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https://en.wikipedia.org/wiki/Collagen%2C%20type%20VI%2C%20alpha%202 | Collagen alpha-2(VI) chain is a protein that in humans is encoded by the COL6A2 gene.
Function
This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy 1, Ullrich congenital muscular dystrophy 1, and autosomal recessive myosclerosis myopathy. Three transcript variants have been identified for this gene.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Congenital Muscular Dystrophy Overview
Collagens |
https://en.wikipedia.org/wiki/Enolase%202 | Gamma-enolase, also known as enolase 2 (ENO2) or neuron specific enolase (NSE), is an enzyme that in humans is encoded by the ENO2 gene. Gamma-enolase is a phosphopyruvate hydratase.
Gamma-enolase is one of the three enolase isoenzymes found in mammals. This isoenzyme, a homodimer, is found in mature neurons and cells of neuronal origin. A switch from alpha enolase to gamma enolase occurs in neural tissue during development in rats and primates.
Interactive pathway map
Utility
Detection of NSE with antibodies can be used to identify neuronal cells and cells with neuroendocrine differentiation. NSE is produced by small-cell carcinomas, which are neuroendocrine in origin. NSE is therefore a useful tumor marker for distinguishing small-cell carcinomas from other tumors.
References
Further reading
External links
EC 4.2.1
Diagnostic neurology |
https://en.wikipedia.org/wiki/B4GALT1 | Beta-1,4-galactosyltransferase 1 is an enzyme that in humans is encoded by the B4GALT1 gene.
This gene is one of seven beta-1,4-galactosyltransferase (beta4GalT) genes. They encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose; all transfer galactose in a beta1,4 linkage to similar acceptor sugars: GlcNAc, Glc, and Xyl. Each beta4GalT has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus and which then remains uncleaved to function as a transmembrane anchor. By sequence similarity, the beta4GalTs form four groups: beta4GalT1 and beta4GalT2, beta4GalT3 and beta4GalT4, beta4GalT5 and beta4GalT6, and beta4GalT7. This gene is unique among the beta4GalT genes because it encodes an enzyme that participates both in glycoconjugate and lactose biosynthesis. For the first activity, the enzyme adds galactose to N-acetylglucosamine residues that are either monosaccharides or the nonreducing ends of glycoprotein carbohydrate chains. The second activity is restricted to lactating mammary tissues where the enzyme forms a heterodimer with alpha-lactalbumin to catalyze UDP-galactose + D-glucose <=> UDP + lactose. The two enzymatic forms result from alternate transcription initiation sites and post-translational processing. Two transcripts, which dif |
https://en.wikipedia.org/wiki/P%20protein | P protein, also known as melanocyte-specific transporter protein or pink-eyed dilution protein homolog, is a protein that in humans is encoded by the oculocutaneous albinism II (OCA2) gene. The P protein is believed to be an integral membrane protein involved in small molecule transport, specifically of tyrosine—a precursor of melanin. Certain mutations in OCA2 result in type 2 oculocutaneous albinism. OCA2 encodes the human homologue of the mouse p (pink-eyed dilution) gene.
The human OCA2 gene is located on the long arm (q) of chromosome 15, specifically from base pair 28,000,020 to base pair 28,344,457 on chromosome 15.
Function
OCA2 provides instructions for making the protein called P protein which is located in melanocytes which are specialized cells that produce melanin, and in the cells of the retinal pigment epithelium. Melanin is responsible for giving color to the skin, hair, and eyes. Moreover, melanin is found in the light-sensitive tissue of the retina of the eye which plays a role in normal vision.
The exact function of protein P is unknown, but it has been found that it is essential for the normal coloring of skin, eyes, and hair; and likely involved in melanin production. This gene seems to be the main determinant of eye color depending on the amount of melanin production in the iris stroma (large amounts giving rise to brown eyes; little to no melanin giving rise to blue eyes).
This gene is mutated in Astyanax mexicanus, a Mexican fish which is charact |
https://en.wikipedia.org/wiki/PDZK1 | Na(+)/H(+) exchange regulatory cofactor NHE-RF3 is a protein that in humans is encoded by the PDZK1 gene.
Interactions
PDZK1 has been shown to interact with:
AKAP10,
CLCN3,
Cystic fibrosis transmembrane conductance regulator
FARP2,
PDZK1IP1,
SLC22A12,
SLC22A4,
SLC34A3,
SLK, and
Sodium-hydrogen antiporter 3 regulator 1.
Related gene problems
TAR syndrome
1q21.1 deletion syndrome
1q21.1 duplication syndrome
References
Further reading |
https://en.wikipedia.org/wiki/KLK6 | Kallikrein-6 is a protein that in humans is encoded by the KLK6 gene. Kallikrein-6 is also referred to as neurosin, protease M, hK6, or zyme. It is a 223 amino acid sequence, derived from its 244 original form, which contains a 16 residue presignal and 5 residue activation peptide.
Function
Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. The encoded enzyme is regulated by steroid hormones. In tissue culture, the enzyme has been found to generate amyloidogenic fragments from the amyloid precursor protein, suggesting a potential for involvement in Alzheimer's disease. Multiple alternatively spliced transcript variants that encode different isoforms have been identified for this gene.
Structure
The secondary structure consists of 13 beta-pleated sheets, 2 alpha-helices, 2 310-helices, and 8 loop regions. In terms of amino acid sequences, hK6 is most similar to myelencephalon-specific protease (MSP), which comes from the rat kvllikrein gene family. MSP and hK6 both target the peptide bond where arginine follows and they both automatically cleave themselves at their Arg positions.
However, structurally, hK6 most resembles trypsin found in cows/oxen. Surrounding the active site, there are sh |
https://en.wikipedia.org/wiki/Poliovirus%20receptor-related%201 | Poliovirus receptor-related 1 (PVRL1), also known as nectin-1 and CD111 (formerly herpesvirus entry mediator C, HVEC) is a human protein of the immunoglobulin superfamily (IgSF), also considered a member of the nectins. It is a membrane protein with three extracellular immunoglobulin domains, a single transmembrane helix and a cytoplasmic tail. The protein can mediate Ca2+-independent cellular adhesion further characterizing it as IgSF cell adhesion molecule (IgSF CAM).
Function
PVRL1 is an adhesion molecule found in a wide range of tissues where it localizes in various junctions such as the adherens junction of epithelial tissue or the chemical synapse of neurons. The cytoplasmic tail of PVRL1 can bind the protein afadin which is a scaffolding protein that binds actin.
In the chemical synapse PVRL1 interacts with PVRL3 (nectin-3) and both proteins can be found in neuronal tissue already in early stages of brain development as well as in aging brains. The two proteins have been found to localize asymmetrically along the chemical synapse, with PVRL1 primarily on the axonal side and PVRL3 on the dendritic side.
The protein has been revealed as one of the key players in mediating cellular entry of the Herpes simplex virus by interacting with the viral glycoprotein D (gD).
See also
Cluster of differentiation
Interactions
PVRL1 has been shown to interact with MLLT4.
References
Further reading
External links
Clusters of differentiation |
https://en.wikipedia.org/wiki/SAFB | Scaffold attachment factor B, also known as SAFB, is a gene with homologs that have been studied in humans and mice.
Function
This gene encodes a DNA-binding protein that has specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there are conflicting views as to whether this protein is a component of chromatin, the nuclear matrix, or both. Scaffold attachment factors are a subset of nuclear matrix proteins (NMP) with enriched binding to AT-rich S/MAR sequences. The SAF-B protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of the heat shock protein 27 transcription and also can act as an estrogen receptor corepressor. This gene is a candidate gene for breast tumorigenesis.
Interactions
SAFB has been shown to interact with:
Estrogen receptor alpha,
HNRPD,
SAFB2, and
TAF15.
References
Further reading |
https://en.wikipedia.org/wiki/SOX10 | Transcription factor SOX-10 is a protein that in humans is encoded by the SOX10 gene.
Function
This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and determination of cell fate. The encoded protein acts as a transcriptional activator after forming a protein complex with other proteins. This protein acts as a nucleocytoplasmic shuttle protein and is important for neural crest and peripheral nervous system development.
In melanocytic cells, there is evidence that SOX10 gene expression may be regulated by MITF.
Mutations
Mutations in this gene are associated with Waardenburg–Shah syndrome and uveal melanoma.
Immunostain
SOX10 is used as an immunohistochemistry marker, being positive in:
Neuroectodermal neoplasms of neural crest origin, especially:
Melanoma, although desmoplastic melanomas may be only focally positive.
Nevus
Interactions
The interaction between SOX10 and PAX3 is studied best in human patients with Waardenburg syndrome, an autosomal dominant disorder that is divided into four different types based upon mutations in additional genes. SOX10 and PAX3 interactions are thought to be regulators of other genes involved in the symptoms of Waardenburg syndrome, particularly MITF, which influences the development of melanocytes as well as neural crest formation. MITF expression can be transactivated by both SOX10 and PAX3 to have an additive effect. The two genes have bindi |
https://en.wikipedia.org/wiki/SULT1A3 | Sulfotransferase 1A3/1A4 is an enzyme that in humans is encoded by the SULT1A3 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 a phenol sulfotransferase with thermolabile enzyme activity. Four sulfotransferase genes are located on the p arm of chromosome 16; this gene and SULT1A4 arose from a segmental duplication. This gene is the most centromeric of the four sulfotransferase genes. Exons of this gene overlap with exons of a gene that encodes a protein containing GIY-YIG domains (GIYD1). Three alternatively spliced variants that encode the same protein have been described.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Thymine-DNA%20glycosylase | G/T mismatch-specific thymine DNA glycosylase is an enzyme that in humans is encoded by the TDG gene. Several bacterial proteins have strong sequence homology with this protein.
Function
The protein encoded by this gene belongs to the TDG/mug DNA glycosylase family. Thymine-DNA glycosylase (TDG) removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of DNA and the mispaired thymine. With lower activity, this enzyme also removes thymine from C/T and T/T mispairings. TDG can also remove uracil and 5-bromouracil from mispairings with guanine. TDG knockout mouse models showed no increase in mispairing frequency suggesting that other enzymes, like the functional homologue MBD4, may provide functional redundancy. This gene may have a pseudogene in the p arm of chromosome 12.
Additionally, in 2011, the human thymine DNA glycosylase (hTDG) was reported to efficiently excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), the key oxidation products of 5-methylcytosine in genomic DNA. Later on, the crystal structure of the hTDG catalytic domain in complex with duplex DNA containing 5caC was published, which supports the role of TDG in mammalian 5-methylcytosine demethylation.
Interactions
Thymine-DNA glycosylase has been shown to interact with:
CREB-binding protein,
Estrogen receptor alpha,
Promyelocytic leukemia protein,
SUMO3, and
Small ubiquitin-related modifier 1.
Interactive pathway map
Referen |
https://en.wikipedia.org/wiki/TLE1 | Transducin-like enhancer protein 1 is a protein that in humans is encoded by the TLE1 gene.
Interactions
TLE1 has been shown to interact with:
Glycoprotein 130,
HES6,
RUNX1,
RUNX3,
SIX3
TLE2, and
UTY.
References
Further reading |
https://en.wikipedia.org/wiki/Translationally%20controlled%20tumor%20protein | Translationally controlled tumor protein (TCTP) is a protein that in humans is encoded by the TPT1 gene. TPT1 is mapped to 13q12-q14 on chromosome 13. The human gene contains five introns and six exons, TPT1 contains a promoter with a canonical TATA-box and several promoter elements, which are well-conserved in mammals. The assay with reporter gene exhibits a strong promoter activity comparable to viral promoters.
TCTP protein is also known as p23, Fortilin, and histamine-releasing factor.
TCTP is a multifunctional and highly conserved protein that existed ubiquitously in different eukaryote species and distributed widely in various tissues and cell types.
TCTP in the human is a growth-related, calcium-binding protein.
History
Translationally controlled tumor protein was first discovered in 1989 as a cDNA sequence obtained from a human mammary carcinoma cDNA library with proves derived from the translationally controlled, growth-related mouse tumor protein TCTP. TCTP was originally described as a growth related protein of tumor cells. Its mRNA accumulates in translationally repressed postpolysomal mRNP-complexes.
Research in 1997 shown that TCTP is not a tumor- or tissue-specific protein, but is expressed ubiquitously from plants to mammals. Later studies show TCTP involvement in a protozoan Trypanosoma brucei.
