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Variations in sequence give rise to differences in structure and function between GA modules in different proteins, which could alter pathogenesis and host specificity due to their varied affinities for different species of albumin. Proteins containing a GA module include PAB from Peptostreptococcus magnus. == References == | https://en.wikipedia.org/wiki/GA_module |
In molecular biology, the GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologues (human GCM1 and GCM2). In GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 amino acids. Sequence conservation is highest in this GCM domain. | https://en.wikipedia.org/wiki/GCM_transcription_factors |
In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3'. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. | https://en.wikipedia.org/wiki/GCM_transcription_factors |
The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. | https://en.wikipedia.org/wiki/GCM_transcription_factors |
The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. == References == | https://en.wikipedia.org/wiki/GCM_transcription_factors |
In molecular biology, the GGDEF domain is a protein domain which appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to act as a diguanylate cyclase and synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria. Enzymatic activity can be strongly influenced by the adjacent domains. | https://en.wikipedia.org/wiki/GGDEF_domain |
Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase. == References == | https://en.wikipedia.org/wiki/GGDEF_domain |
In molecular biology, the GHMP kinase family is a family of kinase enzymes. Members of this family include homoserine kinases EC 2.7.1.39, galactokinases EC 2.7.1.6, and mevalonate kinasesEC 2.7.1.36. These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. | https://en.wikipedia.org/wiki/GHMP_kinase_family |
These enzymes contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, creates a novel nucleotide binding fold. == References == | https://en.wikipedia.org/wiki/GHMP_kinase_family |
In molecular biology, the GRIP domain is a conserved protein domain. The GRIP (golgin-97, RanBP2alpha, Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. It contains a completely conserved tyrosine residue. == References == | https://en.wikipedia.org/wiki/GRIP_domain |
In molecular biology, the GYF domain (glycine-tyrosine-phenylalanine domain) is an approximately 60-amino acid protein domain which contains a conserved GPxxxxxxWxxxYF motif. It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. Binding experiments and mutational analyses have demonstrated the critical importance of the GYF tripeptide in ligand binding. | https://en.wikipedia.org/wiki/GYF_domain |
A GYF domain is also found in several other eukaryotic proteins of unknown function. It has been proposed that the GYF domain found in these proteins could also be involved in proline-rich sequence recognition. Resolution of the structure of the CD2BP2 GYF domain by NMR spectroscopy revealed a compact domain with a beta-beta-alpha-beta-beta topology, where the single alpha-helix is tilted away from the twisted, anti-parallel beta-sheet. The conserved residues of the GYF domain create a contiguous patch of predominantly hydrophobic nature which forms an integral part of the ligand-binding site. There is limited homology within the C-terminal 20-30 amino acids of various GYF domains, supporting the idea that this part of the domain is structurally but not functionally important. | https://en.wikipedia.org/wiki/GYF_domain |
In molecular biology, the GntR-like bacterial transcription factors are a family of transcription factors. | https://en.wikipedia.org/wiki/GntR-like_bacterial_transcription_factors |
In molecular biology, the Guanosine dissociation inhibitors (GDIs) constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic. GDIs bind to the GDP-bound form of Rho and Rab small GTPases and not only prevent exchange (maintaining the small GTPase in an off-state), but also prevent the small GTPase from localizing at the membrane, which is their place of action. This inhibition can be removed by the action of a GDI displacement factor. GDIs also inhibit cdc42 by binding to its tail and preventing its insertion into membranes; hence it cannot trigger WASPs and cannot lead to nucleation of F-actin. | https://en.wikipedia.org/wiki/Guanosine_nucleotide_dissociation_inhibitors |
The GDIs' C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1. REP-1 presents newly synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction. | https://en.wikipedia.org/wiki/Guanosine_nucleotide_dissociation_inhibitors |
