been identified.
In melanocytic cells ATP1A1 gene expression may be regulated by MITF.
Clinical relevance
Mutations in this gene have been associated with aldosterone-producing adenomas and secondary hypertension.
References
Further reading |
https://en.wikipedia.org/wiki/CD47 | CD47 (Cluster of Differentiation 47) also known as integrin associated protein (IAP) is a transmembrane protein that in humans is encoded by the CD47 gene. CD47 belongs to the immunoglobulin superfamily and partners with membrane integrins and also binds the ligands thrombospondin-1 (TSP-1) and signal-regulatory protein alpha (SIRPα). CD-47 acts as a don't eat me signal to macrophages of the immune system which has made it a potential therapeutic target in some cancers, and more recently, for the treatment of pulmonary fibrosis.
CD47 is involved in a range of cellular processes, including apoptosis, proliferation, adhesion, and migration. Furthermore, it plays a key role in immune and angiogenic responses. CD47 is ubiquitously expressed in human cells and has been found to be overexpressed in many different tumor cells. Expression in equine cutaneous tumors has been reported as well.
Structure
CD47 is a 50 kDa membrane receptor that has extracellular N-terminal IgV domain, five transmembrane domains, and a short C-terminal intracellular tail. There are four alternatively spliced isoforms of CD47 that differ only in the length of their cytoplasmic tail.
Form 2 is the most widely expressed form that is found in all circulating and immune cells. The second most abundant isoform is form 4, which is predominantly expressed in the brain and in the peripheral nervous system. Only keratinocytes expressed significant amounts of form 1. Little is known about the functional |
https://en.wikipedia.org/wiki/GADD45A | Growth arrest and DNA-damage-inducible protein GADD45 alpha is a protein that in humans is encoded by the GADD45A gene.
Function
This gene is a member of a group of genes, the GADD45 genes, whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents (mutagens). The DNA damage-induced transcription of this gene is mediated by both p53-dependent and -independent mechanisms. The protein encoded by this gene responds to environmental stresses by mediating activation of the p38/JNK pathway via MTK1/MEKK4 kinase.
Applications
The fact that expression of this gene is an indicator of DNA damage has been exploited to construct an in vitro test for mutagenicity, the GADD45a-GFP GreenScreen HC assay. This assay consists of a cell line which has been engineered so that expression of GADD45A will lead to expression of green fluorescent protein, which can easily be detected. To test a substance for mutagenicity, it is applied to these cells and fluorescence is measured.
Interactions
GADD45A has been shown to interact with:
AURKA,
Cdk1,
CCNB1,
GADD45GIP1
MAP3K4,
P21, and
PCNA.
See also
Gadd45
References
Further reading
External links |
https://en.wikipedia.org/wiki/HLA-DRB3 | HLA class II histocompatibility antigen, DRB3-1 beta chain is a protein that in humans is encoded by the HLA-DRB3 gene.
Function
The protein encoded by this gene belongs to the HLA class II beta chain paralogues. The class II molecule is a heterodimer consisting of an alpha (DRA) and a beta chain (DRB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen-presenting cells (APC: B lymphocytes, dendritic cells, macrophages).
Gene structure and polymorphisms
The beta chain is approximately 26–28 kDa. It is encoded by 6 exons, exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. Within the DR molecule the beta chain contains all the polymorphisms specifying the peptide binding specificities. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation.
Gene expression
DRB1 is expressed at a level five times higher than its paralogues DRB3, DRB4 and DRB5. DRB1 is present in all individuals. Allelic variants of DRB1 are linked with either none or one of the genes DRB3, DRB4 and DRB5. There are 4 related pseudogenes: DRB2, DRB6, DRB7, DRB8 and DRB9.
See also
HLA-DR
References
Further reading
Genes
Human proteins |
https://en.wikipedia.org/wiki/CD82%20%28gene%29 | CD82 (Cluster of Differentiation 82), or KAI1, is a human protein encoded by the gene.
This metastasis suppressor gene product is a membrane glycoprotein that is a member of the tetraspanin/transmembrane 4 superfamily. Expression of this gene has been shown to be downregulated in tumor progression of human cancers and can be activated by p53 through a consensus binding sequence in the promoter. Its expression and that of p53 are strongly correlated, and the loss of expression of these two proteins is associated with poor survival for prostate cancer patients. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
Interactions
CD82 (gene) has been shown to interact with CD19, CD63 and CD234.
CD82 plays a key role in the development of endometriosis.
See also
Cluster of differentiation
References
Further reading
External links
Clusters of differentiation |
https://en.wikipedia.org/wiki/LRP5 | Low-density lipoprotein receptor-related protein 5 is a protein that in humans is encoded by the LRP5 gene. LRP5 is a key component of the LRP5/LRP6/Frizzled co-receptor group that is involved in canonical Wnt pathway. Mutations in LRP5 can lead to considerable changes in bone mass. A loss-of-function mutation causes osteoporosis pseudoglioma syndrome with a decrease in bone mass, while a gain-of-function mutation causes drastic increases in bone mass.
Structure
LRP5 is a transmembrane low-density lipoprotein receptor that shares a similar structure with LRP6. In each protein, about 85% of its 1600-amino-acid length is extracellular. Each has four β-propeller motifs at the amino terminal end that alternate with four epidermal growth factor (EGF)-like repeats. Most extracellular ligands bind to LRP5 and LRP6 at the β-propellers. Each protein has a single-pass, 22-amino-acid segment that crosses the cell membrane and a 207-amino-acid segment that is internal to the cell.
Function
LRP5 acts as a co-receptor with LRP6 and the Frizzled protein family members for transducing signals by Wnt proteins through the canonical Wnt pathway. This protein plays a key role in skeletal homeostasis.
Transcription
The LRP5 promoter contains binding sites for KLF15 and SP1. In addition, 5' region of the LRP5 gene contains four RUNX2 binding sites. LRP5 has been shown in mice and humans to inhibit expression of TPH1, the rate-limiting biosynthetic enzyme for serotonin in enterochromaffin ce |
https://en.wikipedia.org/wiki/MAD2L1 | Mitotic spindle assembly checkpoint protein MAD2A is a protein that in humans is encoded by the MAD2L1 gene.
Function
MAD2L1 is a component of the mitotic spindle assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. MAD2L1 is related to the MAD2L2 gene located on chromosome 1. A MAD2 pseudogene has been mapped to chromosome 14.
Interactions
MAD2L1 has been shown to interact with:
ADAM17,
BUB1B,
CDC20,
CDC27 and
Estrogen receptor beta,
MAD2L2,
Mad1, and
UBD.
References
Further reading |
https://en.wikipedia.org/wiki/MX1 | Interferon-induced GTP-binding protein Mx1 is a protein that in humans is encoded by the MX1 gene.
In mice, the interferon-inducible Mx protein is responsible for a specific antiviral state against influenza virus infection. Furthermore, the human orthologue MxA is a major determinant for influenza viruses of animal origin. The protein encoded by this gene is similar to the mouse protein as determined by its antigenic relatedness, induction conditions, physicochemical properties, and amino acid analysis. This cytoplasmic protein is a member of both the dynamin superfamily and the family of large GTPases.
References
Further reading |
https://en.wikipedia.org/wiki/Glycylpeptide%20N-tetradecanoyltransferase%201 | Glycylpeptide N-tetradecanoyltransferase 1 also known as myristoyl-CoA:protein N-myristoyltransferase 1 (NMT-1) is an enzyme that in humans is encoded by the NMT1 gene. It belongs to the protein N-terminal methyltransferase and glycylpeptide N-tetradecanoyltransferase family of enzymes.
References
Further reading
See also
Myristoylation
N-myristoyltransferase 2
External links
EC 2.3.1
Human proteins |
https://en.wikipedia.org/wiki/Dynamin-like%20120%20kDa%20protein | Dynamin-like 120 kDa protein, mitochondrial is a protein that in humans is encoded by the OPA1 gene. This protein regulates mitochondrial fusion and cristae structure in the inner mitochondrial membrane (IMM) and contributes to ATP synthesis and apoptosis, and small, round mitochondria. Mutations in this gene have been implicated in dominant optic atrophy (DOA), leading to loss in vision, hearing, muscle contraction, and related dysfunctions.
Structure
Eight transcript variants encoding different isoforms, resulting from alternative splicing of exon 4 and two novel exons named 4b and 5b, have been reported for this gene. They fall under two types of isoforms: long isoforms (L-OPA1), which attach to the IMM, and short isoforms (S-OPA1), which localize to the intermembrane space (IMS) near the outer mitochondrial membrane (OMM). S-OPA1 is formed by proteolysis of L-OPA1 at the cleavage sites S1 and S2, removing the transmembrane domain.