Characteristics
TCTP is a 20–25 kDa protein abundantly and ubiquitously expressed in the cell. The protein is transcribed in more than 500 different tissues a |
https://en.wikipedia.org/wiki/SMARCA5 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 is a protein that in humans is encoded by the SMARCA5 gene.
Function
The protein encoded by this gene is a member of the ISWI family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein.
Interactions
SMARCA5 has been shown to interact with RAD21, Histone deacetylase 2, POLE3, SATB1 and BAZ1A.
References
Further reading |
https://en.wikipedia.org/wiki/Herpesvirus%20entry%20mediator | Herpesvirus entry mediator (HVEM), also known as tumor necrosis factor receptor superfamily member 14 (TNFRSF14), is a human cell surface receptor of the TNF-receptor superfamily.
Nomenclature
This protein was originally known as herpesvirus entry mediator A (HveA); HveB and HveC are structurally unrelated proteins of the immunoglobulin superfamily. It is also known as CD270 in the cluster of differentiation classification. Moreover, it is also referred to as ATAR (another TRAF-associated receptor).
Function
The protein encoded by this gene is a member of the TNF-receptor superfamily. The cytoplasmic region of this receptor was found to bind to several TNF receptor associated factor (TRAF) family members, which may mediate the signal transduction pathways that activate the immune response.
In melanocytic cells TNFRSF14 gene expression may be regulated by MITF.
Interactions
TNFRSF14 has been shown to interact with TRAF2, TNFSF14 and TRAF5.
Clinical relevance
Mutations in this gene have been recurrently been associated to cases of diffuse large B-cell lymphoma and pediatric-type follicular lymphoma.
This receptor was identified as a cellular mediator of herpes simplex virus (HSV) entry. Binding of HSV viral envelope glycoprotein D (gD) to this receptor protein has been shown to be part of the viral entry mechanism.
References
Further reading
TNF receptor family |
https://en.wikipedia.org/wiki/ST2%20cardiac%20biomarker | The ST2 cardiac biomarker (also known as soluble interleukin 1 receptor-like 1) is a protein biomarker of cardiac stress encoded by the IL1RL1 gene. ST2 signals the presence and severity of adverse cardiac remodeling and tissue fibrosis, which occurs in response to myocardial infarction, acute coronary syndrome, or worsening heart failure.
ST2 provides prognostic information that is independent of other cardiac biomarkers such as BNP, NT-proBNP, highly sensitive troponin, GDF-15, and galectin-3. One study indicated that discrimination is independent of age, body mass index, history of heart failure, anemia and impaired kidney function or sex.
Protein
ST2 is a member of the interleukin 1 receptor family. The ST2 protein has two isoforms and is directly implicated in the progression of cardiac disease: a soluble form (referred to as soluble ST2 or sST2) and a membrane-bound receptor form (referred to as the ST2 receptor or ST2L). When the myocardium is stretched, the ST2 gene is upregulated, increasing the concentration of circulating soluble ST2. The ligand for ST2 is the cytokine interleukin-33 (IL-33). Binding of IL-33 to the ST2 receptor, in response to cardiac disease or injury, such as an ischemic event, elicits a cardioprotective effect resulting in preserved cardiac function. This cardioprotective IL-33 signal is counterbalanced by the level of soluble ST2, which binds IL-33 and makes it unavailable to the ST2 receptor for cardioprotective signaling. As a result, t |
https://en.wikipedia.org/wiki/TUBA1B | Tubulin alpha-1B chain is a protein that in humans is encoded by the TUBA1B gene.
Interactions
TUBA1B has been shown to interact with PIK3R1.
Antibodies against tubulin alpha 1b can be used as markers for microtubules and spindles.
References
Further reading
External links |
https://en.wikipedia.org/wiki/VKORC1 | The human gene VKORC1 encodes for the enzyme, Vitamin K epOxide Reductase Complex (VKORC) subunit 1. This enzymatic protein complex is responsible for reducing vitamin K 2,3-epoxide to its active form, which is important for effective clotting (coagulation). In humans, mutations in this gene can be associated with deficiencies in vitamin-K-dependent clotting factors.
Function
The VKORC1 protein is a key enzyme in the vitamin K cycle. VKORC1 is a 163 amino acid integral membrane protein associated with the endoplasmic reticulum and VKORC1 mRNA is broadly expressed in many different tissues. VKORC1 is involved in the vitamin K cycle by reduction of vitamin K epoxide to vitamin K, which is the rate-limiting step in the physiological process of vitamin K recycling. The availability of reduced vitamin K is of importance for activation vitamin K 2,3-epoxide. The reduction of vitamin K epoxide is then responsible for the carboxylation of glutamic acid residues in some blood-clotting proteins, including factor VII, factor IX, and factor X. VKORC1 is of therapeutic interest both for its role in contributing to high interpatient variability in coumarin anticoagulant dose requirements and as a potential player in vitamin K deficiency disorders.
Warfarin is a commonly prescribed oral anticoagulant, or blood thinner used to treat blood clots such as deep vein thrombosis and pulmonary embolism and to prevent stroke in people who have atrial fibrillation, valvular heart disease or artif |
https://en.wikipedia.org/wiki/DNA%20replication%20factor%20CDT1 | CDT1 (Chromatin licensing and DNA replication factor 1) is a protein that in humans is encoded by the CDT1 gene. It is a licensing factor that functions to limit DNA from replicating more than once per cell cycle.
Role in pre-replication complexes
The protein encoded by this gene is a key licensing factor in the assembly of pre-replication complexes (pre-RC), which occurs during the G1 phase of the cell cycle. In the assembly of pre-RCs, origin recognition complexes (ORC1-6) recognize and bind to DNA replication origins. CDT1, along with the protein CDC6, are then recruited to the forming pre-RC, followed by minichromosome maintenance complexes (MCM2-7).
The activity of CDT1 during the cell cycle is tightly regulated during the S phase by the protein geminin, which inhibits it, and by SCFSKP2, which ubiquinates the protein to tag it for proteasomal degradation. This regulation is important in preventing relicensing, thus ensuring that DNA is only replicated once per cell cycle.
Orthologs
CDT1 belongs to a family of replication proteins conserved from yeast to humans. Examples of orthologs in other species include:
S. pombe – CDT1 (CDC10-dependent transcript 1)
Drosophila melanogaster – 'double parked' or Dup
Xenopus laevis - CDT1
Interactions
DNA replication factor CDT1 has been shown to interact with SKP2. Cdt1 is recruited by the origin recognition complex in origin licensing. Null-mutations for CDT1 are lethal in yeast; the spores undergo mitosis without DNA repli |
https://en.wikipedia.org/wiki/ACTL6A | Actin-like protein 6A is a protein that in humans is encoded by the ACTL6A gene.
Function
This gene encodes a family member of actin-related proteins (ARPs), which share significant amino acid sequence identity to conventional actins. Both actins and ARPs have an actin fold, which is an ATP-binding cleft, as a common feature. The ARPs are involved in diverse cellular processes, including vesicular transport, spindle orientation, nuclear migration and chromatin remodeling. This gene encodes a 53 kDa subunit protein of the BAF (BRG1/brm-associated factor) complex in mammals, which is functionally related to SWI/SNF complex in S. cerevisiae and Drosophila; the latter is thought to facilitate transcriptional activation of specific genes by antagonizing chromatin-mediated transcriptional repression. Together with beta-actin, it is required for maximal ATPase activity of BRG1, and for the association of the BAF complex with chromatin/matrix. Three transcript variants that encode two different protein isoforms have been described.
Clinical significance
ACTL6A is amplified in head and squamous cancers and confers poor prognosis in patients. In hepatocellular carcinomas, it promotes metastasis.
Interactions
ACTL6A has been shown to interact with SMARCA2, Myc, Transformation/transcription domain-associated protein, RuvB-like 1 and SMARCA4.
References
Further reading
Human proteins |
https://en.wikipedia.org/wiki/AMY1A | Alpha-amylase 1 is an enzyme that in humans is encoded by the AMY1A gene. This gene is found in many organisms.
Amylases are secreted proteins that hydrolyze 1,4-alpha-glucoside bonds in oligosaccharides and polysaccharides, and thus catalyze the first step in digestion of dietary starch and glycogen. The human genome has a cluster of several amylase genes that are expressed at high levels in either salivary gland or pancreas. This gene encodes an amylase isoenzyme produced by the salivary gland. Alternative splicing results in multiple transcript variants encoding the same protein.
See also
AMY2A
References
External links
Further reading |
https://en.wikipedia.org/wiki/Cav1.4 | {{DISPLAYTITLE:Cav1.4}}
Cav1.4 also known as the calcium channel, voltage-dependent, L type, alpha 1F subunit (CACNA1F), is a human gene.
This gene encodes a member of the alpha-1 subunit family; a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. The alpha-1 subunit has 24 transmembrane segments and forms the pore through which ions pass into the cell. There are multiple isoforms of each of the proteins in the complex, either encoded by different genes or the result of alternative splicing of transcripts. Alternate transcriptional splice variants of the gene described here have been observed but have not been thoroughly characterized. Mutations in this gene have been shown to cause incomplete X-linked congenital stationary night blindness type 2 (CSNB2).
See also
Calcium channel
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on X-Linked Congenital Stationary Night Blindness
Ion channels |
https://en.wikipedia.org/wiki/HSD17B10 | 17-β-Hydroxysteroid dehydrogenase X (HSD10) also known as 3-hydroxyacyl-CoA dehydrogenase type-2 is a mitochondrial enzyme that in humans is encoded by the HSD17B10 (hydroxysteroid (17β) dehydrogenase 10) gene. Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. Human HSD10 cDNA was cloned from the brain (NM_004493), and the resulting protein, a homotetramer, was first characterized as a short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD). Active sites of this enzyme can accommodate different substrates; 17β-HSD10 is involved in the oxidation of isoleucine, branched-chain fatty acids, and xenobiotics as well as the metabolism of sex hormones and neuroactive steroids.
Function
17beta-hydroxysteroid dehydrogenase 10 is a member of the short-chain dehydrogenase/reductase superfamily. This homotetrameric mitochondrial multifunctional enzyme catalyzes the oxidation of neuroactive steroids and the degradation of isoleucine. This enzyme is capable of binding to other peptides, such as estrogen receptor α, amyloid-β, and tRNA methyltransferase 10C. Missense mutations of the HSD17B10 gene result in 17β-HSD10 deficiency, an infantile neurodegeneration characterized by progressive psychomotor regression and alteration of mitochondria morphology. 17β-HSD10 exhibits only a negligible alcohol dehydrogenase activity, and is not localized in the endoplasmic reticulum or plasma membrane. Its |
https://en.wikipedia.org/wiki/Indian%20hedgehog%20%28protein%29 | Indian hedgehog homolog (Drosophila), also known as IHH, is a protein which in humans is encoded by the IHH gene. This cell signaling protein is in the hedgehog signaling pathway. The several mammalian variants of the Drosophila hedgehog gene (which was the first named) have been named after the various species of hedgehog; the Indian hedgehog is honored by this one. The gene is not specific to Indian hedgehogs.
Function
The Indian hedgehog protein is one of three proteins in the mammalian hedgehog family, the others being desert hedgehog (DHH) and sonic hedgehog (SHH). It is involved in chondrocyte differentiation, proliferation and maturation especially during endochondral ossification. It regulates its effects by feedback control of parathyroid hormone-related peptide (PTHrP).
Indian Hedge Hog, (Ihh) is one of three signaling molecules from the Hedgehog (Hh) gene family. Genes of the Hh family, Sonic Hedgehog (Shh), Desert Hedgehog (Dhh) and Ihh regulate several fetal developmental processes. The Ihh homolog is involved in the formation of chondrocytes during the development of limbs. The protein is released by small, non-proliferating, mature chondrocytes during endochondral ossification. Recently, Ihh mutations are shown to cause brachydactyly type A1 (BDA1), the first Mendelian autosomal dominant disorder in humans to be recorded. There are seven known mutations to Ihh that cause BDA1. Of particular interest, are mutations involving the E95 residue, which is thought |
https://en.wikipedia.org/wiki/KCNA2 | Potassium voltage-gated channel subfamily A member 2 also known as Kv1.2 is a protein that in humans is encoded by the KCNA2 gene.
Function
Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. The coding region of this gene is intronless, and the gene is clustered with genes KCNA3 and KCNA10 on chromosome 1.
Interactions
KCNA2 has been shown to interact with KCNA4, DLG4, PTPRA, KCNAB2, RHOA and Cortactin.
