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Additional CYCs and other modifications may be necessary to produce linear aromatic polyketides. The Tetracenomycin polyketide synthesis protein, tcmI, from Streptomyces glaucescens catalyses an aromatic rearrangement in the biosynthetic pathway of tetracenomycin C from Streptomyces coelicolor. The protein is a homodimer where each subunit forms a beta-alpha-beta fold belonging to the ferrodoxin fold superfamily. | https://en.wikipedia.org/wiki/Polyketide_synthesis_cyclase_family |
Four strands of antiparallel sheets and a layer of alpha helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase from Streptomyces coelicolor which functions in the actinorhodin biosynthetic pathway. It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates. == References == | https://en.wikipedia.org/wiki/Polyketide_synthesis_cyclase_family |
In molecular biology, the presence of amylase can serve as an additional method of selecting for successful integration of a reporter construct in addition to antibiotic resistance. As reporter genes are flanked by homologous regions of the structural gene for amylase, successful integration will disrupt the amylase gene and prevent starch degradation, which is easily detectable through iodine staining. | https://en.wikipedia.org/wiki/Pancreatic_amylase |
In molecular biology, the protein Sprouty is a developmental protein involved in cell signalling. It works by inhibiting the MAPK/ERK pathway. | https://en.wikipedia.org/wiki/Sprouty_protein |
In molecular biology, the protein domain Adenosine deaminase z-alpha domain refers to an evolutionary conserved protein domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA-editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance. | https://en.wikipedia.org/wiki/Adenosine_deaminase_z-alpha_domain |
In molecular biology, the protein domain S-adenosylmethionine synthetase, C-terminal domain refers to the C terminus of the S-adenosylmethionine synthetase | https://en.wikipedia.org/wiki/S-Adenosylmethionine_synthetase_enzyme |
In molecular biology, the protein domain SAICAR synthase is an enzyme which catalyses a reaction to create SAICAR. In enzymology, this enzyme is also known as phosphoribosylaminoimidazolesuccinocarboxamide synthase (EC 6.3.2.6). It is an enzyme that catalyzes the chemical reaction ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate ⇌ {\displaystyle \rightleftharpoons } ADP + phosphate + (S)-2-succinateThe 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate, and L-aspartate, whereas its 3 products are ADP, phosphate, and (S)-2-succinate. This enzyme belongs to the family of ligases, to be specific those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). | https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazolesuccinocarboxamide_synthase |
The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming). This enzyme participates in purine metabolism. | https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazolesuccinocarboxamide_synthase |
This particular protein family is of huge importance as it is found in all three domains of life. It is the seventh step in the pathway of purine biosynthesis. Purines are vital to all cells as they are involved in energy metabolism and DNA synthesis. Furthermore, they are of specific interest to scientific researchers as the study of the purine biosynthesis pathway could lead to the development of chemotherapeutic drugs. This is because most cancers lack a salvage pathway for adenine nucleotides and rely entirely on the SAICAR pathway. | https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazolesuccinocarboxamide_synthase |
In molecular biology, the protein domain SAND is named after a range of proteins in the protein family: Sp100, AIRE-1, NucP41/75, DEAF-1. It is localised in the cell nucleus and has an important function in chromatin-dependent transcriptional control. It is found solely in eukaryotes. | https://en.wikipedia.org/wiki/SAND_DNA-binding_protein_domain |
In molecular biology, the protein domain SATase is short for Serine acetyltransferase and refers to an enzyme that catalyses the conversion of L-serine to L-cysteine in E. coli. More specifically, its role is to catalyse the activation of L-serine by acetyl-CoA.This entry refers to the N-terminus of the protein which has a sequence that is conserved in plants and bacteria. | https://en.wikipedia.org/wiki/Serine_O-acetyltransferase |
In molecular biology, the protein domain SRCR is short for Scavenger receptor cysteine-rich domain. They are found solely in eukaryotes. These domains are present on the cell membrane and have a role in binding to specific ligands and are often found to be involved with the immune system. | https://en.wikipedia.org/wiki/Scavenger_receptor_cysteine-rich_protein_domain |
In molecular biology, the protein domain SWAP is derived from the term Suppressor-of-White-APricot, a splicing regulator from the model organism Drosophila melanogaster. The protein domain is found in regulators that control splicing. It is found in splicing regulatory proteins. When a gene is expressed the DNA must be transcribed into messenger RNA (mRNA). | https://en.wikipedia.org/wiki/SWAP_protein_domain |