Function
This gene product is a nuclear-encoded mitochondrial protein with similarity to dynamin-related GTPases. It is a component of the mitochondrial network. The OPA1 protein localizes to the inner mitochondrial membrane, where it regulates mitochondrial fusion and cristae structure. OPA1 mediates mitochondrial fusion in cooperation with mitofusins 1 and 2 and participates in cristae remodeling by the oligomerization of two L-OPA1 and one S-OPA1, which then interact with other protein complexes to alter cristae structure. Its cristae r |
https://en.wikipedia.org/wiki/Placental%20growth%20factor | Placental growth factor (PlGF) is a protein that in humans is encoded by the PGF gene.
Placental growth factor (PGF) is a member of the VEGF (vascular endothelial growth factor) sub-family - a key molecule in angiogenesis and vasculogenesis, in particular during embryogenesis. The main source of PGF during pregnancy is the placental trophoblast. PGF is also expressed in many other tissues, including the villous trophoblast.
The placental growth factor (PGF) gene is a protein-coding gene and a member of the vascular endothelial growth factor (VEGF) family. The PGF gene is expressed only in human umbilical vein endothelial cells (HUVE) and the placenta. PGF is ultimately associated with angiogenesis. Specifically, PGF plays a role in trophoblast growth and differentiation. Trophoblast cells, specifically extravillous trophoblast cells, are responsible for invading the uterine wall and the maternal spiral arteries. The extravillous trophoblast cells produce a blood vessel of larger diameter for the developing fetus that is independent of maternal vasoconstriction. This is essential for increased blood flow and reduced resistance. Proper development of blood vessels in the placenta is crucial for the higher blood requirement of the fetus later in pregnancy.
Under normal physiologic conditions, PGF is also expressed at a low level in other organs including the heart, lung, thyroid, and skeletal muscle.
Isoform tissue specificity
There are three isoforms of this protein: P |
https://en.wikipedia.org/wiki/PLCG2 | 1-Phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 is an enzyme that in humans is encoded by the PLCG2 gene.
Function
From OMIM as of March 24, 2020:
Enzymes of the phospholipase C family catalyze the hydrolysis of phospholipids to yield diacylglycerols and water-soluble phosphorylated derivatives of the lipid head groups. A number of these enzymes have specificity for phosphoinositides. Of the phosphoinositide-specific phospholipase C enzymes, C-beta is regulated by heterotrimeric G protein-coupled receptors, while the closely related C-gamma-1 (PLCG1; MIM 172420) and C-gamma-2 enzymes are controlled by receptor tyrosine kinases. The C-gamma-1 and C-gamma-2 enzymes are composed of phospholipase domains that flank regions of homology to noncatalytic domains of the SRC oncogene product, SH2 and SH3.
Interactions
PLCG2 has been shown to interact with:
Bruton's tyrosine kinase,
GAB2,
LYN,
PTPN11, and
SHC1
References
Further reading
EC 3.1.4 |
https://en.wikipedia.org/wiki/Protein%20kinase%20N1 | Serine/threonine-protein kinase N1 is an enzyme that in humans is encoded by the PKN1 gene.
Function
The protein encoded by this gene belongs to the protein kinase C superfamily. This kinase is activated by Rho family of small G proteins and may mediate the Rho-dependent signaling pathway. This kinase can be activated by phospholipids and by limited proteolysis. The 3-phosphoinositide dependent protein kinase-1 (PDPK1/PDK1) is reported to phosphorylate this kinase, which may mediate insulin signals to the actin cytoskeleton. The proteolytic activation of this kinase by caspase-3 or related proteases during apoptosis suggests its role in signal transduction related to apoptosis. Alternatively spliced transcript variants encoding distinct isoforms have been observed.
Interactions
Protein kinase N1 has been shown to interact with:
AKAP9,
Actinin, alpha 1,
CCDC85B,
NEFL,
NEUROD2
Phosphoinositide-dependent kinase-1,
Phospholipase D1,
RHOA, and
Vimentin.
TRAF1.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/PSMD4 | 26S proteasome non-ATPase regulatory subunit 4, also as known as 26S Proteasome Regulatory Subunit Rpn10 (systematic nomenclature), is an enzyme that in humans is encoded by the PSMD4 gene. This protein is one of the 19 essential subunits that contributes to the complete assembly of 19S proteasome complex.
Gene
The gene PSMD4 encodes one of the non-ATPase subunits of the 19S regulator base, subunit Rpn10. Pseudogenes have been identified on chromosomes 10 and 21. The human PSMD4 gene has 10 exons and locates at chromosome band 1q21.3.
Protein
The human protein 26S proteasome non-ATPase regulatory subunit 4 is 41 kDa in size and composed of 377 amino acids. The calculated theoretical pI of this protein is 4.68. An alternative splicing during gene expression generates an isoform of the protein in which the amino acid sequence from 269 to 377 is missing while the amino sequence between 255 and 268 is replaced from DSDDALLKMTISQQ to GERGGIRSPGTAGC.
Complex assembly
26S proteasome complex is usually consisted of a 20S core particle (CP, or 20S proteasome) and one or two 19S regulatory particles (RP, or 19S proteasome) on either one side or both side of the barrel-shaped 20S. The CP and RPs pertain distinct structural characteristics and biological functions. In brief, 20S sub complex presents three types proteolytic activities, including caspase-like, trypsin-like, and chymotrypsin-like activities. These proteolytic active sites located in the inner side of a chamber for |
https://en.wikipedia.org/wiki/SPINK1 | Pancreatic secretory trypsin inhibitor (PSTI) also known as serine protease inhibitor Kazal-type 1 (SPINK1) or tumor-associated trypsin inhibitor (TATI) is a protein that in humans is encoded by the SPINK1 gene.
Mutations in SPINK1 has been associated with hereditary pancreatitis and tropical pancreatitis. Trypsinogen is normally created and stored an inactive zymogen of trypsin in the pancreas, but occasionally will autoactivate itself. PSTI serves to cleave prematurely activated trypsin to prevent the enzyme from causing cellular damage to the organ. Without the function of PSTI, the pancreas is subject to repeated episodes of damage. p.N34S mutation leads to idiopathic pancreatitis (for those reading zarovizsga).
It has also been associated with prostate cancer.
See also
Kazal-type serine protease inhibitor domain
Pancreatitis
References
Further reading |
https://en.wikipedia.org/wiki/SPTB | Spectrin beta chain, erythrocyte is a protein that in humans is encoded by the SPTB gene.
References
Further reading |
https://en.wikipedia.org/wiki/ZFP36 | Tristetraprolin (TTP), also known as zinc finger protein 36 homolog (ZFP36), is a protein that in humans, mice and rats is encoded by the ZFP36 gene. It is a member of the TIS11 (TPA-induced sequence) family, along with butyrate response factors 1 and 2.
TTP binds to AU-rich elements (AREs) in the 3'-untranslated regions (UTRs) of the mRNAs of some cytokines and promotes their degradation. For example, TTP is a component of a negative feedback loop that interferes with TNF-alpha production by destabilizing its mRNA. Mice deficient in TTP develop a complex syndrome of inflammatory diseases.
Interactions
ZFP36 has been shown to interact with 14-3-3 protein family members, such as YWHAH, and with NUP214, a member of the nuclear pore complex.
Regulation
Post-transcriptionally, TTP is regulated in several ways. The subcellular localization of TTP is influenced by interactions with protein partners such as the 14-3-3 family of proteins. These interactions and, possibly, interactions with target mRNAs are affected by the phosphorylation state of TTP, as the protein can be posttranslationally modified by a large number of protein kinases. There is some evidence that the TTP transcript may also be targeted by microRNAs, such as miR-29a.
References
Further reading |
https://en.wikipedia.org/wiki/IQGAP1 | Ras GTPase-activating-like protein IQGAP1 (IQGAP1) also known as p195 is a ubiquitously expressed protein that in humans is encoded by the IQGAP1 gene. IQGAP1 is a scaffold protein involved in regulating various cellular processes ranging from organization of the actin cytoskeleton, transcription, and cellular adhesion to regulating the cell cycle.
History
IQGAP1 was discovered in 1994.
Its name stems from the fact that its RasGAP-related domain (GRD) has sequence homology to the Sar1 GTPase. It was hypothesized that IQGAP1 would act as a GTPase activating protein (GAP) protein, promoting the switch of ras GTPases from the active GTP to GDP-bound forms. However, despite the homology of IQGAP’s GAP domain to sar1 and the fact that IQGAP1 binds Rho GTPases Rac1 and Cdc42, IQGAP does not actually have GAP function. Instead, it binds the active (GTP-bound) forms of RAC1 and CDC42 with higher affinity than GDP-bound forms, and stabilizes the active form in vivo.
IQGAP1 is now recognized as a protein scaffold that integrates signals regulating cell adhesion, actin cytoskeleton, the cell cycle, and other cellular functions. IQGAP is particularly interesting as a therapeutic target since it acts as a node for so many signaling pathways implicated in cancer progression.