Clinical
Mutations in this gene have been associated with hereditary spastic paraplegia.
See also
Voltage-gated potassium channel
Pandinotoxin
References
Further reading
External links
Ion channels |
https://en.wikipedia.org/wiki/LAMP1 | Lysosomal-associated membrane protein 1 (LAMP-1) also known as lysosome-associated membrane glycoprotein 1 and CD107a (Cluster of Differentiation 107a), is a protein that in humans is encoded by the LAMP1 gene. The human LAMP1 gene is located on the long arm (q) of chromosome 13 at region 3, band 4 (13q34).
Lysosomal-associated membrane protein 1 is a glycoprotein from a family of Lysosome-associated membrane glycoproteins. The LAMP-1 glycoprotein is a type I transmembrane protein which is expressed at high or medium levels in at least 76 different normal tissue cell types. It resides primarily across lysosomal membranes, and functions to provide selectins with carbohydrate ligands. CD107a has also been shown to be a marker of degranulation on lymphocytes such as CD8+ and NK cells, and may also play a role in tumor cell differentiation and metastasis.
Structure
Residing primarily across lysosomal membranes, these glycoproteins consist of a large, highly glycosylated end with N-linked carbon chains on the luminal side of the membrane, and a short C-terminal tail exposed to the cytoplasm. The extracytoplasmic region contains a hinge-like structure which can form disulphide bridges homologous to those observed in human immunoglobulin A. Other characteristics of the structure of the LAMP-1 glycoproteins include:
A polypeptide core of ~40kDa
18 {N-glycosylation} sites to help with the addition of sugar chains
Polylactosamine attachments which protect the glyocoprotein from |
https://en.wikipedia.org/wiki/NOV%20%28gene%29 | NOV (nephroblastoma overexpressed) also known as CCN3 is a matricellular protein that in humans is encoded by the NOV gene.
CCN family
NOV is a member of the CCN family of secreted, extracellular matrix (ECM)-associated signaling proteins (see also CCN intercellular signaling protein). The CCN acronym is derived from the first three members of the family being identified, namely CYR61 (cysteine-rich angiogenic inducer 61, or CCN1), CTGF (connective tissue growth factor, or CCN2), and NOV. These proteins, together with WISP1 (CCN4), WISP2 (CCN5), and WISP3 (CCN6) comprise the six-member CCN family in vertebrates and have been renamed CCN1-6 in the order of their discovery by international consensus.
Structure
The human NOV protein contains 357 amino acids with an N-terminal secretory signal peptide followed by four structurally distinct domains with homologies to insulin-like growth factor binding protein (IGFBP), von Willebrand type C repeats (vWC), thrombospondin type 1 repeat (TSR), and a cysteine knot motif within the C-terminal (CT) domain.
Function
NOV regulates multiple cellular activities including cell adhesion, migration, proliferation, differentiation, and survival. It functions by direct binding to integrin receptors, as well as other receptors such as NOTCH1 and fibulin 1c (FBLN1).
NOV is expressed during wound healing and induces angiogenesis in vivo. It is essential for self-renewal of CD34+ hematopoietic stem cells from umbilical cord blood. Nov is reg |
https://en.wikipedia.org/wiki/PSMD3 | 26S proteasome non-ATPase regulatory subunit 3 is an enzyme that in humans is encoded by the PSMD3 gene.
Function
The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the non-ATPase subunits of the 19S regulator lid.
Clinical significance
The proteasome and its subunits are of clinical significance for at least two reasons: (1) a compromised complex assembly or a dysfunctional proteasome can be associated with the underlying pathophysiology of specific diseases, and (2) they can be exploited as drug targets for therapeutic interventions. More recently, more effort has been made to consider the proteasome for the development of novel diagnostic markers and strategies. An improved and comprehensive understanding of the pathophysiology of the proteasome should lead to clinical ap |
https://en.wikipedia.org/wiki/RANGAP1 | Ran GTPase-activating protein 1 is an enzyme that in humans is encoded by the RANGAP1 gene.
Function
RanGAP1, is a homodimeric 65-kD polypeptide that specifically induces the GTPase activity of RAN, but not of RAS by over 1,000-fold. RanGAP1 is the immediate antagonist of RCC1, a regulator molecule that keeps RAN in the active, GTP-bound state. The RANGAP1 gene encodes a 587-amino acid polypeptide. The sequence is unrelated to that of GTPase activators for other RAS-related proteins, but is 88% identical to Rangap1 (Fug1), the murine homolog of yeast Rna1p. RanGAP1 and RCC1 control RAN-dependent transport between the nucleus and cytoplasm. RanGAP1 is a key regulator of the RAN GTP/GDP cycle.
Interactions
RanGAP1 is a trafficking protein which helps transport other proteins from the cytoplasm to the nucleus. Small ubiquitin-related modifier needs to be associated with it before it can be localized at the nuclear pore.
RANGAP1 has been shown to interact with:
Ran, and
UBE2I.
References
Further reading |
https://en.wikipedia.org/wiki/60S%20acidic%20ribosomal%20protein%20P0 | 60S acidic ribosomal protein P0 is a protein that in humans is encoded by the RPLP0 gene.
Ribosomes catalyze protein synthesis and consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein, which is the functional equivalent of the E. coli L10 ribosomal protein, belongs to the L10P family of ribosomal proteins. It is a neutral phosphoprotein with a C-terminal end that is nearly identical to the C-terminal ends of the acidic ribosomal phosphoproteins P1 and P2. The P0 protein can interact with P1 and P2 to form a pentameric complex consisting of P1 and P2 dimers, and a P0 monomer. The protein is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.
References
Further reading
Ribosomal proteins |
https://en.wikipedia.org/wiki/SGTA | Small glutamine-rich tetratricopeptide repeat-containing protein alpha is a protein that in humans is encoded by the SGTA gene. SGTA orthologs have also been identified in several mammals for which complete genome data are available.
Function
This gene encodes a protein which is capable of interacting with the major nonstructural protein of parvovirus H-1 and 70-kDa heat shock cognate protein; however, its function is not known. Since this transcript is expressed ubiquitously in various tissues, this protein may serve a housekeeping function.
Interactions
SGTA has been shown to interact with Growth hormone receptor.
References
Further reading
Co-chaperones |
https://en.wikipedia.org/wiki/FSCN1 | Fascin is a protein that in humans is encoded by the FSCN1 gene.
Interactions
FSCN1 has been shown to interact with Low affinity nerve growth factor receptor and PKC alpha.
References
Further reading |
https://en.wikipedia.org/wiki/Syntrophin%2C%20alpha%201 | Alpha-1-syntrophin is a protein that in humans is encoded by the SNTA1 gene. Alpha-1 syntrophin is a signal transducing adaptor protein and serves as a scaffold for various signaling molecules. Alpha-1 syntrophin contains a PDZ domain, two Pleckstrin homology domain and a 'syntrophin unique' domain.
Function
Dystrophin is a large, rod-like cytoskeletal protein found at the inner surface of muscle fibers. Dystrophin is missing in Duchenne Muscular Dystrophy patients and is present in reduced amounts in Becker Muscular Dystrophy patients. The protein encoded by this gene is a peripheral membrane protein found associated with dystrophin and dystrophin-related proteins. This gene is a member of the syntrophin gene family, which contains at least two other structurally related genes. The PDZ domain of syntrophin-α1(SNTA1), the most abundant isoform in the heart, has been reported to bind to the C-terminal domain of murine cardiac voltage-gated sodium channels (SkM2) causing altering ion channel activity leading to Long QT syndrome.
Interactions
Syntrophin, alpha 1 has been shown to interact with Dystrophin, Nav1.1 and Nav1.5, and Aquaporin 4.
References
Further reading |
https://en.wikipedia.org/wiki/STXBP1 | Syntaxin-binding protein 1 (also known as Munc18-1) is a protein that in humans is encoded by the STXBP1 gene. This gene encodes a syntaxin-binding protein. The encoded protein appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Mutations in this gene have been associated with neurological disorders including epilepsy, intellectual disability, and movement disorders.
Structure
The STXBP1 gene is located on the q arm of chromosome 9 in position 34.11 and has 20 exons spanning 80,510 base pairs. The encoded protein is a peripheral membrane protein located in the cytosol. In the retina and cerebellum, an alternatively spliced transcript variant is expressed, containing an additional exon and totaling 603 amino acids. Alternative splicing can produce an isoform with exon 19 and an isoform without.
Function
The encoded protein may participate in the regulation of synaptic vesicle docking and fusion, possibly through interaction with GTP-binding proteins. It is essential for neurotransmission and binds syntaxin, a component of the synaptic vesicle fusion machinery probably in a 1:1 ratio. It can interact with syntaxins 1, 2, and 3 but not syntaxin 4 and may play a role in determining the specificity of intracellular fusion reactions. This protein functions in a late stage of the intracellular membrane fusion process of exocytosis. Dissociation of this protein from syntaxin determines the kinetics of pos |
https://en.wikipedia.org/wiki/TFDP1 | Transcription factor Dp-1 is a protein that in humans is encoded by the TFDP1 gene.
Function
The E2F transcription factor family (see MIM 189971) regulates the expression of various cellular promoters, particularly those involved in the cell cycle. E2F factors bind to DNA as homodimers or heterodimers in association with dimerization partner DP1. TFDP1 may be the first example of a family of related transcription factors; see TFDP2 (MIM 602160).[supplied by OMIM]
Interactions
TFDP1 has been shown to interact with:
E2F1,
E2F5, and
P53.
References
Further reading |
https://en.wikipedia.org/wiki/Ubiquitin%20C | Polyubiquitin-C is a protein encoded by the UBC gene in humans. Polyubiquitin-C is one of the sources of ubiquitin, along with UBB, UBA52, and RPS27A.
UBC gene is one of the two stress-regulated polyubiquitin genes (UBB and UBC) in mammals. It plays a key role in maintaining cellular ubiquitin levels under stress conditions. Defects of UBC gene could lead to mid-gestation embryonic lethality.
Structure
Gene
UBC gene is located at chromosome 12q24.3, consisting of 2 exons. The promoter of the UBC gene contains putative heat shock elements (HSEs), which mediates UBC induction upon stress. UBC gene differs from UBB gene in the number of Ub coding units they contain. Nine to ten Ub units were in the UBC gene.
Protein
In polyubiquitin-C, the C-terminus of a given ubiquitin molecule is covalently conjugated to either the N-terminal residue or one of seven lysine residues of another ubiquitin molecule. Different linking of ubiquitin chains results in distinct conformations. There are 8 linkage types of polyubiquitin-C, and each type possesses the linkage-dependent dynamics and a linkage-specific conformation.
Function
The diversity of polyubiquitin-C means that ubiquitylation contributes to the regulation of many cellular events. Polyubiquitin-C doesn’t activate the heat-shock response, but it plays a key role in sustaining the response. UBC gene transcription is induced during stress and provides extra ubiquitin necessary to remove damaged/unfolded proteins. Polyubiquitin-C h |
https://en.wikipedia.org/wiki/UBE2L3 | Ubiquitin-conjugating enzyme E2 L3 (UBE2L3), also called UBCH7, is a protein that in humans is encoded by the UBE2L3 gene. As an E2 enzyme, UBE2L3 participates in ubiquitination to target proteins for degradation. The role of UBE2L3 in the ubiquitination of the NF-κB precursor implicated it in various major autoimmune diseases, including rheumatoid arthritis (RA), celiac disease, Crohn's disease (CD), and systemic lupus erythematosus.
Structure
Gene
The UBE2L3 gene is located at chromosome 22q11.21, consisting of 6 exons. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
Protein
There are 38 E2 enzymes in humans. They all contain a conserved catalytic core domain that interacts with E1 and E3 and many E2s possess additional N- and/or C-terminal protein sequences. In contrast to other E2s, residues necessary for lysine reactivity are absent: the D87 and D117 residues (in UBCH5C numbering) are replaced by Pro and His residues.
Function
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s). E2s play a key role in the whole ubiquitin (Ub) transfer pathway and are responsible for Ub cellular signaling. Unlike many E2s that transfer Ub with RINGs, UBE2L3 has E3-independe |
https://en.wikipedia.org/wiki/PLA2G6 | 85 kDa calcium-independent phospholipase A2, also known as 85/88 kDa calcium-independent phospholipase A2, Group VI phospholipase A2, Intracellular membrane-associated calcium-independent phospholipase A2 beta, or Patatin-like phospholipase domain-containing protein 9 is an enzyme that in humans is encoded by the PLA2G6 gene.