However, it sometimes contains intervening or interrupting sequences named introns. mRNA splicing helps to remove these sequences, leaving a more favourable sequence. mRNA splicing is an essential event in the post-transcriptional modification process of gene expression. SWAP helps to control this process in all cells except gametes. | https://en.wikipedia.org/wiki/SWAP_protein_domain |
In molecular biology, the protein domain Saccharopine dehydrogenase (SDH), also named Saccharopine reductase, is an enzyme involved in the metabolism of the amino acid lysine, via an intermediate substance called saccharopine. The Saccharopine dehydrogenase enzyme can be classified under EC 1.5.1.7, EC 1.5.1.8, EC 1.5.1.9, and EC 1.5.1.10. It has an important function in lysine metabolism and catalyses a reaction in the alpha-Aminoadipic acid pathway. | https://en.wikipedia.org/wiki/Saccharopine_dehydrogenase |
This pathway is unique to fungal organisms therefore, this molecule could be useful in the search for new antibiotics. This protein family also includes saccharopine dehydrogenase and homospermidine synthase. It is found in prokaryotes, eukaryotes and archaea. | https://en.wikipedia.org/wiki/Saccharopine_dehydrogenase |
In molecular biology, the protein domain Sda is short for suppressor of dnaA or otherwise known as sporulation inhibitor A. It is found only in bacteria. This protein domain is highly important to cell survival. When starved of nutrients, the cell is under extreme stress so undergoes a series of reactions to increase the chances of survival. One method is to form endospores which can withstand a large amount of environmental pressure. | https://en.wikipedia.org/wiki/Sda_protein_domain |
Sda protein domain is a checkpoint which prevents the formation of spores. The Sda domain affects cell signalling. It prevents the cell communicating the stress that it is under, which is crucial if the cell is to survive. | https://en.wikipedia.org/wiki/Sda_protein_domain |
In molecular biology, the protein domain SdrG C terminal refers to the C terminus domain of an adhesin found only on the cell walls of bacteria. More specifically, SdrG is only found in gram-positive bacteria. This particular domain binds to a glycoprotein named fibrinogen. | https://en.wikipedia.org/wiki/SdrG_C_terminal_protein_domain |
SdrG stands for serine-aspartate dipeptide repeats, which as its name suggests, contains repeats of two amino acids, serine and aspartate.Gram-positive pathogens such as Staphylococci, Streptococci, and Enterococci, contain SdrG anchored to their cell walls; these proteins act as adhesins and help the bacteria adhere to the host tissues via a dock-lock-latch mechanism. This protein domain is of huge significance since it binds to fibrinogen, a glycoprotein involved in important processes such as haemostasis and coagulation. By understanding more about the way they attach to human cells, it is hope a therapeutic target can be developed to prevent diseases such as nosocomial sepsis which are caused by a bacterium which operates in this manner. | https://en.wikipedia.org/wiki/SdrG_C_terminal_protein_domain |
In molecular biology, the protein domain Ste50p mainly in fungi and some other types of eukaryotes. It plays a role in the mitogen-activated protein kinase cascades, a type of cell signalling that helps the cell respond to external stimuli, more specifically mating, cell growth, and osmo-tolerance in fungi. | https://en.wikipedia.org/wiki/Sterile_alpha_motif |
In molecular biology, the protein domain Sterile alpha motif (or SAM) is a putative protein interaction module present in a wide variety of proteins involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins, nevertheless with a low affinity constant.SAM domains also appear to possess the ability to bind RNA. | https://en.wikipedia.org/wiki/Sterile_alpha_motif |
Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. | https://en.wikipedia.org/wiki/Sterile_alpha_motif |
These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces. In the case of the SAM domain of EPHB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures. | https://en.wikipedia.org/wiki/Sterile_alpha_motif |
In molecular biology, the protein domain Stirrup is a domain, found only in found in the domain, archaea. The Stirrup protein domain is found in prokaryotic protein ribonucleotide reductases. It obtains its name due to its resemblance to an old fashioned Japanese stirrup. Stirrip has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface. | https://en.wikipedia.org/wiki/Stirrup_protein_domain |
In molecular biology, the protein domain Sushi 2 is also known as the fifth protein domain of beta-2 glycoprotein 1 (β2-GP1). This protein domain is only found in eukaryotes. The first four domains found in Apolipoprotein H resemble each other, however the fifth one appears to be different. | https://en.wikipedia.org/wiki/Apolipoprotein_H |