The mechanism of REP-1-mediated membrane association of Rab5 is similar to that mediated by Rab GDP dissociation inhibitor (GDI). REP-1 and Rab GDI also share other functional properties, including the ability to inhibit the release of GDP and to remove Rab proteins from membranes. The crystal structure of the bovine alpha-isoform of Rab GDI has been determined to a resolution of 1.81 Angstrom. | https://en.wikipedia.org/wiki/Guanosine_nucleotide_dissociation_inhibitors |
The protein is composed of two main structural units: a large complex multi-sheet domain I, and a smaller alpha-helical domain II. The structural organisation of domain I is closely related to FAD-containing monooxygenases and oxidases. Conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the domain. The two most conserved regions form a compact structure at the apex of the molecule; site-directed mutagenesis has shown these regions to play a critical role in the binding of Rab proteins. | https://en.wikipedia.org/wiki/Guanosine_nucleotide_dissociation_inhibitors |
In molecular biology, the H2TH domain (helix-2turn-helix domain) is a DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity EC 3.2.2.- and AP lyase activity EC 4.2.99.18. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). | https://en.wikipedia.org/wiki/H2TH_domain |
Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; EC 3.2.2.23) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;EC 4.2.99.18). Fpg has a preference for oxidised purines, excising oxidised purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). Its AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. | https://en.wikipedia.org/wiki/H2TH_domain |
Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the H2TH (helix-two-turns-helix) motifs) suggest that the oxidised base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines.Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (EC 3.2.2.-,EC 4.2.99.18), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. | https://en.wikipedia.org/wiki/H2TH_domain |
These proteins contain three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger. == References == | https://en.wikipedia.org/wiki/H2TH_domain |
In molecular biology, the HAMP domain (present in Histidine kinases, Adenylate cyclases, Methyl accepting proteins and Phosphatases) is an approximately 50-amino acid alpha-helical region that forms a dimeric, four-helical coiled coil. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. | https://en.wikipedia.org/wiki/HAMP_domain |
One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. In its most common setting, the HAMP domain transmits conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains and thus regulates the phosphorylation or methylation activity of homodimeric receptors. == References == | https://en.wikipedia.org/wiki/HAMP_domain |
In molecular biology, the HAND domain is a protein domain which adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. This domain confers DNA and nucleosome binding properties to the proteins in which it occurs. It is named the HAND domain because its 4-helical structure resembles an open hand. | https://en.wikipedia.org/wiki/HAND_domain |
HAND domain-containing proteins include proteins involved in nucleosome remodelling, an energy-dependent process that alters histone-DNA interactions within nucleosomes, thereby rendering nucleosomal DNA accessible to regulatory factors. The ATPases involved in nucleosome remodelling belong to the SWI2/SNF2 subfamily of DEAD/H-helicases, which contain a conserved ATPase domain characterised by seven motifs. Proteins within this family differ with regard to domain organisation, their associated proteins and the remodelling complex in which they reside. | https://en.wikipedia.org/wiki/HAND_domain |
The ATPase ISWI is a member of this family. ISWI can be divided into two regions: an N-terminal region that contains the SWI2/SNF2 ATPase domain, and a C-terminal region that is responsible for substrate recognition. The C-terminal region contains 12 alpha-helices and can be divided into three domains and a spacer region: a HAND domain, a SANT domain (c-Myb DNA-binding like), a spacer helix, and a SLIDE domain (SANT-like but with several insertions). == References == | https://en.wikipedia.org/wiki/HAND_domain |
In molecular biology, the HD domain is a conserved protein domain, named after the conserved histidine (H) and/or aspartate (D) amino acid residues. It is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins. == References == | https://en.wikipedia.org/wiki/HD_domain |