Expression
Analysis of IQGAP1 expression in human tissues has indicated that the scaffold is more or less ubiquitously expressed. It is usually found in the nucleus, plasma membrane, and cytoplasm. In other words |
https://en.wikipedia.org/wiki/NDRG1 | Protein NDRG1 is a protein that in humans is encoded by the NDRG1 gene.
This gene is a member of the N-myc downregulated gene family which belongs to the alpha/beta hydrolase superfamily. The protein encoded by this gene is a cytoplasmic protein involved in stress responses, hormone responses, cell growth, and differentiation . Mutations in this gene have been reported to be causative the autosomal-recessive version of Charcot-Marie-Tooth disease known as CMT4D.
It has been reported that NDRG1 localizes to the endosomes and is a Rab4a effector involved in vesicular recycling.
As reviewed by Fang et al., NDRG1 is involved in embryogenesis and development, cell growth and differentiation, lipid biosynthesis and myelination, stress responses, immunity, DNA repair and cell adhesion among other functions. NDRG1 is localised in the cytoplasm, nucleus and mitochondrion, at probabilities of 47.8%, 26.1% and 8.7%, respectively. In response to DNA damage NDRG1 translocates from the cytoplasm to the nucleus, where it may inhibit cell growth and promote DNA repair mechanisms. It is suggested that NDRG1 acts as a stress response gene or potentially as a transcription factor.
Gene
In humans, NDRG1 gene is located on the long arm of chromosome 8 (8q24.22). The gene encodes a 3.0 kilobases (kb) messenger RNA (mRNA) composed of 394 amino acids. NDRG1 belong to the NDRG1 family consisting of four members - NDRG1, NDRG2, NDRG3 and NDRG4 - that share a 53-65 % homology. In contrast to o |
https://en.wikipedia.org/wiki/Sirtuin%201 | Sirtuin 1, also known as NAD-dependent deacetylase sirtuin-1, is a protein that in humans is encoded by the SIRT1 gene.
SIRT1 stands for sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae), referring to the fact that its sirtuin homolog (biological equivalent across species) in yeast (Saccharomyces cerevisiae) is Sir2. SIRT1 is an enzyme located primarily in the cell nucleus that deacetylates transcription factors that contribute to cellular regulation (reaction to stressors, longevity).
Function
Sirtuin 1 is a member of the sirtuin family of proteins, homologs of the Sir2 gene in S. cerevisiae. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. The protein encoded by this gene is included in class I of the sirtuin family.
Sirtuin 1 is downregulated in cells that have high insulin resistance. Furthermore, SIRT1 was shown to de-acetylate and affect the activity of both members of the PGC1-alpha/ERR-alpha complex, which are essential metabolic regulatory transcription factors.
In vitro, SIRT1 has been shown to deacetylate and thereby deactivate the p53 protein, and may have a role in activating T helper 17 cells.
Selective ligands
Activators
Lamin A is a protein that had been identified as a direct activator of S |
https://en.wikipedia.org/wiki/Reticulon%204 | Reticulon 4, also known as Neurite outgrowth inhibitor or Nogo, is a protein that in humans is encoded by the RTN4 gene that has been identified as an inhibitor of neurite outgrowth specific to the central nervous system. During neural development Nogo is expressed mainly by neurons and provides an inhibitory signal for the migration and sprouting of CNS endothelial (tip) cells, thereby restricting blood vessel density.
This gene belongs to the family of reticulon-encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. The product of this gene is a potent neurite outgrowth inhibitor that may also help block the regeneration of the central nervous system in higher vertebrates. Alternatively spliced transcript variants derived both from differential splicing and differential promoter usage and encoding different isoforms have been identified. There are three isoforms: Nogo A, B and C. Nogo-A has two known inhibitory domains including amino-Nogo, at the N-terminus and Nogo-66, which makes up the molecules extracellular loop. Both amino-Nogo and Nogo-66 are involved in inhibitory responses, where amino-Nogo is a strong inhibitor of neurite outgrowth, and Nogo-66 is involved in growth cone destruction.
Research suggests that blocking Nogo-A during neuronal damage (from diseases such as multiple sclerosis) will help to protect or restore the damaged neurons. The inv |
https://en.wikipedia.org/wiki/Alpha-2-HS-glycoprotein | alpha-2-HS-glycoprotein (AHSG, Alpha-2-Heremans-Schmid Glycoprotein) also known as fetuin-A is a protein that in humans is encoded by the AHSG gene. Fetuin-A belongs to the fetuin class of plasma binding proteins and is more abundant in fetal than adult blood.
Function
Alpha2-HS glycoprotein, a glycoprotein present in the serum, is synthesized by hepatocytes and adipocytes. The AHSG molecule consists of two polypeptide chains, which are both cleaved from a proprotein encoded from a single mRNA. It is involved in several functions, such as endocytosis, brain development and the formation of bone tissue. The protein is commonly present in the cortical plate of the immature cerebral cortex and bone marrow hemopoietic matrix, and it has therefore been postulated that it participates in the development of the tissues. However, its exact significance is still obscure.
The choroid plexus is an established extrahepatic expression site. The mature circulating AHSG molecule consists of two polypeptide chains, which are both cleaved from a proprotein encoded from a single mRNA. Multiple post-translational modifications have been reported. Thus AHSG is a secreted partially phosphorylated glycoprotein with complex proteolytic processing that circulates in blood and extracellular fluids. In the test tube AHSG can bind multiple ligands and therefore has been claimed to be involved in several functions, such as endocytosis, brain development and the formation of bone tissue. Most of thes |
https://en.wikipedia.org/wiki/Anaplastic%20lymphoma%20kinase | Anaplastic lymphoma kinase (ALK) also known as ALK tyrosine kinase receptor or CD246 (cluster of differentiation 246) is an enzyme that in humans is encoded by the ALK gene.
Identification
Anaplastic lymphoma kinase (ALK) was originally discovered in 1994 in anaplastic large-cell lymphoma (ALCL) cells. ALCL is caused by a (2;5)(p23:q35) chromosomal translocation that generates the fusion protein NPM-ALK, in which the kinase domain of ALK is fused to the amino-terminal part of the nucleophosmin (NPM) protein. Dimerization of NPM constitutively activates the ALK kinase domain.
The full-length protein ALK was identified in 1997 by two groups. The deduced amino acid sequences revealed that ALK was a novel receptor tyrosine kinase (RTK), having an extracellular ligand-binding domain, a transmembrane domain, and an intracellular tyrosine kinase domain. While the tyrosine kinase domain of human ALK shares a high degree of similarity with that of the insulin receptor, its extracellular domain is unique among the RTK family in containing two MAM domains (meprin, A5 protein and receptor protein tyrosine phosphatase mu), an LDLa domain (low-density lipoprotein receptor class A) and a glycine-rich region. Based on overall homology, ALK is closely related to the leukocyte receptor tyrosine kinase (LTK) and, together with the insulin receptor, forms a subgroup in the RTK superfamily. The human ALK gene encodes a protein 1,620 amino acids long with a molecular weight of 180 kDa.
Since t |
https://en.wikipedia.org/wiki/Collagen%2C%20type%20IV%2C%20alpha%204 | Collagen alpha-4(IV) chain is a protein that in humans is encoded by the COL4A4 gene.
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. This particular collagen IV subunit, however, is only found in a subset of basement membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Mutations in this gene are associated with type II autosomal recessive Alport syndrome (hereditary glomerulonephropathy) and with familial benign hematuria (thin basement membrane disease). Two transcripts, differing only in their transcription start sites, have been identified for this gene and, as is common for collagen genes, multiple polyadenylation sites are found in the 3' UTR.
Disease Database
LOVD Alport gene variant databases (COL4A4, COL4A3, COL4A5)
References
Further reading
Collagens |
https://en.wikipedia.org/wiki/CAMP%20responsive%20element%20modulator | cAMP responsive element modulator is a protein that in humans is encoded by the CREM gene, and it belongs to the cAMP-responsive element binding protein family. It has multiple isoforms, which act either as repressors or activators. CREB family is important for in regulating transcription in response to various stresses, metabolic and developmental signals. CREM transcription factors also play an important role in many physiological systems, such as cardiac function, circadian rhythms, locomotion and spermatogenesis.
Function
This gene encodes a bZIP transcription factor that binds to the cAMP responsive element found in many viral and cellular promoters. It is an important component of cAMP-mediated signal transduction during the spermatogenetic cycle, as well as other complex processes. Alternative promoter and translation initiation site usage allows this gene to exert spatial and temporal specificity to cAMP responsiveness. Multiple alternatively spliced transcript variants encoding several different isoforms have been found for this gene, with some of them functioning as activators and some as repressors of transcription.