In molecular biology, the protein domain TCP is actually a family of transcription factors named after: teosinte branched 1 (tb1, Zea mays (Maize)), cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) and PCF in rice (Oryza sativa). | https://en.wikipedia.org/wiki/TCP_protein_domain |
In molecular biology, the protein domain TyeA is short for Translocation of Yops into eukaryotic cells A. It controls the release of Yersinia outer proteins (Yops) which help Yersinia evade the immune system. More specifically, it interacts with the bacterial protein YopN via hydrophobic residues located on the helices. | https://en.wikipedia.org/wiki/TyeA_protein_domain |
In molecular biology, the protein domain VEK-30, is a 30-amino acid long, internal peptide present within bacterial organisms that acts as an epitope or antigenic determinant. It increases the pathogenicity of the cell. More specifically, it is found in streptococcal M-like plasminogen (Pg)-binding protein (PAM) from gram-positive group-A streptococci (GAS). VEK-30 represents an epitope within PAM that shows high affinity for the lysine binding site (LBS) of the kringle-2 (K2) domain of human (h)Pg. | https://en.wikipedia.org/wiki/VEK-30_protein_domain |
In molecular biology, the protein domain WHEP-TRS refers to helix-turn-helix domains. They are found in variable numbers in glutamyl-prolyl tRNA synthetase (EPRS). This protein domain has an important function in protein–protein interactions between synthetases. WHEP domains exhibit high-affinity interactions with tRNA, indicating a putative evolutionary relationship to facilitate tRNA binding to fused synthetases, thereby enhancing catalytic efficiency. | https://en.wikipedia.org/wiki/WHEP-TRS_protein_domain |
In molecular biology, the protein domain Whirly is a transcription factor commonly found in plants. This means they aid the transcription of genes from DNA into a complementary copy of mRNA. In particular, in plants, they aid the transcription of plant defence genes. | https://en.wikipedia.org/wiki/Whirly |
In molecular biology, the protein domain YopE refers to the secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. It not only infects the host cell but also protects the bacteria. It undergoes several mechanisms to evade the host's immune system. This particular protein domain can be referred to as a Rho GTPase-activating protein (GAP). | https://en.wikipedia.org/wiki/YopE_protein_domain |
In molecular biology, the protein domain Zeta (ζ) toxin refers to a protein domain found in prokaryotes, which acts as a UDP-N-acetylglucosamine kinase. Its function is to inhibit cell wall biosynthesis and it may act as a bactericide in nature. It is also thought that Zeta toxin induces reversible protective dormancy and permeation to propidium iodide (PI). | https://en.wikipedia.org/wiki/Zeta_toxin_protein_domain |
In molecular biology, the protein domain b1 refers to the domain b1 of Protein L. L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains. N-terminus domain contains five homologous B1 repeats of 72-76 amino acids each. == References == | https://en.wikipedia.org/wiki/B1_domain |
In molecular biology, the protein domain eIF4-gamma/eIF5/eIF2-epsilon is a family of evolutionarily related proteins. This domain is found at the C-terminus of several translation Initiation factors. It was first detected at the very C-termini of the yeast protein GCD6, eIF-2B epsilon, and two other eukaryotic translation initiation factors, eIF-4 gamma and eIF-5 and it may be involved in the interaction of eIF-2B, eIF-4 gamma, and eIF-5 with eIF-2. | https://en.wikipedia.org/wiki/EIF-W2_protein_domain |
In molecular biology, the protein domain named the Shugoshin N-terminal coiled-coil region is a domain found on the N-terminal region of the Shugoshin protein in eukaryotes. It has a role in attaching to the kinetochores, structures on the chromatids where microtubules attach. Shugoshin has a conserved coiled-coil N-terminal domain and a highly conserved C-terminal region. Shugoshin is a crucial target of Bub1 kinase that plays a central role in the cohesion of chromosomes during cell division. | https://en.wikipedia.org/wiki/Shugoshin_N_terminal_protein_domain |
In molecular biology, the protein domain selenoprotein P (SelP) is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues. It is a secreted glycoprotein, often found in the plasma. Its precise function remains to be elucidated; however, it is thought to have antioxidant properties. This particular protein contains two domains: the C terminal and N terminal domain. The N-terminal domain is larger than the C terminal and the N-terminal is thought to be glycosylated. | https://en.wikipedia.org/wiki/Selenoprotein_P |
In molecular biology, the protein domain surE refers to survival protein E. It was originally found that cells that did not contain this protein, could not survive in the stationary phase, at above normal temperatures, and in high-salt media. Hence the name, survival protein E. It is a metal ion-dependent phosphatase that is found in bacteria, and eukaryotes. It is an important stress response protein. This domain is found in acid phosphatases (EC), 5'-nucleotidases (EC), 3'-nucleotidases (EC) and exopolyphosphatases (EC). | https://en.wikipedia.org/wiki/SurE,_survival_protein_E |