Structure
The PLA2G6 gene is located on the p arm of chromosome 22 at position 13.1 and it spans 80,605 base pairs. The PLA2G6 gene produces an 18.6 kDa protein composed of 166 amino acids. The resulting protein's structure has been shown to contain a lipase motif and 8 ankyrin repeats. Different from rodent PLA2G6, which is known to share 90% overall amino acid sequence identity with that of the humans, the human PLA2G6 protein contains a 54-residue insertion which codes for a proline-rich region. This insertion has been shown to disrupt the last putative ankyrin repeat, as well as function as a linker region that segregates the N-terminal protein-binding domain from the C-terminal catalytic domain.
Function
The PLA2G6 gene encodes for a phospholipase A2 enzyme, which is a subclass of enzyme that catalyzes the release of fatty acids from phospholipids. This type of enzyme is responsible for breaking down (metabolizing) phospholipids. Phospholipid metabolism is essential for many body processes, including helping to maintain the integrity of the cell membrane.
Specifically, the A2 phospholipase produced from the PLA2G6 gene, sometimes called PLA2 gr |
https://en.wikipedia.org/wiki/TNFSF12 | Tumor necrosis factor ligand superfamily member 12 also known as TNF-related weak inducer of apoptosis (TWEAK) is a protein that in humans is encoded by the TNFSF12 gene.
Function
TWEAK was discovered in 1997. The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein is a ligand for the FN14/TWEAKR receptor. This cytokine has overlapping signaling functions with TNF, but displays a much wider tissue distribution. Leukocytes are the main source of TWEAK including human resting and activated monocytes, dendritic cells and natural killer cells. TWEAK can induce apoptosis via multiple pathways of cell death in a cell type-specific manner. This cytokine is also found to promote proliferation and migration of endothelial cells, and thus acts as a regulator of angiogenesis.
Clinical significance
Excessive activation of the TWEAK pathway in chronic injury has been described to promote pathological tissue changes including chronic inflammation, fibrosis and angiogenesis. In chronic liver disease, for example, TWEAK expression is enhanced and causes hepatic stellate cells, which are key regulators of liver fibrosis, to proliferate.
References
Further reading |
https://en.wikipedia.org/wiki/DLK1 | Protein delta homolog 1, delta like non-canonical Notch ligand 1, fetal antigen 1 or preadipocyte factor 1 is a protein that in humans is encoded by the DLK1 gene.
It is expressed as a transmembrane protein, but a soluble form cleaved off by ADAM17 is active in inhibiting adipogenesis, the differentiation of pre-adipocytes into adipocytes.
It is a member of the EGF-like family of homeotic proteins.
Part of the Dlk1-DIO3 imprinting control region, this gene is one involved in the epigenetic process that causes a subset of genes to be regulated based on their parental origin.
Such imprinted genes are required for the formation of the placenta as well as the development of cellular lineages such as those derived from the mesoderm and ectoderm.
References
Further reading |
https://en.wikipedia.org/wiki/AP2A2 | AP-2 complex subunit alpha-2 is a protein that in humans is encoded by the AP2A2 gene.
Interactions
AP2A2 has been shown to interact with EPN1 and SHC1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/CD48 | CD48 antigen (Cluster of Differentiation 48) also known as B-lymphocyte activation marker (BLAST-1) or signaling lymphocytic activation molecule 2 (SLAMF2) is a protein that in humans is encoded by the CD48 gene.
CD48 is a member of the CD2 subfamily of the immunoglobulin superfamily (IgSF) which includes SLAM (signaling lymphocyte activation molecules) proteins, such as CD84, CD150, CD229 and CD244. CD48 is found on the surface of lymphocytes and other immune cells, dendritic cells and endothelial cells, and participates in activation and differentiation pathways in these cells.
CD48 was the first B-cell-specific cellular differentiation antigen identified in transformed B lymphoblasts.
Structure
The gene for CD48 is located in chromosome 1q23 and contains 4 exons, each exon encoding one of the 4 domains of CD48: signal peptide, variable (V) domain, constant 2 (C2) domain and the glycophosphatidylinositol anchor (GPI anchor). The cDNA sequence of 1137 nucleotides encodes a 243 amino acid polypeptide of about 45 kDa. It consists of a 26 amino acid signal peptide, 194 amino acids of mature CD48 (V and C2 domains) and the C-terminal 23 amino acid segment comprising the GPI anchor. The GPI linkage of CD48 to the cell surface is through serine residue 220. CD48 does not have a transmembrane domain, however, but is held at the cell surface by a GPI anchor via a C-terminal domain which can be cleaved to yield a soluble form of the receptor. The CD48 protein is heavily glycosy |
https://en.wikipedia.org/wiki/CDC27 | Cell division cycle protein 27 homolog is a protein that in humans is encoded by the CDC27 gene.
Function
The protein encoded by this gene shares strong similarity with Saccharomyces cerevisiae protein Cdc27, and the gene product of Schizosaccharomyces pombe nuc 2. This protein is a component of anaphase-promoting complex (APC), which is composed of eight protein subunits and highly conserved in eucaryotic cells. APC catalyzes the formation of cyclin B-ubiquitin conjugate that is responsible for the ubiquitin-mediated proteolysis of B-type cyclins. This protein and 3 other members of the APC complex contain the TPR (tetratricopeptide repeat), a protein domain important for protein-protein interaction. This protein was shown to interact with mitotic checkpoint proteins including Mad2, p55CDC and BUBR1, and thus may be involved in controlling the timing of mitosis.
Interactions
CDC27 has been shown to interact with:
ANAPC10,
ANAPC11,
ANAPC1,
ANAPC4,
ANAPC5,
ANAPC7,
CDC16,
CDC20,
CDC23,
CDH1,
FZR1,
MAD2L1 and
PIN1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/CENPA | Centromere protein A, also known as CENPA, is a protein which in humans is encoded by the CENPA gene. CENPA is a histone H3 variant which is the critical factor determining the kinetochore position(s) on each chromosome in most eukaryotes including humans.
Function
CENPA is a protein which epigenetically defines the position of the centromere on each chromosome, determining the position of kinetochore assembly and the final site of sister chromatid cohesion during mitosis. This proteins is frequently accompanied by "centrochromatin"-associated changes to canonical histones and is constitutively present in centromeres. The CENPA protein is a histone H3 variant which replaces one or both canonical H3 histones in a subset of nucleosomes within centromeric chromatin. CENPA has the greatest sequence divergence of the histone H3 variants, with just 48% similarity to canonical histone H3, and has a highly diverged N-terminal tail that lacks many well characterised histone modification sites including H3K4, H3K9 and H3K27.
Unusually for a histone, CENPA nucleosomes are not loaded together with DNA replication and are loaded at different cell cycle stages in different organisms: G1 phase in human, M phase in drosophila, G2 in S. pombe. To orchestrate this specialised loading there are CENPA-specific histone chaperones: HJURP in human, CAL1 in drosophila and Scm3 in S. pombe. In most eukaryotes CENPA is loaded into large domains of highly repetitive satellite DNA. The position |
https://en.wikipedia.org/wiki/CLIC1 | Chloride intracellular channel protein 1 is a protein that in humans is encoded by the CLIC1 gene.
Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nuclear and plasma membrane chloride ion channel activity.
Interactions
CLIC1 has been shown to interact with TRAPPC2.
See also
Chloride channel
References
Further reading
External links
Ion channels |
https://en.wikipedia.org/wiki/AKR1C1 | Aldo-keto reductase family 1 member C1 also known as 20α-hydroxysteroid dehydrogenase, 3α-hydroxysteroid dehydrogenase, and dihydrodiol dehydrogenase 1/2 is an enzyme that in humans is encoded by the AKR1C1 gene.
This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. These enzymes catalyze the conversion of aldehydes and ketones to their corresponding alcohols by utilizing NADH and/or NADPH as cofactors. The enzymes display overlapping but distinct substrate specificity. This enzyme catalyzes the reduction of progesterone to the inactive form 20-alpha-hydroxy-progesterone. This gene shares high sequence identity with three other gene members, and is clustered with those three genes at chromosome 10p15-p14.
References
External links
Further reading
EC 1.1.1 |
https://en.wikipedia.org/wiki/Exonuclease%201 | Exonuclease 1 is an enzyme that in humans is encoded by the EXO1 gene.
This gene encodes a protein with 5' to 3' exonuclease activity as well as RNase activity (endonuclease activity cleaving RNA on DNA/RNA hybrid). It is similar to the Saccharomyces cerevisiae protein Exo1 which interacts with Msh2 and which is involved in DNA mismatch repair and homologous recombination. Alternative splicing of this gene results in three transcript variants encoding two different isoforms.
Meiosis
ExoI is essential for meiotic progression through metaphase I in the budding yeast Saccharomyces cerevisiae and in mouse.
Recombination during meiosis is often initiated by a DNA double-strand break (DSB) as illustrated in the accompanying diagram. During recombination, sections of DNA at the 5' ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule "invades" the DNA of a homologous chromosome that is not broken, forming a displacement loop (D-loop). After strand invasion, the further sequence of events may follow either of two main pathways leading to a crossover (CO) or a non-crossover (NCO) recombinant (see Genetic recombination and Homologous recombination). The pathway leading to a CO involves a double Holliday junction (DHJ) intermediate. Holliday junctions need to be resolved for CO recombination to be completed.
During meiosis in S. cerevisiae, transcription of the Exo1 gene is highly in |
https://en.wikipedia.org/wiki/SLIT2 | Slit homolog 2 protein is a protein that in humans is encoded by the SLIT2 gene.
Interactions
SLIT2 has been shown to interact with Glypican 1.
References
Further reading
Slit proteins |
https://en.wikipedia.org/wiki/GRAP2 | GRB2-related adapter protein 2 also known as GRB2-related adaptor downstream of Shc (GADS) is a 37 kDa protein that in humans is encoded by the GRAP2 gene.
Function
This gene encodes a member of the GRB2/Sem5/Drk family. This member is an adaptor-like protein involved in leukocyte-specific protein-tyrosine kinase signaling. Like its related family member, GRB2-related adaptor protein (GRAP), this protein contains an SH2 domain flanked by two SH3 domains. This protein interacts with other proteins, such as GRB2-associated binding protein 1 (GAB1) and the SLP-76 leukocyte protein (LCP2), through its SH3 domains. Transcript variants utilizing alternative polyA sites exist.
Interactions
GRAP2 has been shown to interact with:
CCNDBP1,
CD28,
Linker of activated T cells,
Lymphocyte cytosolic protein 2
MAP4K1, and
STAMBP.
References
Further reading |
https://en.wikipedia.org/wiki/ARHGEF6 | Rho guanine nucleotide exchange factor 6 is a protein that, in humans, is encoded by the ARHGEF6 gene.
ARHGEF6 is commonly known as the p21-activated protein kinase exchange factor alpha (alpha-PIX or αPIX), because it was identified by binding to p21-activated kinase (PAK) and also contains a guanine nucleotide exchange factor domain.
Domains and functions
αPIX is a multidomain protein that functions both as a signaling scaffold protein and as an enzyme. αPIX shares this domain structure and signaling function with the highly similar ARHGEF7/βPIX protein.
αPIX contains a central DH/PH RhoGEF domain that functions as a guanine nucleotide exchange factor (GEF) for small GTPases of the Rho family, and specifically Rac and Cdc42. Like other GEFs, αPIX can promote both release of GDP from an inactive small GTP-binding protein and binding of GTP to promote its activation.
Signaling scaffolds bind to specific partners to promote efficient signal transduction by arranging sequential elements of a pathway near each other to facilitate interaction/information transfer, and also by holding these partner protein complexes in specific locations within the cell to promote local or regional signaling. In the case of αPIX, its SH3 domain binds to partner proteins with appropriate polyproline motifs, and particularly to group I p21-activated kinases (PAKs) (PAK1, PAK2 and PAK3). PAK is bound to the αPIX SH3 domain in the inactive state, and activated Rac1 or Cdc42 binding to this PAK st |
https://en.wikipedia.org/wiki/AKAP5 | A-kinase anchor protein 5 is a protein that in humans is encoded by the AKAP5 gene.