In molecular biology, the HECT domain is a protein domain found in ubiquitin-protein ligases. The name HECT comes from 'Homologous to the E6-AP Carboxyl Terminus'. Proteins containing this domain at the C terminus include ubiquitin-protein ligase, which regulates ubiquitination of CDC25. Ubiquitin-protein ligase accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester, and then directly transfers the ubiquitin to targeted substrates. | https://en.wikipedia.org/wiki/HECT_domain |
A cysteine residue is required for ubiquitin-thiolester formation. Human thyroid receptor interacting protein 12 (TRIP12), which also contains this domain, is a component of an ATP-dependent multisubunit protein that interacts with the ligand binding domain of the thyroid hormone receptor. It could be an E3 ubiquitin-protein ligase. | https://en.wikipedia.org/wiki/HECT_domain |
Human E6AP ubiquitin-protein ligase interacts with the E6 protein of the cancer-associated Human papillomavirus type 16 and Human papillomavirus type 18. The E6/E6-AP complex binds to and targets the p53 tumour-suppressor protein for ubiquitin-mediated proteolysis. == References == | https://en.wikipedia.org/wiki/HECT_domain |
In molecular biology, the HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding domain) is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains: Single-domain HEPN proteins found in many bacteria. Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. | https://en.wikipedia.org/wiki/HEPN_domain |
These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug. A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain. | https://en.wikipedia.org/wiki/HEPN_domain |
The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all-alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding. == References == | https://en.wikipedia.org/wiki/HEPN_domain |
In molecular biology, the HMA domain (heavy-metal-associated domain) is a conserved protein domain found in a number of heavy metal transport or detoxification proteins.Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases.The HMA domain, contains two conserved cysteines that are probably involved in metal binding. The fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold. This fold is common to other domains and is classified as "ferredoxin-like". == References == | https://en.wikipedia.org/wiki/HMA_domain |
In molecular biology, the HMG-CoA reductase family is a family of enzymes which participate in the mevalonate pathway, the metabolic pathway that produces cholesterol and other isoprenoids. There are two distinct classes of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase enzymes: class I consists of eukaryotic and most archaeal enzymes EC 1.1.1.34, while class II consists of prokaryotic enzymes EC 1.1.1.88.Class I HMG-CoA reductases catalyse the NADP-dependent synthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). In vertebrates, membrane-bound HMG-CoA reductase is the rate-limiting enzyme in the biosynthesis of cholesterol and other isoprenoids. In plants, mevalonate is the precursor of all isoprenoid compounds. | https://en.wikipedia.org/wiki/HMG-CoA_reductase_family |
The reduction of HMG-CoA to mevalonate is regulated by feedback inhibition by sterols and non-sterol metabolites derived from mevalonate, including cholesterol. In archaea, HMG-CoA reductase is a cytoplasmic enzyme involved in the biosynthesis of the isoprenoids side chains of lipids. Class I HMG-CoA reductases consist of an N-terminal membrane domain (lacking in archaeal enzymes), and a C-terminal catalytic region. | https://en.wikipedia.org/wiki/HMG-CoA_reductase_family |
The catalytic region can be subdivided into three domains: an N-domain (N-terminal), a large L-domain, and a small S-domain (inserted within the L-domain). The L-domain binds the substrate, while the S-domain binds NADP. Class II HMG-CoA reductases catalyse the reverse reaction of class I enzymes, namely the NAD-dependent synthesis of HMG-CoA from mevalonate and CoA. | https://en.wikipedia.org/wiki/HMG-CoA_reductase_family |
Some bacteria, such as Pseudomonas mevalonii, can use mevalonate as the sole carbon source. Class II enzymes lack a membrane domain. | https://en.wikipedia.org/wiki/HMG-CoA_reductase_family |
Their catalytic region is structurally related to that of class I enzymes, but it consists of only two domains: a large L-domain and a small S-domain (inserted within the L-domain). As with class I enzymes, the L-domain binds substrate, but the S-domain binds NAD (instead of NADP in class I). == References == | https://en.wikipedia.org/wiki/HMG-CoA_reductase_family |
In molecular biology, the HMG-box (high mobility group box) is a protein domain which is involved in DNA binding. The domain is composed of approximately 75 amino acid residues that collectively mediate the DNA-binding of chromatin-associated high-mobility group proteins. HMG-boxes are present in many transcription factors and chromatin-remodeling complexes, where they can mediate non-sequence or sequence-specific DNA binding. | https://en.wikipedia.org/wiki/HMG-box |