In molecular biology, the protein domain, WIF N-terminal refers to the N terminal domain of the protein, WIF. It stands for, Wnt-inhibitory factor, whereby wnt is a signalling molecule also known as wingless. Wnt is a molecule in the wnt signaling pathway. The WIF domain binds to the wnt ligand since it inhibits it. | https://en.wikipedia.org/wiki/WIF_domain |
In molecular biology, the protein domain, YTH refers to a member of the YTH family that has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells.This protein domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression. | https://en.wikipedia.org/wiki/YTH_domain |
In molecular biology, the protein domain, Ydc2 (also known as SpCce1), is a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA. | https://en.wikipedia.org/wiki/Ydc2_protein_domain |
In molecular biology, the protein family Dispanin is another name for Interferon-induced transmembrane protein (IFITM). This refers to a family of protein domains which have a specific formation, or in other words, topology containing two alpha helices in within the cell membrane which are called two transmembrane proteins. This includes proteins such as CD225 (Cluster of Differentiation 225). | https://en.wikipedia.org/wiki/Dispanin |
The function of this protein family is to inhibit cell invasion of many harmful, pathogenic viruses, such as HIV. Henceforth, they are being intensively studied in the hope of drug discovery. They mediate the immune response by interferons. | https://en.wikipedia.org/wiki/Dispanin |
In molecular biology, the protein family, Uracil-DNA glycosylase (UDG) is an enzyme that reverts mutations in DNA. The most common mutation is the deamination of cytosine to uracil. UDG repairs these mutations. UDG is crucial in DNA repair, without it these mutations may lead to cancer.This entry represents various uracil-DNA glycosylases and related DNA glycosylases (EC), such as uracil-DNA glycosylase, thermophilic uracil-DNA glycosylase, G:T/U mismatch-specific DNA glycosylase (Mug), and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1).Uracil DNA glycosylases remove uracil from DNA, which can arise either by spontaneous deamination of cytosine or by the misincorporation of dU opposite dA during DNA replication. | https://en.wikipedia.org/wiki/DNA_glycosylases |
The prototypical member of this family is E. coli UDG, which was among the first glycosylases discovered. Four different uracil-DNA glycosylase activities have been identified in mammalian cells, including UNG, SMUG1, TDG, and MBD4. | https://en.wikipedia.org/wiki/DNA_glycosylases |
They vary in substrate specificity and subcellular localization. SMUG1 prefers single-stranded DNA as substrate, but also removes U from double-stranded DNA. In addition to unmodified uracil, SMUG1 can excise 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil bearing an oxidized group at ring C5. | https://en.wikipedia.org/wiki/DNA_glycosylases |
TDG and MBD4 are strictly specific for double-stranded DNA. TDG can remove thymine glycol when present opposite guanine, as well as derivatives of U with modifications at carbon 5. Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas uracil arising in DNA through dU misincorporation is mainly dealt with by UNG. | https://en.wikipedia.org/wiki/DNA_glycosylases |
MBD4 is thought to correct T:G mismatches that arise from deamination of 5-methylcytosine to thymine in CpG sites. MBD4 mutant mice develop normally and do not show increased cancer susceptibility or reduced survival. But they acquire more C T mutations at CpG sequences in epithelial cells of the small intestine.The structure of human UNG in complex with DNA revealed that, like other glycosylases, it flips the target nucleotide out of the double helix and into the active site pocket. UDG undergoes a conformational change from an ‘‘open’’ unbound state to a ‘‘closed’’ DNA-bound state. | https://en.wikipedia.org/wiki/DNA_glycosylases |
In molecular biology, the red chlorophyll catabolite reductase (RCC reductase) family of proteins consists of several red chlorophyll catabolite reductase (RCC reductase) proteins. Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyse the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC). | https://en.wikipedia.org/wiki/Red_chlorophyll_catabolite_reductase |
In molecular biology, the regulator of motility and amylovoran A (RmaA) gene is a bacterial non-coding RNA. It was discovered in genome-wide identification of Hfq binding sRNAs in plant pathogen Erwinia amylovora. Together with Hfq it positively controls motility and negatively controls the production of acidic exopolysaccharide amylovoran in E. amylovora. == References == | https://en.wikipedia.org/wiki/Rma_A_small_RNA |