Function
The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins, which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. This gene is intronless and encodes a member of the AKAP family. The encoded protein binds to the RII-beta regulatory subunit of PKA, and also to protein kinase C and the phosphatase calcineurin. It is predominantly expressed in cerebral cortex and may anchor the PKA protein at postsynaptic densities (PSD) and be involved in the regulation of postsynaptic events. It is also expressed in T lymphocytes and may function to inhibit interleukin 2 transcription by disrupting calcineurin-dependent dephosphorylation of NFAT.
Interactions
AKAP5 has been shown to interact with:
Calcineurin and
GABRB3.
References
External links
Further reading
A-kinase-anchoring proteins |
https://en.wikipedia.org/wiki/ADAMTS1 | A disintegrin and metalloproteinase with thrombospondin motifs 1 is an enzyme that in humans is encoded by the ADAMTS1 gene.
Function
This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The protein encoded by this gene contains two disintegrin loops and three C-terminal TS motifs and has anti-angiogenic activity. The expression of this gene may be associated with various inflammatory processes as well as development of cancer cachexia. This gene is likely to be necessary for normal growth, fertility, and organ morphology and function.
Interactions
ADAMTS1 has been shown to interact with Vascular endothelial growth factor A.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: M12.222
ADAMTS1 on the Atlas of Genetics and Oncology
ADAMTS |
https://en.wikipedia.org/wiki/HDAC9 | Histone deacetylase 9 is an enzyme that in humans is encoded by the HDAC9 gene.
Function
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene has sequence homology to members of the histone deacetylase family. This gene is orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain. It represses MEF2 activity through recruitment of multicomponent corepressor complexes that include CtBP and HDACs. This encoded protein may play a role in hematopoiesis. Multiple alternatively spliced transcripts have been described for this gene but the full-length nature of some of them has not been determined.
Histone deacetylase 9 (HDAC9), a member of class II HDACs, regulates a wide variety of normal and abnormal physiological functions.
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene has sequence homology to members of the histone deacetylase family. This gene is orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain. It represses MEF2 activity through recruitment of multicompo |
https://en.wikipedia.org/wiki/KEAP1 | Kelch-like ECH-associated protein 1 is a protein that in humans is encoded by the Keap1 gene.
Structure
Keap1 has four discrete protein domains. The N-terminal Broad complex, Tramtrack and Bric-à-Brac (BTB) domain contains the Cys151 residue, which is one of the important cysteines in stress sensing. The intervening region (IVR) domain contains two critical cysteine residues, Cys273 and Cys288, which are a second group of cysteines important for stress sensing. A double glycine repeat (DGR) and C-terminal region (CTR) domains collaborate to form a β-propeller structure, which is where Keap1 interacts with Nrf2.
Interactions
Keap1 has been shown to interact with Nrf2, a master regulator of the antioxidant response, which is important for the amelioration of oxidative stress.
Under quiescent conditions, Nrf2 is anchored in the cytoplasm through binding to Keap1, which, in turn, facilitates the ubiquitination and subsequent proteolysis of Nrf2. Such sequestration and further degradation of Nrf2 in the cytoplasm are mechanisms for the repressive effects of Keap1 on Nrf2. Keap1 is not only a tumor suppressor gene, but also a metastasis suppressor gene.
Recently, several interesting studies have also identified a hidden circuit in NRF2 regulations. In the mouse Keap1 (INrf2) gene, Lee and colleagues found that an AREs located on a negative strand can subtly connect Nrf2 activation to Keap1 transcription. When examining NRF2 occupancies in human lymphocytes, Chorley a |
https://en.wikipedia.org/wiki/PSMD6 | 26S proteasome non-ATPase regulatory subunit 6 is an enzyme that in humans is encoded by the PSMD6 gene.
Clinical significance
The proteasome and its subunits are of clinical significance for at least two reasons: (1) a compromised complex assembly or a dysfunctional proteasome can be associated with the underlying pathophysiology of specific diseases, and (2) they can be exploited as drug targets for therapeutic interventions. More recently, more effort has been made to consider the proteasome for the development of novel diagnostic markers and strategies. An improved and comprehensive understanding of the pathophysiology of the proteasome should lead to clinical applications in the future.
The proteasomes form a pivotal component for the Ubiquitin-Proteasome System (UPS) and corresponding cellular Protein Quality Control (PQC). Protein ubiquitination and subsequent proteolysis and degradation by the proteasome are important mechanisms in the regulation of the cell cycle, cell growth and differentiation, gene transcription, signal transduction and apoptosis. Subsequently, a compromised proteasome complex assembly and function lead to reduced proteolytic activities and the accumulation of damaged or misfolded protein species. Such protein accumulation may contribute to the pathogenesis and phenotypic characteristics in neurodegenerative diseases, cardiovascular diseases, inflammatory responses and autoimmune diseases, and systemic DNA damage responses leading to malignan |
https://en.wikipedia.org/wiki/RANBP9 | Ran-binding protein 9 is a protein that in humans is encoded by the RANBP9 gene.
Function
This gene encodes a protein that binds RAN, a small GTP binding protein belonging to the RAS superfamily that is essential for the translocation of RNA and proteins through the nuclear pore complex. The protein encoded by this gene has also been shown to interact with several other proteins, including met proto-oncogene, homeodomain interacting protein kinase 2, androgen receptor, and cyclin-dependent kinase 11.
Interactions
RANBP9 has been shown to interact with:
Androgen receptor,
C-Met,
DISC1,
DYRK1B,
Glucocorticoid receptor,
HIPK2
MKLN1,
S100A7, and
USP11.
References
Further reading
External links |
https://en.wikipedia.org/wiki/SRRM1 | Serine/arginine repetitive matrix protein 1 is a protein that in humans is encoded by the SRRM1 gene.
Interactions
SRRM1 has been shown to interact with CDC5L.
References
Further reading
External links |
https://en.wikipedia.org/wiki/BAIAP2 | Brain-specific angiogenesis inhibitor 1-associated protein 2 is a protein that in humans is encoded by the BAIAP2 gene.
Function
The protein encoded by this gene has been identified as a brain-specific angiogenesis inhibitor (BAI1)-binding protein. This interaction at the cytoplasmic membrane is crucial to the function of this protein, which may be involved in neuronal growth-cone guidance. This protein functions as an insulin receptor tyrosine kinase substrate and suggests a role for insulin in the central nervous system. This protein has also been identified as interacting with the dentatorubral-pallidoluysian atrophy gene, which is associated with an autosomal dominant neurodegenerative disease. It also associates with a downstream effector of Rho small G proteins, which is associated with the formation of stress fibers and cytokinesis. Alternative splicing of the 3'-end of this gene results in three products of undetermined function.
Interactions
BAIAP2 has been shown to interact with:
ATN1,
CDC42,
EPS8,
RAC1,
SHANK1,
WASF1, and
WASF2.
References
External links
Further reading |
https://en.wikipedia.org/wiki/CIB1 | Calcium and integrin-binding protein 1 is a protein that in humans is encoded by the CIB1 gene and is located in Chromosome 15. The protein encoded by this gene is a member of the calcium-binding protein family. The specific function of this protein has not yet been determined; however this protein is known to interact with DNA-dependent protein kinase and may play a role in kinase-phosphatase regulation of DNA end-joining. This protein also interacts with integrin alpha(IIb)beta(3), which may implicate this protein as a regulatory molecule for alpha(IIb)beta(3).
Structure and function
CIB1 is a small protein with a molecular weight of approximately 22 kDa. It has a conserved calcium-binding EF hand domain, which consists of two alpha-helices connected by a loop. CIB1 also has an integrin-binding domain, located near the N-terminus of the protein. In addition, CIB1 has a coiled-coil domain and a C-terminal domain. CIB1 is involved in regulating cell adhesion, migration, and differentiation, as well as other cellular processes. It interacts with integrins, which are transmembrane receptors that play a key role in cell signaling and adhesion to the extracellular matrix. CIB1 has also been shown to regulate other signaling pathways that are important for cell survival and proliferation. Upregulation of CIB1 expression has been observed in several types of cancer, and it has been implicated in cancer development and progression. CIB1 is involved in several cellular processes |
https://en.wikipedia.org/wiki/NFAT5 | Nuclear factor of activated T-cells 5, also known as NFAT5 and sometimes TonEBP, is a human gene that encodes a transcription factor that regulates the expression of genes involved in the osmotic stress.
The product of this gene is a member of the nuclear factors of activated T cells (NFAT) family of transcription factors. Proteins belonging to this family play a central role in inducible gene transcription during the immune response. This protein regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of this protein family, this protein exists as a homodimer and forms stable dimers with DNA elements. Multiple transcript variants encoding different isoforms have been found for this gene.
Osmotic stress
Tissues that comprise the kidneys, skin, and eyes are often subjected to osmotic stresses. When the extracellular environment is hypertonic, cells lose water and consequently, shrink. To counteract this, cells increase their sodium uptake in order to lose less water. However, an increase in intracellular ionic concentration is harmful to the cell. Cells can alternatively synthesize enzymes and transporters that increase intracellular concentration of organic osmolytes, which are less toxic than excess ions but which also aid in water retention. Under conditions of hyperosmolarity, NFAT5 is synthesized and accumulates in the nucleus. NFAT5 stimulates the transcription of genes for aldose reductase (AR), the sodium chloride-betaine co |
https://en.wikipedia.org/wiki/RALBP1 | RalA-binding protein 1 is a protein that in humans is encoded by the RALBP1 gene.
Interactions
RALBP1 has been shown to interact with:
Cyclin B1,
HSF1,
RALA,
RALB, and
REPS2.
References
Further reading |
https://en.wikipedia.org/wiki/TOPBP1 | DNA topoisomerase 2-binding protein 1 (TOPBP1) is a scaffold protein that in humans is encoded by the TOPBP1 gene.
TOPBP1 was first identified as a protein binding partner of DNA topoisomerase-IIβ by a yeast 2-hybrid screen, giving it its name. TOPBP1 is involved in a variety of nuclear specific events. These include DNA damage repair, DNA replication, transcriptional regulation, and cell cycle checkpoint activation. TOPBP1 primarily regulates the DNA damage repair response through its ability to activate the damage response kinase, ataxia-telangiectasia mutated and RAD3-related (ATR). It also plays a critical role in DNA replication initiation and regulation of the cell cycle. Changes in TOPBP1 gene expression are associated with pulmonary hypertension, breast cancer, glioblastoma, non-small cell lung cancer, and sarcomas.
Structure
BRCT domains
The TOPBP1 gene encodes a scaffold protein which facilitates interactions between different proteins at specific times and locations. It accomplishes these interactions with other protein partners through its breast cancer associated gene 1 C-terminus (BRCT) domains. A BRCT domain is structurally defined by a 4 member β sheet that is bookended by one α-helix (α2) and two other α-helices (α1 and α3). The amino acid residues that make up these core features are highly conserved, with protein specific deviations occurring in the loops that connect these subunits. BRCT domains canonically act in pairs, with one domain acting as the |
https://en.wikipedia.org/wiki/Dedicator%20of%20cytokinesis%20protein%201 | Dedicator of cytokinesis protein 1 (Dock1), also (DOCK180), is a large (~180 kDa) protein encoded in the human by the DOCK1 gene, involved in intracellular signalling networks. It is the mammalian ortholog of the C. elegans protein CED-5 and belongs to the DOCK family of guanine nucleotide exchange factors (GEFs).
Discovery
DOCK180 was identified, using a far-western blotting approach, as a binding partner of the adaptor protein Crk that was able to induce morphological changes in 3T3 fibroblasts. Subsequently it was reported that DOCK180 was able to activate the small GTP-binding protein (G protein) Rac1 and this was later shown to happen via its ability to act as a GEF.
Structure and function
DOCK180 is part of a large class of proteins (GEFs) which contribute to cellular signalling events by activating small G proteins. In their resting state G proteins are bound to Guanosine diphosphate (GDP) and their activation requires the dissociation of GDP and binding of guanosine triphosphate (GTP). GEFs activate G proteins by promoting this nucleotide exchange.
DOCK180 and related proteins differ from other GEFs in that they do not possess the canonical structure of tandem DH-PH domains known to elicit nucleotide exchange. Instead they possess a DHR2 domain which mediates Rac activation by stabilising it in its nucleotide-free state. DOCK180-related proteins also possess a DHR1 domain which has been shown, in vitro, to bind phospholipids and which may be involved in their inte |
https://en.wikipedia.org/wiki/Eyes%20absent%20homolog%201 | Eyes absent homolog 1 is a protein that in humans is encoded by the EYA1 gene.