In molecular biology, the HORMA domain (named after the Hop1p, Rev7p and MAD2 proteins) is a protein domain that has been suggested to recognise chromatin states resulting from DNA adducts, double stranded breaks or non-attachment to the spindle and act as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity. | https://en.wikipedia.org/wiki/HORMA_domain |
In molecular biology, the Hsp17 thermometer is an RNA element (RNA thermometer) found in the 5' UTR of Hsp17 mRNA. Hsp17 is a cyanobacterial heat shock protein belonging to the Hsp20 family.At physiological temperature (28 degrees Celsius) the Hsp17 thermometer forms a hairpin structure, preventing translation of Hsp17. Under heat shock conditions the hairpin structure melts and translation takes place. | https://en.wikipedia.org/wiki/Hsp17_thermometer |
In molecular biology, the IMD domain (IRSp53 and MIM (missing in metastases) homology Domain) is a BAR-like domain of approximately 250 amino acids found at the N-terminus in the insulin receptor tyrosine kinase substrate p53 (IRSp53/BAIAP2) and in the evolutionarily related IRSp53/MIM (MTSS1) family. In IRSp53, a ubiquitous regulator of the actin cytoskeleton, the IMD domain acts as conserved F-actin bundling domain involved in filopodium formation. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 (Rho-family GTPases) and is SH3-independent. The IRSp53/MIM family is a novel F-actin bundling protein family that includes invertebrate relatives: Vertebrate MIM (missing in metastasis) (MTSS1), an actin-binding scaffold protein that may be involved in cancer metastasis. | https://en.wikipedia.org/wiki/IMD_domain |
Vertebrate ABBA-1 (MTSS1L), a MIM-related protein. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) or insulin receptor tyrosine kinase substrate p53 (IRSp53), a multifunctional adaptor protein that links Rac1 with a Wiskott–Aldrich syndrome family verprolin-homologous protein 2 (WAVE2/WASF2) to induce lamellipodia or Cdc42 with Mena to induce filopodia. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2-like proteins 1 and 2 (BAI1-associated protein 2-like proteins 1 and 2, BAIAP2L1 and BAIAP2L2). | https://en.wikipedia.org/wiki/IMD_domain |
Drosophila melanogaster (Fruit fly) CG32082-PA. Caenorhabditis elegans M04F3.5 protein.The vertebrate IRSp53/MIM family is divided into two major groups: the IRSp53 subfamily and the MIM/ABBA subfamily. The putative invertebrate homologues are positioned between them. | https://en.wikipedia.org/wiki/IMD_domain |
The IRSp53 subfamily members contain an SH3 domain, and the MIM/ABBA subfamily proteins contain a WH2 (WASP-homology 2) domain. The vertebrate SH3-containing subfamily is further divided into three groups according to the presence or absence of the WWB and the half-CRIB motif. The IMD domain can bind to and bundle actin filaments, bind to membranes and interact with the small GTPase Rac.The IMD domain folds as a coiled coil of three extended alpha-helices and a shorter C-terminal helix. | https://en.wikipedia.org/wiki/IMD_domain |
Helix 4 packs tightly against the other three helices, and thus represents an integral part of the domain. The fold of the IMD domain closely resembles that of the BAR (Bin-Amphiphysin-RVS) domain, a functional module serving both as a sensor and inducer of membrane curvature. The IMD domain is also known as the I-BAR domain because of its inverse curvature of the membrane binding surface compared to that of the BAR domain. The WH2 domain performs a scaffolding function. == References == | https://en.wikipedia.org/wiki/IMD_domain |
In molecular biology, the IMPDH/GMPR family of enzymes includes IMP dehydrogenase and GMP reductase. These enzymes are involved in purine metabolism. These enzymes adopt a TIM barrel structure. == References == | https://en.wikipedia.org/wiki/IMPDH/GMPR_family |
In molecular biology, the KduI/IolB isomerase family is a family of isomerase enzymes that includes 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (5-keto 4-deoxyuronate isomerase) (KduI) and 5-deoxy-glucuronate isomerase (5DG isomerase) (IolB). KduI is involved in pectin degradation by free-living soil bacteria that use pectin as a carbon source, breaking it down to 2-keto-3-deoxygluconate, which can ultimately be converted to pyruvate. KduI catalyses the fourth step in pectin degradation, namely the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate. KduI has a TIM-barrel fold.This family also includes several bacterial Myo-inositol catabolism proteins, such as IolB, which is encoded by the inositol operon (iolABCDEFGHIJ) in Bacillus subtilis. | https://en.wikipedia.org/wiki/KduI/IolB_isomerase_family |