Gene location
The chromosomal location of CREM gene is at 10p11.21, where it starts at 35415769 and ends at 35501886 bp from pter ( according to hg19-Feb_2009)
Interactions
CAMP responsive element modulator has been shown to interact with FHL5.
Disease relevance of CREM
Panic disorder
One study reported the DNA sequence variations in the gene |
https://en.wikipedia.org/wiki/FANCA | Fanconi anaemia, complementation group A, also known as FAA, FACA and FANCA, is a protein which in humans is encoded by the FANCA gene. It belongs to the Fanconi anaemia complementation group (FANC) family of genes of which 12 complementation groups are currently recognized and is hypothesised to operate as a post-replication repair or a cell cycle checkpoint. FANCA proteins are involved in inter-strand DNA cross-link repair and in the maintenance of normal chromosome stability that regulates the differentiation of haematopoietic stem cells into mature blood cells.
Mutations involving the FANCA gene are associated with many somatic and congenital defects, primarily involving phenotypic variations of Fanconi anaemia, aplastic anaemia, and forms of cancer such as squamous cell carcinoma and acute myeloid leukaemia.
Function
The Fanconi anaemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, and FANCL. The previously defined group FANCH is the same as FANCA. The members of the Fanconi anaemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. The FANCA gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms.
Gene and protein
In humans, the gene FANCA is 79 kilobases (kb) in length, and is located on chromosome 16 (16q24.3). The FANC |
https://en.wikipedia.org/wiki/HLA-F | HLA class I histocompatibility antigen, alpha chain F is a protein that in humans is encoded by the HLA-F gene. It is an empty intracellular molecule that encodes a non-classical heavy chain anchored to the membrane and forming a heterodimer with a β-2 microglobulin light chain. It belongs to the HLA class I heavy chain paralogues that separate from most of the HLA heavy chains. HLA-F is localized in the endoplasmic reticulum and Golgi apparatus, and is also unique in the sense that it exhibits few polymorphisms in the human population relative to the other HLA genes; however, there have been found different isoforms from numerous transcript variants found for the HLA-F gene. Its pathways include IFN-gamma signaling and CDK-mediated phosphorylation (cyclin-dependent kinase) and removal of the Saccharomyces cerevisiae Cdc6 protein, which is crucial for functional DNA replication.
HLA-F
The Major Histocompatibility Complex (MHC) is a group of cell surface proteins that in humans is also called the Human Leukocyte Antigen (HLA) complex. These proteins are encoded by a cluster of genes known as the HLA locus. The HLA locus occupies a ~ 3Mbp stretch that is located on the short arm of chromosome 6, specifically on 6p21.1-21.3. The MHC proteins are classified into three main categories, namely class I, II, and III. There are over 140 genes within the HLA locus and they are often called HLA genes. HLA-A, B, and C are the classical class I genes and HLA-E, F and G are the nonclass |
https://en.wikipedia.org/wiki/HNRPD | Heterogeneous nuclear ribonucleoprotein D0 (HNRNPD) also known as AU-rich element RNA-binding protein 1 (AUF1) is a protein that in humans is encoded by the HNRNPD gene. Alternative splicing of this gene results in four transcript variants.
Function
This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are nucleic acid binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). The interaction sites on the RNA are frequently biased towards particular sequence motifs. These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two repeats of quasi-RRM domains that bind to RNAs. It localizes to both the nucleus and the cytoplasm. This protein is implicated in the regulation of mRNA stability.
Interactions
HnRNP D has been shown to interact with SAFB and Hsp27. It also has been reported to interact with mRNAs such as Mef2c mRNA.
References
Further reading
External links
PDBe-KB provides an overview of all the structure information available in the PDB for Human Heterogeneous nuclear ribonucleoprotein D0 (HNRPD) |
https://en.wikipedia.org/wiki/Homeobox%20A10 | Homeobox protein Hox-A10 is a protein that in humans is encoded by the HOXA10 gene.
Function
In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor that may regulate gene expression, morphogenesis, and differentiation. More specifically, it may function in fertility, embryo viability, and regulation of hematopoietic lineage commitment. Alternatively spliced transcript variants encoding different isoforms have been described.
Downregulation of HOXA10 is observed in the human and baboon decidua after implantation and this downregulation promotes trophoblast invasion by activating STAT3.
Interactions
Homeobox A10 has been shown to interact with PTPN6.
See also
Homeobox
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/HSPA4 | Heat shock 70 kDa protein 4 is a protein that in humans is encoded by the HSPA4 gene.
The protein encoded by this gene was originally suggested to be a member of the heat shock protein 70 family. However it is now known that human HSPA4 is an equivalent to mouse the Apg-2 protein and is a member of the Hsp110 family.
Interactions
HSPA4 has been shown to interact with:
APAF1
DNAJB1,
HDAC1,
HSF1,
HSPBP1,
Histone deacetylase 2,
NAD(P)H dehydrogenase (quinone 1),
STUB1, and
TTC1.
References
Further reading
External links
Heat shock proteins |
https://en.wikipedia.org/wiki/INPP5D | Src homology 2 (SH2) domain containing inositol polyphosphate 5-phosphatase 1 (SHIP1) is an enzyme with phosphatase activity. SHIP1 is structured by multiple domain and is encoded by the INPP5D gene in humans. SHIP1 is expressed predominantly by hematopoietic cells but also, for example, by osteoblasts and endothelial cells. This phosphatase is important for the regulation of cellular activation. Not only catalytic but also adaptor activities of this protein are involved in this process. Its movement from the cytosol to the cytoplasmic membrane, where predominantly performs its function, is mediated by tyrosine phosphorylation of the intracellular chains of cell surface receptors that SHIP1 binds. Insufficient regulation of SHIP1 leads to different pathologies.
Structure and regulation of activity
SHIP1 is a 145 kDa large protein and member of the inositol polyphosphate-5-phosphatase (INPP5) family. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
At the N-terminus of the protein, SH2 domain is formed. This domain is important for the interaction of SHIP1 with the phosphorylated protein chains that SHIP1 binds. Highly conserved phosphatase domain is in central part of the protein. This catalytic domain is flanked on the N-terminal side by the PH-like domain that binds phosphatidylinositol-3,4,5-triphosphate (PI(3,4,5)P3) and is overlapped on C-terminus with the C2 domain that binds phosphatidylinositol-3,4-bisphosphate (PI(4 |
https://en.wikipedia.org/wiki/INSL3 | Insulin-like 3 is a protein that in humans is encoded by the INSL3 gene.
Function
The protein encoded by this gene is an insulin like hormone produced mainly in gonadal tissues in males and females. Studies of the mouse counterpart suggest that this gene may be involved in the development of urogenital tract and female fertility. INSL-3 initiates meiotic progression in follicle-enclosed oocytes by mediating a reduction in intra-oocyte cAMP concentration by activating leucine-rich repeat-containing G protein-coupled receptor 8 (LGR8). It may also act as a hormone to regulate growth and differentiation of gubernaculum, and thus mediating intra-abdominal testicular descent. The mutations in this gene may lead to, but not a frequent cause of, cryptorchidism.
References
Further reading |
https://en.wikipedia.org/wiki/Transportin%201 | Transportin-1 (or Importin-β 2) is a protein that in humans is encoded by the TNPO1 gene.
Function
This protein is a karyopherin which interacts with nuclear localization sequence to target nuclear proteins to the nucleus. The classical karyopherin receptor complex, such as the complex that uses Importin-β1 (encoded by gene KPNB1), is a heterodimer of an alpha subunit which recognizes the nuclear localization signal and a beta subunit which docks the complex at nucleoporins. However, Transportin-1 can directly bind to the cargo proteins and may not need importin alpha subunit to do it.
Transportin-1 is thought to use the same principal mechanism to carry out nuclear transport as other Importins. It mediates docking to the nuclear pore complex through binding to nucleoporin and is subsequently translocated through the pore by an energy requiring mechanism. Then, in the nucleus Ran binds to Transportin-1, it dissociates from cargo, and Transportin-1 is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. Then Transportin-1 is free to bind new cargo.
In addition, Transportin-1 is implicated in helping protein transport into primary cilium. The function of Transportin-1 in this case is thought to be similar to carrying proteins into the nucleus through a nuclear pore. Transportin-1 binds cargo and then is helping this cargo to pass through a pore at the base of the cilium. Ran and nucleoporins are also implicated in this mechanism.
Alternate splic |
https://en.wikipedia.org/wiki/Laminin%2C%20alpha%205 | Laminin subunit alpha-5 is a protein that in humans is encoded by the LAMA5 gene.
Function
Components of the extracellular matrix exert myriad effects on tissues throughout the body. In particular, the laminins, a family of heterotrimeric extracellular glycoproteins, affect tissue development and integrity in such diverse organs as the kidney, lung, skin, and nervous system. It is thought that laminins mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Laminins function as heterotrimeric complexes of alpha, beta, and gamma chains, with each chain type representing a different subfamily of proteins. The protein encoded by this gene belongs to the alpha subfamily of laminin chains and is a major component of basement membranes. Two transcript variants encoding different isoforms have been found for this gene, but the full-length nature of one of them has not been determined.