In molecular biology, the sea anemone cytotoxic proteins are lethal pore-forming proteins, known collectively as actinoporins, a sub-class of cytolysins. There are several different groups of cytolysins based on their structure and function. This entry represents the most numerous group, the 20kDa highly basic peptides. | https://en.wikipedia.org/wiki/Sea_anemone_cytotoxic_protein |
These cytolysins form cation-selective pores in sphingomyelin-containing membranes. Examples include equinatoxins (from Actinia equina), sticholysins (from Stichodactyla helianthus), magnificalysins (from Heteractis magnifica), and tenebrosins (from Actinia tenebrosa), which exhibit pore-forming, haemolytic, cytotoxic, and heart stimulatory activities. Cytolysins adopt a stable soluble structure, which undergoes a conformational change when brought in contact with a membrane, leading to an active, membrane-bound form that inserts spontaneously into the membrane. | https://en.wikipedia.org/wiki/Sea_anemone_cytotoxic_protein |
They often oligomerise on the membrane surface, before puncturing the lipid bilayers, causing the cell to lyse. The 20kDa sea anemone cytolysins require a phosphocholine lipid headgroup for binding, however sphingomyelin is required for the toxin to promote membrane permeability. The crystal structures of equinatoxin II and sticholysin II both revealed a compact beta-sandwich consisting of ten strands in two sheets flanked on each side by two short alpha-helices, which is a similar topology to osmotin. It is believed that the beta sandwich structure attaches to the membrane, while a three-turn alpha helix lying on the surface of the beta sheet may be involved in membrane pore formation, possibly by the penetration of the membrane by the helix. == References == | https://en.wikipedia.org/wiki/Sea_anemone_cytotoxic_protein |
In molecular biology, the single-domain protein SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae (Baker's yeast) but it is also found in other eukaryotes and prokaryotes as well as archaea. It is otherwise known as Eukaryotic translation initiation factor 1 (eIF1) in eukaryotes or YciH in bacteria. | https://en.wikipedia.org/wiki/SUI1 |
In molecular biology, the small nucleolar RNA ACA40 belongs to the H/ACA family of snoRNAs and guides the pseudouridylation of 28S rRNA subunit at position U4565. snoRNA ACA40 was discovered using large-scale cloning by Kiss et al. (2004) from a HeLa cell extract immunoprecipitated with an anti-GAR1 antibody. It is predicted to guide the pseudouridylation of residues 28S rRNA U4546 and 18S rRNA 1174. The pseudouridylation of these residues was reported by Ofengand and Bakin (1997) and Maden (1990). ACA1, ACA8, ACA18, ACA25, ACA32 and ACA40 and the C/D box snoRNAs mgh28S-2409 and mgh28S-2411 share the same host gene (MGC5306). | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA40 |
In molecular biology, the small nucleolar RNA SNORA73 (also called U17/E1 RNA) belongs to the H/ACA class of small nucleolar RNAs (snoRNAs). Vertebrate U17 is intron-encoded and ranges in length from 200-230 nucleotides, longer than most snoRNAs. It is one of the most abundant snoRNAs in human cells and is essential for the cleavage of pre-rRNA within the 5' external transcribed spacer (ETS). This cleavage leads to the formation of 18S rRNA. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA73 |
Regions of the U17 RNA are complementary to rRNA and act as guides for RNA/RNA interactions, although these regions do not seem to be well conserved between organisms.There is evidence that SNORA73 (isoforms: SNORA73A and SNORA73B) functions as a regulator of chromatin function. SNORA73 is chromatin-associated RNA (caRNA) and stably linked to chromatin. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA73 |
Notably, SNORA73 can bind to PARP1, leading to the activation of its ADPRylation (PAR) function. SNORA73 Interacts with the PARP1 DNA-Binding Domain. In addition, the snoRNA-activated PARP1 ADPRylates DDX21 in cells to promote cell proliferation. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA73 |
In molecular biology, the snoRNA ACA53 belongs to the H/ACA family of pseudouridylation guide snoRNAs. This H/ACA box RNA was cloned by Kiss et al. (2004) from a HeLa cell extract immunoprecipitated with an anti-GAR1 antibody. It has no identified target RNA. RNA residues targeted for pseudouridylation by this molecule have not been identified. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA53 |
In molecular biology, the snoRNA snR48 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_snR48 |
snR48 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.snR48 was identified in yeast (Saccharomyces cerevisiae) by computational screening of the yeast genome. This snoRNA is predicted to guide the 2'O ribosose methylation of 28S ribosomal RNA (rRNA) residues Gm2788 and Gm2790. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_snR48 |