IolB is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR. Members of this family possess a Cupin like structure. == References == | https://en.wikipedia.org/wiki/KduI/IolB_isomerase_family |
In molecular biology, the KilA-N domain is a conserved DNA-binding domain found at the N-terminus of the poxvirus D6R/NIR proteins. It is also found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. Putative proteins with homology to the KilA-N domain have also been identified in Maverick transposable elements of the parabasalid protozoa Trichomonas vaginalis. The KilA-N domain has been suggested to be homologous to the fungal DNA-binding APSES domain. | https://en.wikipedia.org/wiki/KilA-N_domain |
In all proteins shown to contain the KilA-N domain, it occurs at the extreme amino terminus accompanied by a wide range of distinct carboxy-terminal domains. These carboxy-terminal modules may be enzymes, such as the nuclease domains, or might mediate additional, specific interactions with nucleic acids or proteins, like the RING or CCCH fingers in the poxviruses. | https://en.wikipedia.org/wiki/KilA-N_domain |
The KilA-N domain is predicted to adopt an alpha-beta fold with four conserved strands and at least two conserved helices. Some proteins known to contain a KilA-N domain are listed below: Bacteriophage P1 protein kilA Fowlpox virus (FPV) protein FPV236. Trichomonas vaginalis G3 Putative uncharacterised protein Vaccinia virus hypothetical 21.7 kDa HindIII-C protein == References == | https://en.wikipedia.org/wiki/KilA-N_domain |
In molecular biology, the LIM domain-binding protein family is a family of proteins which binds to the LIM domain of LIM (LIN-11, Isl-1 and MEC-3) homeodomain proteins which are transcriptional regulators of development. | https://en.wikipedia.org/wiki/LIM_domain-binding_protein_family |
In molecular biology, the LisH domain (lis homology domain) is a protein domain found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerisation motif, and that other structural elements are likely to play an important role in dimerisation.The LisH domain is found in the Saccharomyces cerevisiae SIF2 protein, a component of the SET3 complex which is responsible for repressing meiotic genes In SIF2 the LisH domain has been shown to mediate dimer and tetramer formation. It has been shown that the LisH domain helps mediate interaction with components of the SET3 complex. == References == | https://en.wikipedia.org/wiki/LisH_domain |
In molecular biology, the Lon protease family is a family of enzymes that break peptide bonds in proteins resulting in smaller peptides or amino acids. They are found in archaea, bacteria and eukaryotes. Lon proteases are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (Lon protease family, clan SJ). | https://en.wikipedia.org/wiki/Lon-A_peptidase |
In the eukaryotes the majority of the Lon proteases are located in the mitochondrial matrix. In yeast, the Lon protease PIM1 is located in the mitochondrial matrix. It is required for mitochondrial function, it is constitutively expressed but is increased after thermal stress, suggesting that PIM1 may play a role in the heat shock response. Lon proteases have two specific subfamilies: LonA and LonB, differentiated by the number of AAA+ domains found in the protein. | https://en.wikipedia.org/wiki/Lon-A_peptidase |
In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. It is present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
The DNA-binding HTH domain is usually located in the C-terminal region of the protein; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers.LuxR-type HTH proteins can be activated by one of four different mechanisms: 1. | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis comA (involved in expression of late-expressing competence genes)2. Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria: Vibrio fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) Acinetobacter baumannii abaR (activates operon for production of surfactant-like lipopeptide acinetin-505)3. | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
Autonomous effector domain regulators, without a regulatory domain, represented by gerE. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation)4. Multiple ligand-binding regulators, exemplified by malT. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose) == References == | https://en.wikipedia.org/wiki/LuxR-type_DNA-binding_HTH_domain |