Interactions
Laminin, alpha 5 has been shown to interact with BCAM.
References
Further reading
Laminins |
https://en.wikipedia.org/wiki/Microsomal%20triglyceride%20transfer%20protein | Microsomal triglyceride transfer protein large subunit is a protein that in humans is encoded by the MTTP gene.
MTP encodes the large subunit of the heterodimeric microsomal triglyceride transfer protein. Protein disulfide isomerase (PDI) completes the heterodimeric microsomal triaglyceride transfer protein, which has been shown to play a central role in lipoprotein assembly. Mutations in MTP can cause abetalipoproteinemia.
Apolipoprotein B48 on chylomicra and Apolipoprotein B100 on LDL, IDL, and VLDL are important for MTP binding.
Interactive pathway map
Pharmacology
Drugs that inhibit MTTP prevent the assembly of apo B-containing lipoproteins thus inhibiting the synthesis of chylomicrons and VLDL and leading to decrease in plasma levels of LDL-C.
Lomitapide (Juxtapid) was approved by the US FDA for adjunctive treatment of homozygous familial hypercholesterolemia.
Dirlotapide (Slentrol) and mitratapide (Yarvitan) are veterinary drugs for the management of obesity in dogs.
References
Further reading
Human proteins |
https://en.wikipedia.org/wiki/PSMB9 | Proteasome subunit beta type-9 as known as 20S proteasome subunit beta-1i is a protein that in humans is encoded by the PSMB9 gene.
This protein is one of the 17 essential subunits (alpha subunits 1-7, constitutive beta subunits 1-7, and inducible subunits including beta1i, beta2i, beta5i) that contributes to the complete assembly of 20S proteasome complex. In particular, proteasome subunit beta type-5, along with other beta subunits, assemble into two heptameric rings and subsequently a proteolytic chamber for substrate degradation. This protein contains "Trypsin-like" activity and is capable of cleaving after basic residues of peptide. The eukaryotic proteasome recognized degradable proteins, including damaged proteins for protein quality control purpose or key regulatory protein components for dynamic biological processes. The constitutive subunit beta1, beta2, and beta 5 (systematic nomenclature) can be replaced by their inducible counterparts beta1i, 2i, and 5i when cells are under the treatment of interferon-γ. The resulting proteasome complex becomes the so-called immunoproteasome. An essential function of the modified proteasome complex, the immunoproteasome, is the processing of numerous MHC class-I restricted T cell epitopes.
Structure
Gene
The gene PSMB9 encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This gene is located in the class II region of the MHC (major histocompatibility complex). Expre |
https://en.wikipedia.org/wiki/PSMC2 | 26S protease regulatory subunit 7, also known as 26S proteasome AAA-ATPase subunit Rpt1, is an enzyme that in humans is encoded by the PSMC2 gene This protein is one of the 19 essential subunits of a complete assembled 19S proteasome complex. Six 26S proteasome AAA-ATPase subunits (Rpt1 (this protein), Rpt2, Rpt3, Rpt4, Rpt5, and Rpt6) together with four non-ATPase subunits (Rpn1, Rpn2, Rpn10, and Rpn13) form the base sub complex of 19S regulatory particle for proteasome complex.
Gene
The gene PSMC2 encodes one of the ATPase subunits, a member of the triple-A family of ATPases which have a chaperone-like activity. This subunit has been shown to interact with several of the basal transcription factors so, in addition to participation in proteasome functions, this subunit may participate in the regulation of transcription. This subunit may also compete with PSMC3 for binding to the HIV tat protein to regulate the interaction between the viral protein and the transcription complex. The human PSMC2 gene has 13 exons and locates at chromosome band 7q22.1-q22.3.
Protein
The human protein 26S protease regulatory subunit 7 is 48.6kDa in size and composed of 433 amino acids. The calculated theoretical pI of this protein is 526S protease regulatory subunit 5.71. One expression isoform is generated by alternative splicing, in which 1–137 of the amino acid sequence is missing.
Complex assembly
26S proteasome complex is usually consisted of a 20S core particle (CP, or 20S prote |
https://en.wikipedia.org/wiki/PTPN12 | Tyrosine-protein phosphatase non-receptor type 12 is an enzyme that in humans is encoded by the PTPN12 gene.
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains a C-terminal PEST motif, which serves as a protein–protein interaction domain, and may be related to protein intracellular half-life. This PTP was found to bind and dephosphorylate the product of oncogene c-ABL, thus may play a role in oncogenesis. This PTP was shown to interact with, and dephosphorylate, various of cytoskeleton and cell adhesion molecules, such as p130 (Cas), CAKbeta/PTK2B, PSTPIP1, and paxillin, which suggested its regulatory roles in controlling cell shape and mobility.
Interactions
PTPN12 has been shown to interact with BCAR1, Grb2, PSTPIP1, TGFB1I1, Paxillin and SHC1.
References
Further reading |
https://en.wikipedia.org/wiki/Protein%20SET | Protein SET, also known as Protein SET 1, is a protein that in humans is encoded by the SET gene.
Interactions
Protein SET has been shown to interact with:
Acidic leucine-rich nuclear phosphoprotein 32 family member A,
CDK5R1,
KLF5,
NME1, and
TAF1A.
References
Further reading
Histone Acetyltransferase Inhibitor |
https://en.wikipedia.org/wiki/Natural%20resistance-associated%20macrophage%20protein%201 | Natural resistance-associated macrophage protein 1 is a protein that in humans is encoded by the SLC11A1 gene.
Function
This gene is a member of the solute carrier family 11 (proton-coupled divalent metal ion transporters) family and encodes a multi-pass membrane protein. The protein functions as a divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Mutations in this gene have been associated with susceptibility to infectious diseases such as tuberculosis and leprosy, and inflammatory diseases such as rheumatoid arthritis and Crohn's disease. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined.
See also
Solute carrier family
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/VAMP2 | Vesicle-associated membrane protein 2 (VAMP2) is a protein that in humans is encoded by the VAMP2 gene.
Function
Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein SNAP25 are the main components of a protein complex involved in the docking and/or fusion of synaptic vesicles with the presynaptic membrane. VAMP2 is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. VAMP2 is thought to participate in neurotransmitter release at a step between docking and fusion. Mice lacking functional synaptobrevin2/VAMP2 gene cannot survive after birth, and have a dramatically reduced synaptic transmission, around 10% of control. The protein forms a stable complex with syntaxin, synaptosomal-associated protein, 25 kD, and complexin. It also forms a distinct complex with synaptophysin.
Clinical significance
Heterozygous mutations in VAMP2 cause a neurodevelopmental disorder with hypotonia and autistic features (with or without hyperkinetic movements).
Interactions
VAMP2 has been shown to interact with:
RABAC1,
SNAP-25,
SNAP23,
STX1A, and
STX4.
References
Further reading |
https://en.wikipedia.org/wiki/Endothelial%20protein%20C%20receptor | Endothelial protein C receptor (EPCR) also known as activated protein C receptor (APC receptor) is a protein that in humans is encoded by the PROCR gene. PROCR has also recently been designated CD201 (cluster of differentiation 201).
The protein encoded by this gene is a receptor for protein C that enhances its activation. Protein C is an anti-coagulant serine protease activated by the blood coagulation pathway.
Structure
EPCR protein is an N-glycosylated type I membrane protein that enhances the activation of protein C. It belongs to the MHC class I/CD1 family of proteins, that is characterized by having a deep groove, that in other proteins in the family (but not in EPCR) is usually used for antigen binding.
Like the CD1 series, EPCR has a lipid in the corresponding groove. The bound lipid in EPCR is usually phosphatidylcholine, but it may be phosphatidylethanolamine, and it contributes to protein C binding, though probably not through direct contact
Clinical significance
Mutations in this gene have been associated with venous thromboembolism and myocardial infarction, as well as with late fetal loss during pregnancy.
The protein is also involved in Plasmodium falciparum malaria as subtypes of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family use EPCR of the host as a receptor.
References
Further reading
External links
Clusters of differentiation |
https://en.wikipedia.org/wiki/Alpha-actinin-2 | Alpha-actinin-2 is a protein which in humans is encoded by the ACTN2 gene. This gene encodes an alpha-actinin isoform that is expressed in both skeletal and cardiac muscles and functions to anchor myofibrillar actin thin filaments and titin to Z-discs.