In molecular biology, the sulfonylurea receptors (SUR) are membrane proteins which are the molecular targets of the sulfonylurea class of antidiabetic drugs whose mechanism of action is to promote insulin release from pancreatic beta cells. More specifically, SUR proteins are subunits of the inward-rectifier potassium ion channels Kir6.x (6.1 and 6.2). The association of four Kir6.x and four SUR subunits form an ion conducting channel commonly referred to as the KATP channel.Three forms of the sulfonylurea receptor are known, SUR1 encoded by the ABCC8 gene, and SUR2A and SUR2B, which are splice variants arising from a single ABCC9 gene. | https://en.wikipedia.org/wiki/Sulfonylurea_receptor |
In molecular biology, the ter site, also known as DNA replication terminus binding-site, refers to a protein domain which binds to the DNA replication terminus site. Ter-binding proteins are found in some bacterial species, and include the tus protein which is part of the common ter-tus binding domain. They are required for the termination of DNA replication and function by binding to DNA replication terminator sequences, thus preventing the passage of replication forks. The termination efficiency is affected by the affinity of a particular protein for the terminator sequence. | https://en.wikipedia.org/wiki/Ter_protein |
In E. coli, there are 10 closely ter related sites encoded in the chromosome. The sites are designated TerA, TerB, ..., TerJ. Each site is 23 base pairs. | https://en.wikipedia.org/wiki/Ter_protein |
In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure. The term entered popular culture with the publication in 1968 of The Double Helix: A Personal Account of the Discovery of the Structure of DNA by James Watson. | https://en.wikipedia.org/wiki/Watson-Crick_model |
The DNA double helix biopolymer of nucleic acid is held together by nucleotides which base pair together. In B-DNA, the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn. The double helix structure of DNA contains a major groove and minor groove. In B-DNA the major groove is wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove. | https://en.wikipedia.org/wiki/Watson-Crick_model |
In molecular biology, the term molten globule (MG) refers to protein states that are more or less compact (hence the "globule"), but are lacking the specific tight packing of amino acid residues which creates the solid state-like tertiary structure of completely folded proteins. It was found, for example, in cytochrome c, which conserves a native-like secondary structure content but without the tightly packed protein interior, under low pH and high salt concentration. For cytochrome c and some other proteins, it has been shown that the molten globule state is a "thermodynamic state" clearly different both from the native and the denatured state, demonstrating for the first time the existence of a third equilibrium (i.e., intermediate) state. The term "molten globule" may be used to describe various types of partially-folded protein states found in slightly denaturing conditions such as low pH (generally pH = 2), mild denaturant, or high temperature. | https://en.wikipedia.org/wiki/Molten_globule |
Molten globules are collapsed and generally have some native-like secondary structure but a dynamic tertiary structure as seen by far and near circular dichroism (CD) spectroscopy, respectively. These traits are similar to those observed in the transient intermediate states found during the folding of certain proteins, especially globular proteins that undergo hydrophobic collapse, and therefore the term "molten globule" is also used to refer to certain protein folding intermediates corresponding to the narrowing region of the folding funnel higher in energy than the native state but lower than the denatured state. The molten globule ensembles sampled during protein folding and unfolding are thought to be roughly similar. | https://en.wikipedia.org/wiki/Molten_globule |
The MG structure is believed to lack the close packing of amino acid side chains that characterize the native state ( N {\displaystyle {\ce {N}}} ) of a protein. The transition from a denatured ( U {\displaystyle {\ce {U}}} ) state to a molten globule may be a two state process U ⟷ MG {\displaystyle {\ce {U <-> MG}}} Or it may be a continuous transition, with no cooperativity and no apparent "switch" from one form to the other. The folding of some proteins can be modeled as a three-state kinetic process: U ⟷ MG ⟷ N {\displaystyle {\ce {U <-> MG <-> N}}} One of the difficulties in de novo protein design is achieving the side chain packing needed to create a stable native state rather than an ensemble of molten globules. Given a desired backbone conformation, side chain packing can be designed using variations of the dead-end elimination algorithm; however, attempts to design proteins of novel folds have difficulty using this method due to an absence of plausible backbone models. | https://en.wikipedia.org/wiki/Molten_globule |
In molecular biology, the transcriptional activator LAG-3 is a transcriptional activator protein. The C. elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. == References == | https://en.wikipedia.org/wiki/Transcriptional_activator_LAG-3 |