In molecular biology, the Macro domain (often also written macrodomain) or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose, an NAD metabolite, or related ligands. Binding to ADP-ribose can be either covalent or non-covalent: in certain cases it is believed to bind non-covalently, while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. | https://en.wikipedia.org/wiki/Macro_domain |
In molecular biology, the NAD+ five-prime cap (NAD+ 5’ cap) refers to a molecule of nicotinamide adenine dinucleotide (NAD+), a nucleoside-containing metabolite, covalently bonded the 5’ end of cellular mRNA. While the more common methylated guanosine (m7G) cap is added to RNA by a capping complex that associates with RNA polymerase II (RNAP II), the NAD cap is added during transcriptional initiation by the RNA polymerase itself, acting as a non-canonical initiating nucleotide (NCIN). As such, while m7G capping can only occur in organisms possessing specialized capping complexes, because NAD capping is performed by RNAP itself, it is hypothesized to occur in most, if not all, organisms.The NAD+ 5’ cap has been observed in bacteria, contrary to the long-held belief that prokaryotes lacked 5’-capped RNA, as well as on the 5’ cap of eukaryotic mRNA, in place of the m7G cap. | https://en.wikipedia.org/wiki/NAD+_Five-prime_cap |
This modification also potentially allows for selective degradation of RNA]within prokaryotes as different pathways are involved in the degradation of NAD+-capped and uncapped 5′-triphosphate-RNAs. In eukaryotic cells, while the more commonly observed m7G cap promotes the stability of the mRNA and supports translation, the NAD+ cap targets the RNA transcript for decay, facilitated by the non-canonical decapping enzyme, DXO. Considering the centrality of NAD in redox chemistry and post-translational protein modification, its attachment to RNA represents potentially undiscovered pathways in RNA metabolism and regulation. | https://en.wikipedia.org/wiki/NAD+_Five-prime_cap |
In molecular biology, the NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 7 family of proteins (also known as NADH-ubiquinone oxidoreductase subunit B14.5a or Complex I-B14.5a) form a part of NADH dehydrogenase (complex I). In mammals, it is encoded by the NDUFA7 gene. == References == | https://en.wikipedia.org/wiki/NADH_dehydrogenase_(ubiquinone)_1_alpha_subcomplex_subunit_7 |
In molecular biology, the NELF (negative elongation factor) is a four-subunit protein complex (NELF-A, NELF-B, NELF-C/NELF-D, and NELF-E) that negatively impacts transcription by RNA polymerase II (Pol II) by pausing about 20-60 nucleotides downstream from the transcription start site (TSS). | https://en.wikipedia.org/wiki/Negative_elongation_factor |
In molecular biology, the OmpA domain is a conserved protein domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins, such as porin-like integral membrane proteins (such as ompA), small lipid-anchored proteins (such as pal), and MotB proton channels. The N-terminal half of these proteins is variable although some of the proteins in this group have the OmpA-like transmembrane domain at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules. MotB (and MotA) serve two functions in E. coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor. | https://en.wikipedia.org/wiki/OmpA_domain |
In molecular biology, the PRINTS database is a collection of so-called "fingerprints": it provides both a detailed annotation resource for protein families, and a diagnostic tool for newly determined sequences. A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces. | https://en.wikipedia.org/wiki/PRINTS |
The particular diagnostic strength of fingerprints lies in their ability to distinguish sequence differences at the clan, superfamily, family and subfamily levels. This allows fine-grained functional diagnoses of uncharacterised sequences, allowing, for example, discrimination between family members on the basis of the ligands they bind or the proteins with which they interact, and highlighting potential oligomerisation or allosteric sites. PRINTS is a founding partner of the integrated resource, InterPro, a widely used database of protein families, domains and functional sites. | https://en.wikipedia.org/wiki/PRINTS |
In molecular biology, the PYP domain (photoactive yellow protein) is a p-coumaric acid-binding protein domain. They are present in various proteins in bacteria. PYP is a highly soluble globular protein with an alpha/beta fold structure. | https://en.wikipedia.org/wiki/Photoactive_yellow_protein |