Structure
Alpha-actinin-2 is a 103.8 kDa protein composed of 894 amino acids. Each molecule is rod-shaped (35 nm in length) and it homodimerizes in an anti-parallel fashion. Each monomer has an N-terminal actin-binding region composed of two calponin homology domains, two C-terminal EF hand domains, and four tandem spectrin-like repeats form the rod domain in the central region of the molecule. The high-resolution crystal structure of human alpha-actinin 2 at 3.5 Å was recently resolved. Alpha actinins belong to the spectrin gene superfamily which represents a diverse group of actin-binding cytoskeletal proteins, including spectrin, dystrophin, utrophin and fimbrin. Skeletal, cardiac, and smooth muscle isoforms are localized to the Z-disc and analogous dense bodies, where they help anchor the myofibrillar actin filaments. Alpha-actinin 2 has been shown to interact with KCNA5, DLG1, DISC1, MYOZ1, GRIN2B, ADAM12, ACTN3, MYPN, PDLIM3, PKN, MYOT, TTN, NMDAR, SYNPO2, LDB3, and FATZ.
Function
The primary function of alpha-actinin-2 is to crosslink filamentous actin molecules and titin molecules from adjoining sarcomeres at Z-discs, a function that is modulated by phospholipids. It is clear from studies by Hampton et al. that t |
https://en.wikipedia.org/wiki/CHRNA4 | Neuronal acetylcholine receptor subunit alpha-4, also known as nAChRα4, is a protein that in humans is encoded by the CHRNA4 gene. The protein encoded by this gene is a subunit of certain nicotinic acetylcholine receptors (nAChR). Alpha4-containing nAChRs (specifically the alpha4beta2 subtype) appear to play a crucial role in the addictive response to nicotine..
The nicotinic acetylcholine receptors (nAChRs) are members of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. After binding acetylcholine, these pentameric receptors respond by undergoing an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. The protein encoded by this gene is an integral membrane receptor subunit that can interact with either nAChR beta-2 or nAChR beta-4 to form a functional receptor.
Mutations in this gene appear to account for a small proportion of the cases of nocturnal frontal lobe epilepsy. It has also been associated with a rare form of movement disorder characterised by dyskinesia during periods of exercise or activity called paroxysmal kinesogenic dyskinesia.
Interactive pathway map
See also
Nicotinic acetylcholine receptor
References
Further reading
External links
Nicotinic acetylcholine receptors |
https://en.wikipedia.org/wiki/Collagen%2C%20type%20IV%2C%20alpha%202 | Collagen alpha-2(IV) chain is a protein that in humans is encoded by the COL4A2 gene.
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter.
References
Further reading
Collagens |
https://en.wikipedia.org/wiki/Coxsackievirus%20and%20adenovirus%20receptor | Coxsackievirus and adenovirus receptor (CAR) is a protein that in humans is encoded by the CXADR gene. The protein encoded by this gene is a type I membrane receptor for group B coxsackie viruses and subgroup C adenoviruses. CAR protein is expressed in several tissues, including heart, brain, and, more generally, epithelial and endothelial cells. In cardiac muscle, CAR is localized to intercalated disc structures, which electrically and mechanically couple adjacent cardiomyocytes. CAR plays an important role in the pathogenesis of myocarditis, dilated cardiomyopathy, and in arrhythmia susceptibility following myocardial infarction or myocardial ischemia. In addition, an isoform of CAR (CAR-SIV) has been recently identified in the cytoplasm of pancreatic beta cells. It's been suggested that CAR-SIV resides in the insulin secreting granules and might be involved in the virus infection of these cells.
Structure
Human CAR protein has a theoretical molecular weight of 40.0 kDa and is composed of 365 amino acids. The human CAR gene (CXADR) is found on chromosome 21. Alternative splicing is known to produce at least 2 splice variants known as hCAR1 and hCAR2 and are each composed of at least 7 exons. Pseudogenes of this gene are found on chromosomes 15, 18, and 21.
CAR is a transmembrane bound protein with two Ig-like extracellular domains, a transmembrane domain, a cytoplasmic domain, and two N-linked glycosylation sites. CAR contains two disulfide bonded loops (residues 35-1 |
https://en.wikipedia.org/wiki/RNA%20Helicase%20A | ATP-dependent RNA helicase A (RHA; also known as DHX9, LKP, and NDHI) is an enzyme that in humans is encoded by the DHX9 gene.
Function
DEAD/DEAH box helicases are proteins, and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein with RNA helicase activity. It may participate in melting of DNA:RNA hybrids, such as those that occur during transcription, and may play a role in X-linked gene expression. It contains 2 copies of a double-stranded RNA-binding domain, a DEXH core domain and an RGG box. The RNA-binding domains and RGG box influence and regulate RNA helicase activity. The DHX9 gene is located on the long arm q of chromosome 1.
Interactions
DHX9 has been shown to interact with:
AKAP8L,
BRCA1,
DDX17 (p72)
DDX5 (p68),
KHDRBS1,
MIZF,
NXF1,
PRMT1,
RELA, and
SMN1.
References
Further reading |
https://en.wikipedia.org/wiki/DEFA1 | Defensin, alpha 1 also known as human alpha defensin 1, human neutrophil peptide 1 (HNP-1) or neutrophil defensin 1 is a human protein that is encoded by the DEFA1 gene. Human alpha defensin 1 belongs to the alpha defensin family of antimicrobial peptides.
Function
Defensins are a family of microbicidal and cytotoxic peptides thought to be involved in host defense. They are abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the intestine, respiratory tract, urinary tract, and vagina. Members of the defensin family are highly similar in protein sequence and distinguished by a conserved cysteine motif. Several alpha defensin genes are clustered on chromosome 8. The protein encoded by this gene, defensin, alpha 1, is found in the microbicidal granules of neutrophils and likely plays a role in phagocyte-mediated host defense. It differs from the defensins, alpha 2 and alpha 3 by only one amino acid.
Biosynthesis
HNPs are generated as 94 amino acids preproHNPs, which are co-translationally cleaved to 75 amino acids pro-peptides with a N-terminal prosegment having a negative charge that neutralizes the highly positively charged C terminal peptide. Processing of proHNPs occurs mainly in late promyelocytes, where the 75 amino acids proHNPs are cleaved to a 56 amino acids intermediate form and onward to 29-30 amino acids mature peptides designated HNPs. Cationic 29-30 amino acids HNPs associate with the negatively charg |
https://en.wikipedia.org/wiki/Beta%20defensin%201 | Beta-defensin 1 is a protein that in humans is encoded by the DEFB1 gene.
Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Members of the defensin family are highly similar in protein sequence. This gene encodes defensin, beta 1, an antimicrobial peptide implicated in the resistance of epithelial surfaces to microbial colonization. This gene maps in close proximity to defensin family member defensin, alpha 1, and has been implicated in the pathogenesis of cystic fibrosis. Single-nucleotide polymorphisms in the DEFB1 gene were associated with plasma kynurenine concentrations in major depressive disorder patients in a genome-wide association study.
References
Further reading
Defensins |
https://en.wikipedia.org/wiki/FASN | FASN may refer to
the FASN gene that encodes Fatty acid synthase
Fellowship of the American Society of Nephrology |
https://en.wikipedia.org/wiki/Tyrosine-protein%20kinase%20Fes/Fps | Tyrosine-protein kinase Fes/Fps also known as proto-oncogene c-Fes/Fps is an enzyme that in humans is encoded by the FES gene. FES was originally cloned as a retroviral oncogene from feline (v-FES) and avian (v-FPS) sarcomas. This triggered the subsequent identification and cloning of the cellular FES (c-FES) genes (also referred to as FPS) in birds and mammals.
Function
This gene encodes the human cellular counterpart of a feline sarcoma retrovirus protein with transforming capabilities. The gene product has tyrosine-specific protein kinase activity and that activity is required for maintenance of cellular transformation. Its chromosomal location has linked it to a specific translocation event identified in patients with acute promyelocytic leukemia but it is also involved in normal hematopoiesis. A truncated transcript has been identified that is generated utilizing a start site in one of the far downstream exons but a protein product associated with this transcript has not been identified.
Interactions
Feline sarcoma oncogene has been shown to interact with BCAR1 and BCR gene.
References
Further reading
External links
Tyrosine kinases |
https://en.wikipedia.org/wiki/GNB1 | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 is a protein that in humans is encoded by the GNB1 gene.
Function
Heterotrimeric guanine nucleotide-binding proteins (G proteins), which integrate signals between receptors and effector proteins, are composed of an alpha, a beta, and a gamma subunit. These subunits are encoded by families of related genes. This gene encodes a beta subunit. Beta subunits are important regulators of alpha subunits, as well as of certain signal transduction receptors and effectors. This gene uses alternative polyadenylation signals.
Interactive pathway map
Interactions
GNB1 has been shown to interact with GNG4.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Laminin%20subunit%20gamma-2 | Laminin subunit gamma-2 is a protein that in humans is encoded by the LAMC2 gene.
Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene.
Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the gamma chain isoform laminin, gamma 2. The gamma 2 chain, formerly thought to be a truncated version of beta chain (B2t), is highly homologous to the gamma 1 chain; however, it lacks domain VI, and domains V, IV and III are shorter. It is expressed in |
https://en.wikipedia.org/wiki/SH2D1A | SH2 domain–containing protein 1A is a protein that in humans is encoded by the SH2D1A gene. It is often called SLAM-associated protein (symbol SAP), where "SLAM" refers to signaling lymphocytic activation molecules. It is a SH2 domain–containing molecule (part of a family of such molecules) that plays a role in SLAM signaling. A putative function is as an adaptor for Fyn and competitor of phosphatases, leading to modulation of SLAM family function. SAP has been implicated in autoimmunity, and a mutation of it is associated with X-linked lymphoproliferative disease. At least 32 disease-causing mutations in this gene have been discovered.
Interactions
SH2D1A has been shown to interact with:
CD84,
DOK1,
FYN,
LY9 and
SLAMF1.
References
Further reading
Ex |
https://en.wikipedia.org/wiki/Ectonucleotide%20pyrophosphatase/phosphodiesterase%201 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (PC-1, CD203a) is an enzyme that in humans is encoded by the ENPP1 gene.
Structure
This gene is a member of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family. The encoded protein is a type II transmembrane glycoprotein comprising two identical disulfide-bonded subunits.
Function
ENPP1 has broad specificity and cleaves a variety of substrates, including phosphodiester bonds of nucleotides and nucleotide sugars. ENPP1 protein may function to hydrolyze nucleoside 5′-triphosphates to their corresponding monophosphates and may also hydrolyze diadenosine polyphosphates.
The main substrate of ENNP1 is adenosine triphosphate (ATP), which is cleaved into adenosine monophosphate (AMP) and diphosphate. Another notable nucleotide substrate is nicotinamide adenine dinucleotide (NAD+) which can be hydrolyzed to produce AMP. ADPR can also be hydrolyzed by ENNP1 to produce AMP.
Clinical significance
Mutations in this gene have been associated with Generalized arterial calcification of infancy, ossification of the posterior longitudinal ligament of the spine (OPLL), Hypophosphatemic rickets autosomal recessive 2 (ARHR2), and insulin resistance.
In a tumor microenvironment, AMP generated by ENNP1 can lead to production of adenosine, which suppresses the anti-cancer function of the immune system.
Interactions
Ectonucleotide pyrophosphatase/phosphodiesterase 1 has been shown to interact with Insulin r |
https://en.wikipedia.org/wiki/Prohibitin | Prohibitin, also known as PHB, is a protein that in humans is encoded by the PHB gene.
The Phb gene has also been described in animals, fungi, plants, and unicellular eukaryotes. Prohibitins are divided in two classes, termed Type-I and Type-II prohibitins, based on their similarity to yeast PHB1 and PHB2, respectively. Each organism has at least one copy of each type of prohibitin gene.
Discovery
Prohibitins are evolutionarily conserved genes that are ubiquitously expressed. The human prohibitin gene, located on the BRCA1 chromosome region 17q21, was originally thought to be a negative regulator of cell proliferation and a tumor suppressor. This anti-proliferative activity was later attributed to the 3' UTR of the PHB gene, and not to the actual protein. Mutations in human PHB have been linked to sporadic breast cancer. However, over-expression of PHB has been associated with a reduction in the androgen receptor activity and a reduction in PSA gene expression resulting in a decrease of androgen-dependent growth of cancerous prostate cells.
Prohibitin is expressed as two transcripts with varying lengths of 3' untranslated region. The longer transcript is present at higher levels in proliferating tissues and cells, suggesting that this longer 3' untranslated region may function as a trans-acting regulatory RNA.
Function
Prohibitins may have multiple functions including:
Mitochondrial function and morphology
Prohibitins are assembled into a ring-like structure with 16 |
https://en.wikipedia.org/wiki/PIM1 | Proto-oncogene serine/threonine-protein kinase Pim-1 is an enzyme that in humans is encoded by the PIM1 gene.
Pim-1 is a proto-oncogene which encodes for the serine/threonine kinase of the same name. The pim-1 oncogene was first described in relation to murine T-cell lymphomas, as it was the locus most frequently activated by the Moloney murine leukemia virus. Subsequently, the oncogene has been implicated in multiple human cancers, including prostate cancer, acute myeloid leukemia and other hematopoietic malignancies. Primarily expressed in spleen, thymus, bone marrow, prostate, oral epithelial, hippocampus and fetal liver cells, Pim-1 has also been found to be highly expressed in cell cultures isolated from human tumors. Pim-1 is mainly involved in cell cycle progression, apoptosis and transcriptional activation, as well as more general signal transduction pathways. Pim-1's role in oncogenic signalling has led to it becoming a widely studied target in cancer research, with numerous drug candidates under investigation which target it.
Gene
Located on chromosome 6 (6p21.2), the gene encompasses 5Kb of DNA, including 6 exons and 5 introns. Expression of Pim-1 has been shown to be regulated by the JAK/STAT pathway. Direct binding of transcription factors STAT3 and STAT5 to the Pim-1 promoter results in the transcription of Pim-1. The Pim-1 gene has been found to be conserved in dogs, cows, mice, rats, zebrafish and C. elegans. Pim-1 deficient mice have been shown to be pheno |
https://en.wikipedia.org/wiki/PRKAA2 | 5'-AMP-activated protein kinase catalytic subunit alpha-2 is an enzyme that in humans is encoded by the PRKAA2 gene.
Function
The protein encoded by this gene is a catalytic subunit of the AMP-activated protein kinase (AMPK). AMPK is a heterotrimer consisting of an alpha catalytic subunit, and non-catalytic beta and gamma subunits. AMPK is an important energy-sensing enzyme that monitors cellular energy status. In response to cellular metabolic stresses, AMPK is activated, and thus phosphorylates and inactivates acetyl-CoA carboxylase (ACC) and beta-hydroxy beta-methylglutaryl-CoA reductase (HMGCR), key enzymes involved in regulating de novo biosynthesis of fatty acid and cholesterol. Studies of the mouse counterpart suggest that this catalytic subunit may control whole-body insulin sensitivity and is necessary for maintaining myocardial energy homeostasis during ischemia.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/PTPRA | Receptor-type tyrosine-protein phosphatase alpha is an enzyme that in humans is encoded by the PTPRA gene.
Function
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. This PTP has been shown to dephosphorylate and activate Src family tyrosine kinases, and is implicated in the regulation of integrin signaling, cell adhesion and proliferation. Three alternatively spliced variants of this gene, which encode two distinct isoforms, have been reported.
Interactions
PTPRA has been shown to interact with Grb2 and KCNA2.
References
Further reading |
https://en.wikipedia.org/wiki/Telomerase%20RNA%20component | Telomerase RNA component, also known as TR, TER or TERC, is an ncRNA found in eukaryotes that is a component of telomerase, the enzyme used to extend telomeres. TERC serves as a template for telomere replication (reverse transcription) by telomerase. Telomerase RNAs differ greatly in sequence and structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the template sequence. The vertebrate telomerase RNAs have a 3' H/ACA snoRNA-like domain.
Structure
TERC is a Long non-coding RNA (lncRNA) ranging in length from ~150nt in ciliates to 400-600nt in vertebrates, and 1,300nt in yeast (Alnafakh). Mature human TERC (hTR) is 451nt in length. TERC has extensive secondary structural features over 4 principal conserved domains. The core domain, the largest domain at the 5’ end of TERC, contains the CUAAC Telomere template sequence. Its secondary structure consists of a large loop containing the template sequence, a P1 loop-closing helix, and a P2/P3 pseudoknot. The core domain and CR4/CR5 conserved domain associate with TERT, and are the only domains of TERC necessary for in vitro catalytic activity of telomerase. The 3’ end of TERC consists of a conserved H/ACA domain, a 2 hairpin structure connected by a single-stranded hinge and bordered on the 3’ end by a single-stranded ACA sequence. The H/ACA domain binds Dyskerin, GAR1, NOP10, NHP2, to form an H/ACA RNP complex. The conserved CR7 domain is also localized at the 3’ end of TERC, and c |
https://en.wikipedia.org/wiki/XPA | DNA repair protein complementing XP-A cells is a protein that in humans is encoded by the XPA gene.
Function
Nucleotide excision repair (NER) is a major pathway for repairing a variety of bulky DNA damages including those introduced by UV irradiation. The XPA protein appears to play a key role in NER at sites of damage as a scaffold for other repair proteins in order to ensure that the damages are appropriately excised. Among the repair proteins with which XPA interacts is a protein complex (including the ERCC1 protein) that is capable of incising DNA at sites of damage.
Xpa mutant individuals often show the severe clinical symptoms of xeroderma pigmentosum, a condition involving extreme sensitivity to sunlight and a high incidence of skin cancer.
Interactions
XPA has been shown to interact with ERCC1, Replication protein A1 and XAB2.