This gene encodes a member of the eyes absent (EYA) subfamily of proteins. The encoded protein may play a role in the developing kidney, branchial arches, eye, and ear. Mutations of this gene have been associated with branchiootorenal dysplasia syndrome, branchiootic syndrome, and sporadic cases of congenital cataracts and ocular anterior segment anomalies. A similar protein in mice can act as a transcriptional activator. Four transcript variants encoding three distinct isoforms have been identified for this gene.
Interactions
EYA1 has been shown to interact with SIX1.
References
Further reading |
https://en.wikipedia.org/wiki/Axon%20reflex | The axon reflex (or the flare response) is the response stimulated by peripheral nerves of the body that travels away from the nerve cell body and branches to stimulate target organs. Reflexes are single reactions that respond to a stimulus making up the building blocks of the overall signaling in the body's nervous system. Neurons are the excitable cells that process and transmit these reflex signals through their axons, dendrites, and cell bodies. Axons directly facilitate intercellular communication projecting from the neuronal cell body to other neurons, local muscle tissue, glands and arterioles. In the axon reflex, signaling starts in the middle of the axon at the stimulation site and transmits signals directly to the effector organ skipping both an integration center and a chemical synapse present in the spinal cord reflex. The impulse is limited to a single bifurcated axon, or a neuron whose axon branches into two divisions and does not cause a general response to surrounding tissue.
The axon reflex arc is distinct from the spinal cord reflex arc. In the spinal cord reflex pathway the afferent neuron transmits information to spinal cord interneurons. These interneurons act collectively, process and make sense of inbound stimuli, and stimulate effector neurons acting as an integration center. The effector neurons leaving the integration center transmit a response to the original tissue the reflex arose resulting in a response. The axon reflex results in a localized re |
https://en.wikipedia.org/wiki/FER%20%28gene%29 | Proto-oncogene tyrosine-protein kinase FER is an enzyme that in humans is encoded by the FER gene.
Fer protein is a member of the FPS/FES family of nontransmembrane receptor tyrosine kinases. It regulates cell-cell adhesion and mediates signaling from the cell surface to the cytoskeleton via growth factor receptors.
Interactions
FER (gene) has been shown to interact with TMF1 and Cortactin.
References
Further reading
Tyrosine kinases |
https://en.wikipedia.org/wiki/GABRB2 | The GABAA beta-2 subunit is a protein that in humans is encoded by the GABRB2 gene. It combines with other subunits to form the ionotropic GABAA receptors. GABA (γ-aminobutyric acid) system is the major inhibitory system in the brain, and its dominant GABAA receptor subtype is composed of α1, β2, and γ2 subunits with the stoichiometry of 2:2:1, which accounts for 43% of all GABAA receptors.
Alternative splicing of the GABRB2 gene leads at least to four isoforms, viz. β2-long (β2L) and β2-short (β2S, β2S1, and β2S2). Alternatively spliced variants displayed similar but non-identical electrophysiological properties. GABRB2 is subjected to positive selection and known to be both an alternative splicing and a recombination hotspot; it is regulated via epigenetic regulation including imprinting and gene and promoter methylation
GABRB2 has been associated with a number of neuropsychiatric disorders, and found to display altered expression in cancer.
Structure
GABRB2 encodes the GABAA receptor beta-2 subunit. It is highly expressed in the brain with dominance in the gray matter. In humans, it is located on chromosome 5q34, with 11 exons and 10 introns spanning more than 260 kb, and a promoter region ranging from 1000 bp upstream to 689 bp downstream of exon 1. Alternative splicing of the gene product yields at least four isoforms, viz. β2-long (β2L), β2-short (β2S) and two additional short isoforms β2S1 and β2S2. These isoforms, composed of 512, 474, 313, and 372 amino acids re |
https://en.wikipedia.org/wiki/GATA6 | Transcription factor GATA-6, also known as GATA-binding factor 6 (GATA6), is protein that in humans is encoded by the GATA6 gene. The gene product preferentially binds (A/T/C)GAT(A/T)(A) of the consensus binding sequence.
Clinical significance
Mutations in the gene have been linked with pancreatic agenesis and congenital heart defects.
Lung Endodermal Epithelial Development
GATA-6, a zinc finger transcription factor, is important in the endodermal differentiation of organ tissues. It is also indicated in proper lung development by controlling the late differentiation stages of alveolar epithelium and aquaporin-5 promoter activation. Furthermore, GATA-6 has been linked to the production of LIF, a cytokine that encourages proliferation of endodermal embryonic stem cells and blocks early epiblast differentiation. If left unregulated in the developing embryo, this cytokine production and chemical signal contributes to the phenotypes discussed further below.
Upon the disruption of GATA-6 in an embryo, the distal lung epithelial development is stunted in transgenic mice models The progenitor cells, or stem cells, for alveolar epithelial tissues develop and are specified appropriately, however further differentiation does not occur. Also the distal-proximal bronchiole development is affected, resulting in a reduced quantity of airway exchange sites.
This branching deficit, which will cause bilateral pulmonary hypoplasia after birth, has been locally associated with areas lac |
https://en.wikipedia.org/wiki/GRK6 | This gene encodes a member of the G protein-coupled receptor kinase subfamily of the Ser/Thr protein kinase family, and is most highly similar to GRK4 and GRK5. The protein phosphorylates the activated forms of G protein-coupled receptors to regulate their signaling.
Function
G protein-coupled receptor kinases phosphorylate activated G protein-coupled receptors, which promotes the binding of an arrestin protein to the receptor. Arrestin binding to phosphorylated, active receptor prevents receptor stimulation of heterotrimeric G protein transducer proteins, blocking their cellular signaling and resulting in receptor desensitization. Arrestin binding also directs receptors to specific cellular internalization pathways, removing the receptors from the cell surface and also preventing additional activation. Arrestin binding to phosphorylated, active receptor also enables receptor signaling through arrestin partner proteins. Thus the GRK/arrestin system serves as a complex signaling switch for G protein-coupled receptors.
GRK6 and the closely related GRK5 phosphorylate receptors at sites that encourage arrestin-mediated signaling rather than arrestin-mediated receptor desensitization, internalization and trafficking (in contrast to GRK2 and GRK3, which have the opposite effect). This difference is one basis for pharmacological biased agonism (also called functional selectivity), where a drug binding to a receptor may bias that receptor’s signaling toward a particular subset of |
https://en.wikipedia.org/wiki/Stream%20restoration | Stream restoration or river restoration, also sometimes referred to as river reclamation, is work conducted to improve the environmental health of a river or stream, in support of biodiversity, recreation, flood management and/or landscape development.
Stream restoration approaches can be divided into two broad categories: form-based restoration, which relies on physical interventions in a stream to improve its conditions; and process-based restoration, which advocates the restoration of hydrological and geomorphological processes (such as sediment transport or connectivity between the channel and the floodplain) to ensure a stream's resilience and ecological health. Form-based restoration techniques include deflectors; cross-vanes; weirs, step-pools and other grade-control structures; engineered log jams; bank stabilization methods and other channel-reconfiguration efforts. These induce immediate change in a stream, but sometimes fail to achieve the desired effects if degradation originates at a wider scale. Process-based restoration includes restoring lateral or longitudinal connectivity of water and sediment fluxes and limiting interventions within a corridor defined based on the stream's hydrology and geomorphology. The beneficial effects of process-based restoration projects may sometimes take time to be felt since changes in the stream will occur at a pace that depends on the stream dynamics.
Despite the significant number of stream-restoration projects worldwide, th |
https://en.wikipedia.org/wiki/Histone%20H2A.Z | Histone H2A.Z is a protein that in humans is encoded by the H2AZ1 gene.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. The H2AFZ gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.
Histone H2AZ is a variant of histone H2A, and is used to mediate the thermosensory response, and is essential to perceive the ambient temperature. Nucleosome occupancy of H2A.Z decreases with temperature, and in vitro assays show that H2A.Z-containing nucleosomes wrap DNA more tightly than canonical H2A nucleosomes in Arabidopsis.(Cell 140: 136–147, 2010) However, some of the other studies (Nat. Genet. 41, 941–945 and Genes Dev., 21, 1519–1529) have shown that incorporation of H2A.Z in nucleosomes, when it co-occurs with H3.3, makes them weaker. Positioning of H2A.Z containing nucleosomes around transcription start sites has now been shown to affect the do |
https://en.wikipedia.org/wiki/HCLS1 | Hematopoietic lineage cell-specific protein is a protein that in humans is encoded by the HCLS1 gene.
Interactions
HCLS1 has been shown to interact with Caspase 3.
References
Further reading |
https://en.wikipedia.org/wiki/HOXB6 | Homeobox protein Hox-B6 is a protein that in humans is encoded by the HOXB6 gene.
Function
This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development, including that of lung and skin, and has been localized to both the nucleus and cytoplasm. Altered expression of this gene or a change in the subcellular localization of its protein is associated with some cases of acute myeloid leukemia and colorectal cancer.
During development
HOX B6 gene is only expressed in erythoid progenitor cells, which are the precursor to red blood cells used for transport of oxygen and carbon dioxide throughout the body. During development, the formation of the HOX gene factor happens in the first stages of fetal development, namely soon after the establishment of the mesoderm, which is the “middle layer” of the future embryo. However, HOX B6 is only expressed once the undifferentiated stem cells of the embryo distinguish themselves into the erythpoietic phase. The research has shown that HOX B6 is not expressed in hematopoietic stem cells located in the red bone marrow, which are the precursor cells to all types of blood cells, or primordial germ cells (PGCs), the precursor to cells passed on in each generation. Since it is a transcriptional factor, HOX B6 regulates er |
https://en.wikipedia.org/wiki/HPGD | Hydroxyprostaglandin dehydrogenase 15-(NAD) (the HUGO-approved official symbol = HPGD; HGNC ID, HGNC:5154), also called 15-hydroxyprostaglandin dehydrogenase [NAD+], is an enzyme that in humans is encoded by the HPGD gene.
In melanocytic cells HPGD gene expression may be regulated by MITF.
Functions
15-hydroxy prostaglandin dehydrogenase (HPGD) is an enzyme belongs to the family of oxidoreductases, specifically the short chain dehydrogenase/reductase family 36C member 1. This protein coding gene encodes a member of the short chain alcohol dehydrogenase protein family. HPGD catalyzes the first step in the catabolic pathway of prostaglandins and is therefore responsible for the metabolic/catabolic inactivation of prostaglandins. This inactivation process will oxidize the 15-hydroxyl group of prostaglandins and yield the corresponding 15-keto (oxo) metabolite.
Prostaglandins have a critical role in the signaling pathways that are involved in reproduction (establishment of pregnancy, maintenance of pregnancy, and initiation of labor), blood pressure homeostasis (vasoconstriction and vasodilation), sexual dimorphism, and the immune system (inflammation). HPGD is has a critical role in the regulation of prostaglandin expression.
Expression
HPGD RNA-seq was performed in tissue samples from 95 human individuals representing 27 different tissues to determine tissue-specificity of all protein-coding genes. HPGD was expressed in the adrenal, appendix, bone marrow, brain, colon, du |
https://en.wikipedia.org/wiki/DNAJB1 | DnaJ homolog subfamily B member 1 is a protein that in humans is encoded by the DNAJB1 gene.
A fusion protein of DNAJB1 and PRKACA drives fibrolemallar hepatocellular carcinoma, a type of rare liver cancer.
Interactions
DNAJB1 has been shown to interact with:
HSPA4, and
STUB1
References
Further reading
Heat shock proteins |
https://en.wikipedia.org/wiki/IFI16 | Gamma-interferon-inducible protein Ifi-16 (Ifi-16) also known as interferon-inducible myeloid differentiation transcriptional activator is a protein that in humans is encoded by the IFI16 gene.
Function
This gene encodes a member of the HIN-200 (hematopoietic interferon-inducible nuclear antigens with 200 amino acid repeats) family of cytokines. The encoded protein contains domains involved in DNA binding, transcriptional regulation, and protein-protein interactions. The protein localizes to the nucleoplasm and nucleoli, and interacts with p53, retinoblastoma-1 and BRCA1. It modulates p53 function, and inhibits cell growth in the Ras/Raf signaling pathway. IFI16 has been shown to play a role in the sensing of intracellular DNA - a hallmark of virally infected cells - and has also been linked to the death of HIV-infected helper CD4 T cells by pyroptosis, a highly inflammatory form of programmed cell death. Recently, it has been shown how IFI16, once extracellularly released, can induce inflammation upon TLR4 binding, acting as a DAMP.