In molecular biology, the trappin protein transglutaminase binding domain or cementoin is a protein domain found at the N-terminus of Whey Acidic Protein (WAP) domain-containing protease inhibitors such as trappin-2. This N-terminal domain enables it to become cross-linked to extracellular matrix proteins by transglutaminase. This domain contains several repeated motifs with the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond. == References == | https://en.wikipedia.org/wiki/Trappin_protein_transglutaminase_binding_domain |
In molecular biology, the type IV collagen C4 domain (or collagen IV NC1 domain) is a duplicated domain present at the C-terminus of type IV collagens. Each type IV collagen contains a long triple-helical collagenous domain flanked by a short 7S domain of 25 amino acids and a globular non-collagenous C4 domain of ~230 amino acids at the N and C terminus, respectively. In protomer assembly, the C4 domains of three chains interact, forming a C4 trimer, to select and register chains for triple helix formation. In network assembly, the C4 trimers of two protomers interact, forming a C4 hexamer structure, to select and connect protomers.The collagen IV C4 domain contains 12 cysteines, and all of them are involved in disulphide bonds. | https://en.wikipedia.org/wiki/Type_IV_collagen_C4_domain |
It folds into a tertiary structure with predominantly beta-strands. The collagen IV C4 domain is composed of two similarly folded subdomains stabilised by 3 intrachain disulphide bonds involving the following pairs: C1-C6, C2-C5, and C3-C4. Each subdomain represents a compact disulphide-stabilised triangular structure, from which a finger-like hairpin loop projects into an incompletely formed six-stranded beta-sheet of an adjacent subdomain of the same or of an adjacent chain clamping the subdomains tightly together. == References == | https://en.wikipedia.org/wiki/Type_IV_collagen_C4_domain |
In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin (vitamin B12). It can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain. | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (EC 2.1.1.13), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (EC 5.4.99.2), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (EC 5.4.3.4). | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
Prokaryotic glutamate mutase (EC 5.4.99.1). Prokaryotic methyleneglutarate mutase (EC 5.4.99.4). Prokaryotic isobutyryl-CoA mutase (EC 5.4.99.13).The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha). | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices. This N-terminal domain forms a 4-helical bundle cap, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. == References == | https://en.wikipedia.org/wiki/Vitamin_B12-binding_domain |
In molecular biology, the xyloglucan endo-transglycosylase (XET) is an enzyme that is involved in the metabolism of xyloglucan, which is a component of plant cell walls. This enzyme is part of glycoside hydrolase family 16. | https://en.wikipedia.org/wiki/Xyloglucan_endo-transglycosylase |
In molecular biology, the δ (delta) subunit of DNA polymerase III is encoded by the holA gene in E. coli and other bacteria. Along with the γ, δ', χ, and ψ subunits that make up the core polymerase, and the β accessory proteins, the δ subunit is responsible for the high speed and processivity of polIII. == References == | https://en.wikipedia.org/wiki/DNA_polymerase_III,_delta_subunit |
In molecular biology, this entry refers to a protein domain called, the Vitelline membrane outer layer protein I (VMO-I). It is a structure found on the outside of an egg, in the vitelline membrane. | https://en.wikipedia.org/wiki/Vitelline_membrane_outer_layer_protein_I_(VMO-I) |
In molecular biology, this protein domain belongs to the terpene synthase family (TPS). Its role is to synthesize terpenes, which are part of primary metabolism, such as sterols and carotene, and also part of the secondary metabolism. This entry will focus on the C terminal domain of the TPS protein. | https://en.wikipedia.org/wiki/Terpene_synthase_C_terminal_domain |
In molecular biology, this protein domain belongs to the terpene synthase family (TPS). Its role is to synthesize terpenes, which are part of primary metabolism, such as sterols and carotene, and also part of the secondary metabolism. This entry will focus on the N terminal domain of the TPS protein. | https://en.wikipedia.org/wiki/Terpene_synthase_N_terminal_domain |
In molecular biology, this protein domain has been termed SRA-YDG, which is the abbreviation for SET and Ring finger Associated, YDG motif. Additional characteristics of the domain include conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The protein domain is mainly found in plants and animals and in bacteria. | https://en.wikipedia.org/wiki/YDG_SRA_protein_domain |
In molecular biology, this protein domain is found at the C terminus of the GTP-binding protein, YchF-GTPase found in both prokaryotes and eukaryotes. | https://en.wikipedia.org/wiki/YchF-GTPase_C_terminal_protein_domain |
In molecular biology, this protein domain of unknown function is found in numerous prokaryote organisms. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. | https://en.wikipedia.org/wiki/YbaK_protein_domain |