References
Further reading
External links
GeneReviews/NIH/NCBI/UW entry on Xeroderma Pigmentosum |
https://en.wikipedia.org/wiki/DEK%20%28gene%29 | The human DEK gene encodes the DEK protein.
Function
This gene encodes a protein with one SAP domain. The protein binds to cruciform DNA and DNA coiled into a superhelix, thereby inducing positive supercoils into closed circular DNA. It is also involved in splice site selection during mRNA processing. Chromosomal aberrations involving this region increased expression of this gene and the presence of antibodies against this protein are all associated with various diseases.
Interactions
DEK interacts with TFAP2A.
References
Further reading
External links
PDBe-KB provides an overview of all the structure information available in the PDB for Human Protein DEK
Oncogenes |
https://en.wikipedia.org/wiki/CDK5R1 | Cyclin-dependent kinase 5 activator 1 is an enzyme that in humans is encoded by the CDK5R1 gene.
Function
The protein encoded by this gene (p35) is a neuron-specific activator of cyclin-dependent kinase 5 (CDK5); the activation of CDK5 is required for proper development of the central nervous system. The p35 form of this protein is proteolytically cleaved by calpain, generating a p25 form. The cleavage of p35 into p25 results in relocalization of the protein from the cell periphery to nuclear and perinuclear regions. P25 deregulates CDK5 activity by prolonging its activation and changing its cellular location. The p25 form accumulates in the brain neurons of patients with Alzheimer's disease. This accumulation correlates with an increase in CDK5 kinase activity, and may lead to aberrantly phosphorylated forms of the microtubule-associated protein tau, which contributes to Alzheimer's disease.
In melanocytic cells CDK5R1 gene expression may be regulated by MITF.
Interactions
CDK5R1 has been shown to interact with:
Actinin, alpha 1
Amphiphysin,
Beta-catenin,
CAMK2A,
CDK5RAP2,
Cyclin-dependent kinase 5,
Protein SET,
See also
CDK5RAP1
CDK5RAP2
CDK5RAP3
References
Further reading
External links |
https://en.wikipedia.org/wiki/WASL%20%28gene%29 | Neural Wiskott–Aldrich syndrome protein is a protein that in humans is encoded by the WASL gene.
The Wiskott–Aldrich syndrome (WAS) family of proteins share similar domain structure, and are involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton. The presence of a number of different motifs suggests that they are regulated by a number of different stimuli, and interact with multiple proteins. Recent studies have demonstrated that these proteins, directly or indirectly, associate with the small GTPase, Cdc42, known to regulate formation of actin filaments, and the cytoskeletal organizing complex, Arp2/3. The WASL gene product is a homolog of WAS protein, however, unlike the latter, it is ubiquitously expressed and shows highest expression in neural tissues. It has been shown to bind Cdc42 directly, and induce formation of long actin microspikes.
According to one study, mouse DAB1 regulates actin cytoskeleton through N-WASP.
Diseases associated with WASL include Wiskottt-Aldrich Syndrome and Vaccinia.
Interactions
WASL (gene) has been shown to interact with:
CDC42,
Cortactin
NCK1,
Profilin 1, and
RHOQ.
References
Further reading |
https://en.wikipedia.org/wiki/Major%20vault%20protein | Major vault protein is a protein that in humans is encoded by the MVP gene. 78 copies of the protein assemble into the large compartments called vaults.
Function
This gene encodes the major vault protein which is a lung infection resistance-related protein. Vaults are multi-subunit structures that may be involved in nucleo-cytoplasmic transport. This protein mediates drug resistance, perhaps via a transport process. It is widely distributed in normal tissues, and overexpressed in multidrug-resistant cancer cells. The protein overexpression is a potentially useful marker of clinical drug resistance. This gene produces two transcripts by using two alternative exon 2 sequences; however, the open reading frames are the same in both transcripts.
Interactions
Major vault protein has been shown to interact with Estrogen receptor alpha, PTEN and PARP4.
References
Further reading
Human proteins |
https://en.wikipedia.org/wiki/Alpha-actinin-4 | Alpha-actinin-4 is a protein that in humans is encoded by the ACTN4 gene.
Alpha actinins belong to the spectrin gene superfamily which represents a diverse group of cytoskeletal proteins, including the alpha and beta spectrins and dystrophins. Alpha actinin is an actin-binding protein with multiple roles in different cell types. In nonmuscle cells, the cytoskeletal isoform is found along microfilament bundles and adherens-type junctions, where it is involved in binding actin to the membrane. In contrast, skeletal, cardiac, and smooth muscle isoforms are localized to the Z-disc and analogous dense bodies, where they help anchor the myofibrillar actin filaments. This gene encodes a nonmuscle, alpha actinin isoform which is concentrated in the cytoplasm, and thought to be involved in metastatic processes. Mutations in this gene have been associated with focal and segmental glomerulosclerosis.
Interactions
Alpha-actinin-4 has been shown to interact with PDLIM1, Sodium-hydrogen exchange regulatory cofactor 2, Collagen, type XVII, alpha 1, CAMK2A, CAMK2B, MAGI1 and TRIM3.
See also
Focal segmental glomerulosclerosis
References
Further reading
External links
EF-hand-containing proteins
Human proteins |
https://en.wikipedia.org/wiki/ATP1A2 | Sodium/potassium-transporting ATPase subunit alpha-2 is a protein which in humans is encoded by the ATP1A2 gene.
Function
The protein encoded by this gene belongs to the family of P-type cation transport ATPases and to the subfamily of Na+/K+-ATPases. Na+/K+-ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+-ATPase is encoded by multiple genes. This gene encodes an alpha 2 subunit.
Clinical significance
Mutations in ATP1A2 have been found to cause hemiplegic migraine and epilepsy in an autosomal dominant fashion, sometimes co-occurring in families. Additionally, it has been associated with an unusual form of migraine called alternating hemiplegia of childhood.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Familial Hemiplegic Migraine |
https://en.wikipedia.org/wiki/Dystonin | Dystonin (DST), also known as bullous pemphigoid antigen 1 (BPAG1), isoforms 1/2/3/4/5/8, is a protein that in humans is encoded by the DST gene.
This gene encodes a member of the plakin protein family of adhesion junction plaque proteins. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the full-length nature of some variants has not been defined. It has been known that some isoforms are expressed in neural and muscle tissue, anchoring neural intermediate filaments to the actin cytoskeleton, and some isoforms are expressed in epithelial tissue, anchoring keratin-containing intermediate filaments to hemidesmosomes. Consistent with the expression, mice defective for this gene show skin blistering and neurodegeneration.
Interactions
Dystonin has been shown to interact with collagen, type XVII, alpha 1, DCTN1, MAP1B and erbin.
Loss of function in neurological disease
Several Dst mutant mouse lines have been described which share the common feature of having sensory neuron degeneration. In humans, loss of dystonin function can cause hereditary sensory and autonomic neuropathy type VI and axonal Charcot-Marie-Tooth disease. In both human diseases, pathology is likely attributable to the loss of the dystonin-a2 protein isoform, which plays a role in neuronal autophagy.
See also
Bullous pemphigoid
References
Further reading
EF-hand-containing proteins
Plakins |
https://en.wikipedia.org/wiki/C1QBP | Complement component 1 Q subcomponent-binding protein, mitochondrial is a protein that in humans is encoded by the C1QBP gene.
The human complement subcomponent C1q associates with C1r and C1s in order to yield the first component of the serum complement system. The protein encoded by this gene is known to bind to the globular heads of C1q molecules and inhibit C1 activation. This protein has also been identified as the p32 subunit of pre-mRNA splicing factor SF2, as well as a hyaluronic acid-binding protein.
Protein subunit
C1QBP is 282 amino acid in length and has three homologous subunit with its N-terminal 73 amino acid residues cleaved off to produce mature C1QBP. C1QBP appears as a monomer around 33 kDa on SDS-PAGE gel under both reducing and nonreducing condition but migrates as a trimer on size-exclusion chromatography (gel filtration).
Protein structure
The crystal structure of C1QBP at 2.25 Å resolution shows a homotrimeric ring displaying symmetry. The individual subunits are held together by noncovalent interactions and forms a doughnut shaped quaternary structure with a central cavity of 20 Å in diameter. Each Subunit of C1QBP has seven β-strand (β1- β7) and three α-helices (α1- α3). C1QBP is negatively charged on its soluble face while the membrane face is predominantly positively charged.
Interactions
C1QBP has been shown to interact with Protein kinase D1, BAT2, PRKCD, PKC alpha and Protein kinase Mζ.
Other interacting partners of C1QBP include protein dom |
https://en.wikipedia.org/wiki/Calpastatin | Calpastatin is a protein that in humans is encoded by the CAST gene.
The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1–4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length natures of only some have been determined.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: LI27.001
Proteases
EC 3.4 |
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