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/Interleukin%2012%20receptor%2C%20beta%201%20subunit | Interleukin-12 receptor, beta 1, or IL-12Rβ1 in short, is a subunit of the interleukin 12 receptor and the interleukin 23 receptor. IL12RB1, is the name of its human gene. IL-12Rβ1 is also known as CD212 (cluster of differentiation 212).
The protein encoded by this gene is a type I transmembrane protein that belongs to the hemopoietin receptor superfamily.
This protein binds to interleukin-12 (IL-12) with a low affinity, and is part of the IL-12 receptor complex. This protein forms a disulfide-linked oligomer, which is required for its IL-12 binding activity. The coexpression of this and IL-12Rβ2 protein was shown to lead to the formation of high-affinity IL-12 binding sites and reconstitution of IL-12 dependent signaling.
IL-12Rβ1 can also bind interleukin-23 (IL-23) as part of the IL-23 receptor complex. This complex forms a disulfide-linked oligomer, which is required for its IL-23 binding activity. The coexpression of this and IL-23R protein was shown to lead to the formation of IL-23 binding sites.
Various mutations in this gene were found to result in the immunodeficiency of patients with severe mycobacterial and Salmonella infections. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported.
All mutations known in the IL12RB1 gene, as well as many polymorphisms, have been collected in a mutation database
References
Further reading
External links
Clusters of differentiation |
https://en.wikipedia.org/wiki/Integrin%20alpha%207 | Alpha-7 integrin is a protein that in humans is encoded by the ITGA7 gene. Alpha-7 integrin is critical for modulating cell-matrix interactions. Alpha-7 integrin is highly expressed in cardiac muscle, skeletal muscle and smooth muscle cells, and localizes to Z-disc and costamere structures. Mutations in ITGA7 have been associated with congenital myopathies and noncompaction cardiomyopathy, and altered expression levels of alpha-7 integrin have been identified in various forms of muscular dystrophy.
Structure
ITGA7 encodes the protein alpha-7 integrin. Alpha-7 integrin is 128.9 kDa in molecular weight and 1181 amino acids in length. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. Alpha-7 integrin undergoes post-translational cleavage within the extracellular domain to yield disulfide-linked light and heavy chains that join with beta 1 to form an integrin that binds to the extracellular matrix protein laminin-1. The primary binding partners of alpha-7 integrin are laminin-1 (alpha1-beta1-gamma1), laminin-2 (alpha2-beta1-gamma1) and laminin-4 (alpha2-beta2-gamma1). Alpha-7/beta-1 is the major integrin complex expressed in differentiated muscle cells.
Splice variants of alpha-7 integrin that differ in both the extracellular and cytoplasmic domains exist in the mouse and are developmentally regulated in mouse and rat muscle tissue. The X1/X2 alternative splicing region lies in the extracellular domain and alters the ligand bin |
https://en.wikipedia.org/wiki/KIR2DL1 | Killer cell immunoglobulin-like receptor 2DL1 is a protein that in humans is encoded by the KIR2DL1 gene.
Function
Killer-cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR2DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response.
Interactions
KIR2DL1 has been shown to interact with HLA-C.
See also
Cluster of differentiation
References
Further reading
Clusters of differentiation
Immunoglobulin superfamily |
https://en.wikipedia.org/wiki/MAP1A | Microtubule-associated protein 1A is a protein that in humans is encoded by the MAP1A gene.
Function
This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1A heavy chain and LC2 light chain. Expression of this gene is almost exclusively in the brain. Studies of the rat microtubule-associated protein 1A gene suggested a role in early events of spinal cord development.
Interactions
MAP1A has been shown to interact with DISC1.
References
Further reading |
https://en.wikipedia.org/wiki/MSMB | Beta-microseminoprotein is a protein that in humans is encoded by the MSMB gene. For historical reasons, the scientific literature may also refer to this protein as Prostate secretory protein 94 (PSP94), microseminoprotein (MSP), microseminoprotein-beta (MSMB), beta-inhibitin, prostatic inhibin peptide (PIP), and inhibitin like material (ILM).
Distribution
MSMB is one of the three major proteins secreted by the epithelial cells of the prostate and has a concentration in seminal plasma of 0.5 to 1 mg/mL Two comprehensive studies of beta-microseminoprotein in tissue have shown that it is secreted by epithelial cells in many other organs: liver, lung, breast, kidney, colon, stomach, pancreas, esophagus, duodenum, salivary glands, fallopian tube, corpus uteri, bulbourethral glands and cervix. This list corresponds closely to the sites from which all late onset cancers develop.
Evolution and structure
MSMB is a rapidly evolving protein. Solution structures of human and porcine MSMB show remarkable similarity despite having only 51% of amino acids in common. The C-terminus domain of MSMB contains two two-stranded β-sheets; these have no resemblance to other structural motifs. The rapid evolution of MSMB can be attributed to either sexual selection or innate pathogen defense; the wide distribution of MSMB in the body and the fungicidal properties of the C-terminus suggest that innate pathogen defense plays a role in driving this evolution.
Function
Beta-microseminoprotein i |
https://en.wikipedia.org/wiki/CD93 | CD93 (Cluster of Differentiation 93) is a protein that in humans is encoded by the CD93 gene. CD93 is a C-type lectin transmembrane receptor which plays a role not only in cell–cell adhesion processes but also in host defense.
Family
CD93 belongs to the Group XIV C-Type lectin family, a group containing three other members, endosialin (CD248), CLEC14A and thrombomodulin, a well characterized anticoagulant. All of them contain a C-type lectin domain, a series of epidermal growth factor like domains, a highly glycosylated mucin-like domain, a unique transmembrane domain and a short cytoplasmic tail. Due to their strong homology and their close proximity on chromosome 20, CD93 has been suggested to have arisen from the thrombomodulin gene through a duplication event.
Expression
CD93 was originally identified in mice as an early B cell marker through the use of AA4.1 monoclonal antibody. Then this molecule was shown to be expressed on an early population of hematopoietic stem cells, which give rise to the entire spectrum of mature cells in the blood. Now CD93 is known to be expressed by a wide variety of cells such as platelets, monocytes, microglia and endothelial cells. In the immune system CD93 is also expressed on neutrophils, activated macrophages, B cell precursors until the T2 stage in the spleen, a subset of dendritic cells and of natural killer cells. Molecular characterization of CD93 revealed that this protein is identical with C1qRp, a human protein identified |
https://en.wikipedia.org/wiki/SNW1 | SNW domain-containing protein 1 is a protein that in humans is encoded by the SNW1 gene.
Function
This gene, a member of the SNW gene family, encodes a coactivator that enhances transcription from some Pol II promoters. This coactivator can bind to the ligand-binding domain of the vitamin D receptor and to retinoid receptors to enhance vitamin D-, retinoic acid-, estrogen-, and glucocorticoid-mediated gene expression. It can also function as a splicing factor by interacting with poly(A)-binding protein 2 to directly control the expression of muscle-specific genes at the transcriptional level. Finally, the protein may be involved in oncogenesis since it interacts with a region of SKI oncoproteins that is required for transforming activity.
Interactions
SNW1 has been shown to interact with:
CIR,
Calcitriol receptor,
Histone deacetylase 2,
Mothers against decapentaplegic homolog 2,
Mothers against decapentaplegic homolog 3,
NOTCH1
Nuclear receptor co-repressor 2,
Nuclear receptor coactivator 1,
PABPN1,
RBPJ,
Retinoblastoma protein, and
SKI protein.
References
Further reading |
https://en.wikipedia.org/wiki/SGK3 | Serine/threonine-protein kinase Sgk3 is an enzyme that in humans is encoded by the SGK3 gene.
Function
This gene is a member of the serine/threonine protein kinase family and encodes a phosphoprotein with a PX (phox homology) domain. The protein phosphorylates several target proteins and has a role in neutral amino acid transport and activation of potassium and chloride channels. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
In melanocytic cells SGK3 gene expression may be regulated by MITF.
Interactions
SGK3 has been shown to interact with GSK3B.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/PRPF31 | PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae), also known as PRPF31, is a protein which in humans is encoded by the PRPF31 gene.
Function
PRPF31 is the gene coding for the splicing factor hPRP31. It is essential for the formation of the spliceosome hPRP31 is associated with the U4/U6 di-snRNP and interacts with another splicing factor, hPRP6, to form the U4/U6-U5 tri-snRNP. It has been shown that when hPRP31 is knocked down by RNAi, U4/U6 di-snRNPs accumulate in the Cajal bodies and the U4/U6-U5 tri-snRNP cannot form.
PRPF31 is recruited to introns following the attachment of U4 and U6 RNAs and the 15.5K protein NHP2L1. The addition of PRPF31 is crucial for the transition of the spliceosomal complex to the activated state.
Clinical significance
A mutation in PRPF31 is one of 4 known mutations in splicing factors which are known to cause retinitis pigmentosa. The first mutation in PRPF31 was discovered by Vithana et al. in 2001. Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of retinal dystrophies characterized by a progressive degeneration of photoreceptors, eventually resulting in severe visual impairment.
Inheritance
Mutations in PRPF31 are inherited in an autosomal dominant manner, accounting for 2.5% of cases of autosomal dominant retinitis pigmentosa (adRP) in a mixed UK population. However, the inheritance pattern of PRPF31 mutations is atypical of dominant inheritance, showing the phenomenon of partial penetrance, |
https://en.wikipedia.org/wiki/UBQLN1 | Ubiquilin-1 is a protein that in humans is encoded by the UBQLN1 gene.
Ubiquilins contain two domains, an N-terminal ubiquitin-like domain and a C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases, and thus are thought to functionally link the ubiquitination machinery to the proteasome to effect in vivo protein degradation.
Functions
Ubiquilin-1 is associated with protein degradation and aggregation of misfolded proteins, and may be involved in neurodegenerative diseases. Ubiquilin-1 has been reported to act as a molecular chaperone for amyloid precursor protein (APP), a protein associated with Alzheimer's disease.
Ubiquilin-1 was first identified through its interactions with presenilins. Two transcript variants encoding different isoforms have been found for this gene.
Related proteins
Human UBQLN1 shares a high degree of similarity with related ubiquilins including UBQLN2 and UBQLN4.
Interactions
UBQLN1 has been shown to interact with
HERPUD1,
MTOR,
P4HB,
PSEN1
PSEN2, and
UBE3A.
TMCO6,
References
Further reading |
https://en.wikipedia.org/wiki/ATP2B1 | Plasma membrane calcium-transporting ATPase 1 also known as Plasma membrane calcium pump isoform 1 is a plasma membrane ATPase, an enzyme that in humans is encoded by the ATP2B1 gene. It's a transport protein, a translocase, a calcium pump .
The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues.
Clinical significance
ATP2B1 is a critical host factor supporting cytotoxicity caused by Chironex fleckeri (a type of box jellyfish) stings. Blocking ATP2B1 is believed to have therapeutic potential for treating pain and skin necrosis caused by these stings.
Mutations of the ATP2B1 gene cause a neurodevelopmental delay with mild to moderately impaired intellectual development and mild speech delay.
References
External links
Further reading
|
https://en.wikipedia.org/wiki/MSR1 | Macrophage scavenger receptor 1, also known as MSR1, is a protein which in humans is encoded by the MSR1 gene. MSR1 has also been designated CD204 (cluster of differentiation 204).
Function
This gene encodes the class A macrophage scavenger receptors, which include three different types (1, 2, 3) generated by alternative splicing of this gene. These receptors or isoforms are trimeric integral membrane glycoproteins and have been implicated in many macrophage-associated physiological and pathological processes including atherosclerosis, Alzheimer's disease, and host defense. They were thought to be expressed macrophage-specific, but recently shown to be present on different dendritic cells classes, too.
The isoforms type 1 and type 2 are functional receptors and are able to mediate the endocytosis of modified low density lipoproteins (LDLs). The isoform type 3 does not internalize modified LDL (acetyl-LDL) despite having the domain shown to mediate this function in the types 1 and 2 isoforms. It has an altered intracellular processing and is trapped within the endoplasmic reticulum, making it unable to perform endocytosis. The isoform type 3 can inhibit the function of isoforms type 1 and type 2 when co-expressed, indicating a dominant negative effect and suggesting a mechanism for regulation of scavenger receptor activity in macrophages.