It is a member of the PAS domain superfamily, which also contains a variety of other kinds of photosensory proteins. PYP was first discovered in 1985.A recently (2016) developed chemogenetic system named FAST (Fluorescence-Activating and absorption Shifting Tag) was engineered from PYP to specifically and reversibly bind a series of hydroxybenzylidene rhodanine (HBR) derivatives for their fluorogenic properties. Upon interaction with FAST, the fluorogen is locked into a fluorescent conformation unlike when in solution. This new protein labelling system is used in a variety of microscopy and cytometry setups. | https://en.wikipedia.org/wiki/Photoactive_yellow_protein |
In molecular biology, the PsbZ (Ycf9) is a protein domain, which is low in molecular weight. It is a transmembrane protein and therefore is located in the thylakoid membrane of chloroplasts in cyanobacteria and plants. More specifically, it is located in Photosystem II (PSII) and in the light-harvesting complex II (LHCII). Ycf9 acts as a structural linker, that stabilises the PSII-LHCII supercomplexes. Moreover, the supercomplex fails to form in PsbZ-deficient mutants, providing further evidence to suggest Ycf9's role as a structural linker. This may be caused by a marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII.Ycf is an acronym originally standing for hypothetical chloroplast open reading frame. | https://en.wikipedia.org/wiki/Ycf9_protein_domain |
In molecular biology, the RNase E 5′ UTR element is a cis-acting element located in the 5′ UTR of ribonuclease (RNase) E messenger RNA (mRNA). RNase E is a key regulatory enzyme in the pathway of mRNA degradation in Escherichia coli. It is able to auto-regulate the degradation of its own mRNA in response to changes in RNase E activity. This rne 5′ UTR element acts as a sensor of cellular RNase E concentration enabling tight regulation of RNase E concentration and synthesis. | https://en.wikipedia.org/wiki/RNase_E_5′_UTR_element |
In molecular biology, the SAG1 protein domain is an example of a group of glycosylphosphatidylinositol (GPI)-linked proteins named SRSs (SAG1 related sequence). SAG1 is found on the surface of a protozoan parasite Toxoplasma gondii. This parasite infects almost any warm-blooded vertebrate. The surface of T. gondii is coated with a family of developmentally regulated glycosylphosphatidylinositol (GPI)-linked proteins (SRSs), of which SAG1 is the prototypic member. | https://en.wikipedia.org/wiki/SAG1_protein_domain |
In molecular biology, the SR1 RNA is a small RNA (sRNA) produced by species of Bacillus and closely related bacteria. It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA. SR1 RNA is involved in the regulation of arginine catabolism. | https://en.wikipedia.org/wiki/SR1_RNA |
SR1 RNA binds to complementary stretches of ahrC mRNA (also known as argR and inhibits translation. AhrC endodes an arginine repressor protein which represses synthesis of arginine biosynthetic enzymes and activates arginine catabolic enzymes via regulation of the rocABC and rocDEF operons.In addition to acting as a sRNA, SR1 also encodes a small peptide, SR1P. SR1P binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilises the gapA operon mRNAs.SR1 expression is regulated by CcpA and CcpN. | https://en.wikipedia.org/wiki/SR1_RNA |
In molecular biology, the Shroom protein family is a small group of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. The Shroom (Shrm) protein family is found only in animals. Proteins of this family are predicted to be utilised in multiple morphogenic and developmental processes across animal phyla to regulate cells shape or intracellular architecture in an actin and myosin-dependent manner. While the founding member of the Shrm family is Shrm1 (formerly Apx), it appears that this protein is found only in Xenopus. | https://en.wikipedia.org/wiki/Shroom_protein_family |
In mice and humans, the Shrm family of proteins consists of: Shrm2 (formerly Apxl), a protein involved in the morphogenesis, maintenance, and/or function of vascular endothelial cells. Shrm3 (formerly Shroom), a protein necessary for neural tube closure in vertebrate development as deficiency in Shrm results in spina bifida. Shrm3 is also conserved in some invertebrates, as orthologues can be found in sea urchins. | https://en.wikipedia.org/wiki/Shroom_protein_family |
Shrm4, a regulator of cyto-skeletal architecture that may play an important role in vertebrate development. It is implicated in X-linked intellectual disability in humans.This protein family is based on the conservation of a specific arrangement of an N-terminal PDZ domain, a centrally positioned sequence motif termed ASD1 (Apx/Shrm Domain 1) and a C-terminal motif termed ASD2. Shrm2 and Shrm3 contain all three domains, while Shrm4 contains the PDZ and ASD2 domains, but lacks a discernible ASD1 element. | https://en.wikipedia.org/wiki/Shroom_protein_family |