In molecular biology, this protein domain represents Tbf5 which stands for TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1 a type of nucleotide excision repair (NER) proteins. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. The function of this protein is to aid transcription. | https://en.wikipedia.org/wiki/Tbf5_protein_domain |
In molecular biology, trans-activating crispr RNA (tracrRNA) is a small trans-encoded RNA. It was first discovered by Emmanuelle Charpentier in her study of human pathogen Streptococcus pyogenes, a type of bacteria that causes harm to humanity. In bacteria and archaea; CRISPR-Cas (clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins) constitute an RNA-mediated defense system which protects against viruses and plasmids. This defensive pathway has three steps. | https://en.wikipedia.org/wiki/Trans-activating_crRNA |
First a copy of the invading nucleic acid is integrated into the CRISPR locus. Next, CRISPR RNAs (crRNAs) are transcribed from this CRISPR locus. The crRNAs are then incorporated into effector complexes, where the crRNA guides the complex to the invading nucleic acid and the Cas proteins degrade this nucleic acid. | https://en.wikipedia.org/wiki/Trans-activating_crRNA |
There are several CRISPR system subtypes. Type II CRISPR-Cas systems require a tracrRNA which plays a role in the maturation of crRNA. The tracrRNA is partially complementary to and base pairs with a pre-crRNA forming an RNA duplex. This is cleaved by RNase III, an RNA-specific ribonuclease, to form a crRNA/tracrRNA hybrid. This hybrid acts as a guide for the endonuclease Cas9, which cleaves the invading nucleic acid. | https://en.wikipedia.org/wiki/Trans-activating_crRNA |
In molecular biology, transcription factor DP (Dimerization Partner) is a family of proteins which function as transcription factors. DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer and negatively regulates the G1-S transition. | https://en.wikipedia.org/wiki/Transcription_factor_DP |
In molecular biology, translation initiation factor IF-3 (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consists of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit. The chloroplast homolog enhances the poly(A,U,G)-dependent binding of the initiator tRNA to its ribosomal 30s subunits. | https://en.wikipedia.org/wiki/Translation_initiation_factor_IF-3 |
IF1–IF3 may also perform ribosome recycling.IF3 is not universally found in all bacterial species. However, in E. coli, it is required for the 30S subunit to bind to the initiation site in mRNA. In addition, it has several other jobs including the stabilization of free 30S subunits, enables 30S subunits to bind to mRNA and checks for accuracy against the first aminoacyl-tRNA. | https://en.wikipedia.org/wiki/Translation_initiation_factor_IF-3 |
It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly. IF3 is required by the small subunit to form initiation complexes, but has to be released to allow the 50S subunit to bind. IF3 is made up of two domains connected by a flexible linker. | https://en.wikipedia.org/wiki/Translation_initiation_factor_IF-3 |
Together they allow IF3 to carry out its function.Human mitochondria use a nuclear-encoded homolog MTIF3 for translation initiation. Some bacteria, chloroplasts, and mitochondria have multiple copies of IF3. == References == | https://en.wikipedia.org/wiki/Translation_initiation_factor_IF-3 |
In molecular biology, treadmilling is a phenomenon observed within protein filaments of the cytoskeletons of many cells, especially in actin filaments and microtubules. It occurs when one end of a filament grows in length while the other end shrinks, resulting in a section of filament seemingly "moving" across a stratum or the cytosol. This is due to the constant removal of the protein subunits from these filaments at one end of the filament, while protein subunits are constantly added at the other end. | https://en.wikipedia.org/wiki/Treadmilling |
Treadmilling was discovered by Wegner, who defined the thermodynamic and kinetic constraints. Wegner recognized that: “The equilibrium constant (K) for association of a monomer with a polymer is the same at both ends, since the addition of a monomer to each end leads to the same polymer.”; a simple reversible polymer can’t treadmill; ATP hydrolysis is required. GTP is hydrolyzed for microtubule treadmilling. | https://en.wikipedia.org/wiki/Treadmilling |
In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.TAAs are just one of many methods bacteria use to infect their hosts, infection resulting in diseases such as pneumonia, sepsis, and meningitis. | https://en.wikipedia.org/wiki/Trimeric_autotransporter_adhesin |
Most bacteria infect their host through a method named the secretion pathway. TAAs are part of the secretion pathway, to be more specific the type Vc secretion system.Trimeric autotransporter adhesins have a unique structure. The structure they hold is crucial to their function. | https://en.wikipedia.org/wiki/Trimeric_autotransporter_adhesin |
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