Biotechnology application
Macrophage scavenger receptor has been shown to mediate adhesion of macrophages and other cell lines to tis |
https://en.wikipedia.org/wiki/NEK2 | Serine/threonine-protein kinase Nek2 is an enzyme that in humans is encoded by the NEK2 gene.
Interactions
NEK2 has been shown to interact with MAPK1 and NDC80.
Protein kinase which is involved in the control of centrosome separation and bipolar spindle formation in mitotic cells and chromatin condensation in meiotic cells. Regulates centrosome separation (essential for the formation of bipolar spindles and high-fidelity chromosome separation) by phosphorylating centrosomal proteins such as CROCC, CEP250 and NINL, resulting in their displacement from the centrosomes. Regulates kinetochore microtubule attachment stability in mitosis via phosphorylation of NDC80. Involved in regulation of mitotic checkpoint protein complex via phosphorylation of CDC20 and MAD2L1. Plays an active role in chromatin condensation during the first meiotic division through phosphorylation of HMGA2. Phosphorylates: PPP1CC; SGOL1; NECAB3 and NPM1. Essential for localization of MAD2L1 to kinetochore and MAPK1 and NPM1 to the centrosome. Isoform 1 phosphorylates and activates NEK11 in G1/S-arrested cells. Isoform 2, which is not present in the nucleolus, does not [Uniprot].
References
Further reading
Human proteins |
https://en.wikipedia.org/wiki/PAK3 | PAK3 (p21-activated kinase 2, beta-PAK) is one of three members of Group I PAK family of evolutionary conserved serine/threonine kinases. PAK3 is preferentially expressed in neuronal cells and involved in synapse formation and plasticity and mental retardation.
Discovery
PAK3 was initially cloned from a murine fibroblast cDNA library and from a murine embryo cDNA library. Like other group I PAKs, PAK3 is stimulated by activated Cdc42 and Rac1.
Gene and spliced variants
The human PAK3 gene, the longest group I family member, is 283-kb long. The PAK3 gene is composed of 22 exons of which 6 exons are for 5’-UTR and generates 13 alternative spliced transcripts. Among PAK3 transcripts, 11 transcripts are for coding proteins ranging from 181- to 580-amino acids long, while remaining two transcripts are non-coding RNAs. The murine PAK3 gene contains 10 transcripts, coding six proteins from 544 amino acids and 559 amino acids long, and four smaller polypeptides from 23 to 366 amino acids.
Protein domains
Similar to PAK1, PAK2 contains a p21-binding domain (PBD) and an auto-inhibitory domain (AID) and exists in an inactive conformation.
Activators and inhibitors
PAK3 activity is stimulated by Dbl, Cdc42 and Cool-2, and by AP1 transcription factor. Stimulation of PAK3 activity by upstream stimulators such as Dbl or Cdc42 is inhibited by p50 (Cool-1) PAK3 activity is inhibited by FRAX597, a PAN inhibitor of PAKs.
Functions
PAK3 is overexpressed in neuroendocrine/carcinoids tu |
https://en.wikipedia.org/wiki/PDK4 | Pyruvate dehydrogenase lipoamide kinase isozyme 4, mitochondrial (PDK4) is an enzyme that in humans is encoded by the PDK4 gene. It codes for an isozyme of pyruvate dehydrogenase kinase.
This gene is a member of the PDK/BCKDK protein kinase family and encodes a mitochondrial protein with a histidine kinase domain. This protein is located in the matrix of the mitochondria and inhibits the pyruvate dehydrogenase complex by phosphorylating one of its subunits, reducing the conversion of pyruvate, which is produced from the oxidation of glucose and amino acids, to acetyl-CoA and contributing to the regulation of glucose metabolism. Expression of this gene is regulated by glucocorticoids, retinoic acid and insulin. PDK4 is increased in hibernation and helps to decrease metabolism and conserve glucose by decreasing its conversion to acetyl-CoA, which enters the citric acid cycle and is converted to ATP.
Structure
The mature protein encoded by the PDK4 gene contains 294 amino acids in its sequence. To form the active protein, two of the polypeptide chains come together to form an open conformation. Specifically, the two subunits come together to form a nucleotide-binding pocket; this pocket is targeted most often by inhibitors.
Function
The pyruvate dehydrogenase (PDH) complex must be tightly regulated due to its central role in general metabolism. Within the complex, there are three serine residues on the E1 component that are sites for phosphorylation; this phosphorylation |
https://en.wikipedia.org/wiki/PMM2 | Phosphomannomutase 2 is an enzyme that in humans is encoded by the PMM2 gene.
Function
Phosphomannomutase 2 catalyzes the isomerization of mannose 6-phosphate to mannose 1-phosphate. Mannose 1-phosphate is a precursor to GDP-mannose necessary for the synthesis of dolichol-P-oligosaccharides. Mutations in the gene have been shown to cause defects in the protein glycosylation pathway which manifest as the congenital disorder of glycosylation PMM2 deficiency.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Congenital Disorders of Glycosylation Overview
GeneReviews/NIH/NCBI/UW entry on PMM2-CDG (CDG-Ia)Carbohydrate-Deficient Glycoprotein Syndrome, Type 1a; Congenital Disorder of Glycosylation Type 1a; Jaeken Syndrome
OMIM entries on Carbohydrate-Deficient Glycoprotein Syndrome, Type 1a; Congenital Disorder of Glycosylation Type 1a; Jaeken Syndrome |
https://en.wikipedia.org/wiki/PPP2R1B | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform is an enzyme that in humans is encoded by the PPP2R1B gene.
Function
This gene encodes a constant regulatory subunit of protein phosphatase 2. Protein phosphatase 2 is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The constant regulatory subunit A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. This gene encodes a beta isoform of the constant regulatory subunit A. Defects in this gene could be the cause of some lung and colon cancers. At least two transcript variants encoding different isoforms have been found for this gene.
Interactions
PPP2R1B has been shown to interact with:
PPP2CA,
PPP2CB,
PPP2R2A,
PPP2R3B,
PPP2R5A,
PPP2R5B,
PPP2R5C,
PPP2R5D, and
PPP2R5E.
References
Further reading |
https://en.wikipedia.org/wiki/PTK6 | Tyrosine-protein kinase 6 is an enzyme that in humans is encoded by the PTK6 gene.
Function
Tyrosine-protein kinase 6—also known as BRK (breast tumor kinase)—is a cytoplasmic non-receptor protein kinase which may function as an intracellular signal transducer in epithelial tissues. The encoded protein has been shown to undergo autophosphorylation.
Clinical significance
Overexpression of this gene in mammary epithelial cells leads to sensitization of the cells to epidermal growth factor and results in a partially transformed phenotype. Expression of this gene has been detected at low levels in some breast tumors but not in normal breast tissue.
Interactions
PTK6 has been shown to interact with STAP2 and KHDRBS1.
References
Further reading
Tyrosine kinases |
https://en.wikipedia.org/wiki/RAD52 | RAD52 homolog (S. cerevisiae), also known as RAD52, is a protein which in humans is encoded by the RAD52 gene.
Function
The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Rad52, a protein important for DNA double-strand break repair and homologous recombination. This gene product was shown to bind single-stranded DNA ends, and mediate the DNA-DNA interaction necessary for the annealing of complementary DNA strands. It was also found to interact with DNA recombination protein RAD51, which suggested its role in RAD51-related DNA recombination and repair.
Role in DNA recombination repair
RAD52 mediates RAD51 function in homologous recombinational repair (HRR) in both yeast Saccharomyces cerevisiae and in mammalian cells of mice and humans. However, the RAD52 protein has distinctly different functions in HRR of yeast and humans. In S. cerevisiae, Rad52 protein, acting alone, facilitates the loading of Rad51 protein onto single-stranded DNA pre-coated with replication protein A in the presynaptic phase of recombination.
In mice and humans, however, BRCA2 primarily mediates orderly assembly of RAD51 on ssDNA, the form that is active for homologous pairing and strand invasion. BRCA2 also redirects RAD51 from dsDNA and prevents dissociation from ssDNA. In addition, the four paralogs of RAD51, consisting of RAD51B (RAD51L1), RAD51C (RAD51L2), RAD51D (RAD51L3), XRCC2 form a complex called the BCDX2 complex. This complex participates in RAD51 recr |
https://en.wikipedia.org/wiki/RHAG | Rh-associated glycoprotein (RHAG) is an ammonia transporter protein that in humans is encoded by the RHAG gene. RHAG has also recently been designated CD241 (cluster of differentiation 241). Mutations in the RHAG gene can cause stomatocytosis.
Function
The Rh blood group antigens (MIM 111700) are associated with human erythrocyte membrane proteins of approximately 30 kD, the so-called Rh30 polypeptides. Heterogeneously glycosylated membrane proteins of 50 and 45 kD, the Rh50 glycoproteins, are coprecipitated with the Rh30 polypeptides on immunoprecipitation with anti-Rh-specific mono- and polyclonal antibodies. The Rh antigens appear to exist as a multisubunit complex of CD47 (MIM 601028), LW (MIM 111250), glycophorin B (MIM 111740), and play a critical role in the Rh50 glycoprotein [supplied by OMIM].
Interactions
RHAG has been shown to interact with ANK1.
See also
Rh deficiency syndrome
References
Further reading
External links
RhAG blood group system in the BGMUT blood group antigen gene mutation database
Clusters of differentiation
Solute carrier family
Blood antigen systems
Transfusion medicine |
https://en.wikipedia.org/wiki/S100A11 | S100 calcium-binding protein A11 (S100A11) is a protein that in humans is encoded by the S100A11 gene.
Function
The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100A11, also known as calgizzarin or 100C, is a small acidic protein. Along with all 13 members of the S100 family, are located as a cluster on chromosome 1q21. It was first found in 1989, and later isolated from chicken gizzard muscles.
The protein may function in motility, invasion, and tubulin polymerization. Chromosomal rearrangements and altered expression of this gene have been implicated in tumor metastasis.
Its high expression has been found in many tissues including lung, pancreas, heart, placenta, kidney, and low levels in skeletal muscle, liver, and brain tissue.
S100A11 is implicated in membrane and cytoskeletal dynamics, vesicular transportation and processes of endo and exocytosis. It has been shown that S100A11 interacts with many cytoskeletal structures as tubulin, actin, intermediate filaments also with annexin I and annexin II. S100A11 is able to control reorganization of actin and it is important in forming protrusion by metastatic cells.
It lacks enzymatic activity, it functions by binding to other proteins, it regulates activity of other enzymes. It is associated with cell cycle, growth, survival and apoptosis. It has been identified as dual growth mediator. Suppression of S100A11 by small interfering RNA caused cells t |
https://en.wikipedia.org/wiki/Ferritin%20light%20chain | Ferritin light chain is a protein that in humans is encoded by the FTL gene. Ferritin is the major protein responsible for storing intracellular iron in prokaryotes and eukaryotes. It is a heteropolymer consisting of 24 subunits, heavy and light ferritin chains. This gene has multiple pseudogenes.
It is abnormally expressed in fetuses of both IVF and ICSI, which may contribute to the increase risk of birth defects in these assisted reproductive technologies.
Function
Iron is extremely important in the development of neurons, transport through iron-sulfur clusters, the electron transport chain, and synthesis and breakdown of neurotransmitters. The function of the FTL is to act as both an iron reservoir and to remove excess iron from the body. Since iron plays a role in electron transfer, there is potential for the generation of free, highly toxic radicals which makes the role of the FTL as an iron detoxifier very significant. The rates of iron uptake and release may be affected by changes to the components of the ferritin light chains and heavy chains. Although the ferritin light chain unlike the ferritin heavy chain has no ferroxidase activity, the light chain may be responsible for the electron transfer across the ferritin protein cage.
Clinical significance
Oxidative stress caused by iron radicals generated in the ETC and an increase in iron levels caused by defects in the FTL gene has been known to be a cause of the onset of neurodegenerative diseases and hyperferr |
https://en.wikipedia.org/wiki/SERPINB3 | Serpin B3 is a protein that in humans is encoded by the SERPINB3 gene.
See also
Serpin
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: I04.008
Serine protease inhibitors |
https://en.wikipedia.org/wiki/TRA2B | Transformer-2 protein homolog beta, also known as TRA2B previously known as splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) (SFRS10), is a protein that in humans is encoded by the TRA2B gene.
Interactions
TRA2B has been shown to interact with RBMX.
References
Further reading |
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