To date, the ASD1 and ASD2 elements have only been found in Shrm-related proteins and do not appear in combination with other conserved domains. ASD1 is required for targeting actin, while ASD2 is capable of eliciting an actomyosin based constriction event. ASD2 is the most highly conserved sequence element shared by Shrm1, Shrm2, Shrm3, and Shrm4. | https://en.wikipedia.org/wiki/Shroom_protein_family |
It possesses a well conserved series of leucine residues that exhibit spacing consistent with that of a leucine zipper motif.Shroom2 is both necessary and sufficient to govern the localization of pigment granules at the apical surface of epithelial cells. Shroom2 is a central regulator of RPE pigmentation. | https://en.wikipedia.org/wiki/Shroom_protein_family |
Despite their diverse biological roles, Shroom family proteins share a common activity. Since the locus encoding human SHROOM2 lies within the critical region for two distinct forms of ocular albinism, it is possible that SHROOM2 mutations may contribute to human visual system disorders. == References == | https://en.wikipedia.org/wiki/Shroom_protein_family |
In molecular biology, the Signal Peptide Peptidase (SPP) is a type of protein that specifically cleaves parts of other proteins. It is an intramembrane aspartyl protease with the conserved active site motifs 'YD' and 'GxGD' in adjacent transmembrane domains (TMDs). Its sequences is highly conserved in different vertebrate species. SPP cleaves remnant signal peptides left behind in membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins. | https://en.wikipedia.org/wiki/Signal_peptide_peptidase |
In molecular biology, the Small nucleolar RNA J26 is a non-coding RNA (ncRNA) molecule identified in rice (Oryza sativa) 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. J26 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. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_J26 |
In molecular biology, the Small nucleolar RNA J33 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_J33 |
snoRNA J33 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. Plant snoRNA J33 was identified in a screen of Oryza sativa. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_J33 |
In molecular biology, the Small nucleolar RNA MBI-1 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is 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". snoRNA MBI-1 was originally cloned from mouse brain tissues and belongs to the H/ACA box class of snoRNAs as it has the predicted hairpin-hinge-hairpin-tail structure and has the conserved H/ACA-box motifs. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_MBI-1 |
In molecular biology, the Small nucleolar RNA MBI-161 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is 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".snoRNA MBI-161 was originally cloned from mouse brain tissues and belongs to the H/ACA box class of snoRNAs as it has the predicted hairpin-hinge-hairpin-tail structure and has the conserved H/ACA-box motifs. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_MBI-161 |
In molecular biology, the Small nucleolar RNA Me18S-Gm1358 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_Me18S-Gm1358 |
snoRNA Me18S-Gm1358 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. It is predicted that this family directs 2'-O-methylation of 18S G-1358. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_Me18S-Gm1358 |
In molecular biology, the Small nucleolar RNA U2-19 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_U2-19 |
snoRNA U2-19 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. snoRNA U2-19 directs 2'-O-methylation of U2 spliceosomal RNA G-19. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_U2-19 |
In molecular biology, the Small nucleolar RNA snoR1 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_snoR1 |
snoRNA snoR1 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. Plant snoRNA snoR1 was identified in a screen of Arabidopsis thaliana. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_snoR1 |
In molecular biology, the TATA box (also called the Goldberg–Hogness box) is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence. The TATA box is considered a non-coding DNA sequence (also known as a cis-regulatory element). It was termed the "TATA box" as it contains a consensus sequence characterized by repeating T and A base pairs. | https://en.wikipedia.org/wiki/Hogness_box |
How the term "box" originated is unclear. In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" at the -31 position. When consensus nucleotides and alternative ones were compared, homologous regions were "boxed" by the researchers. | https://en.wikipedia.org/wiki/Hogness_box |
The boxing in of sequences sheds light on the origin of the term "box". The TATA box was first identified in 1978 as a component of eukaryotic promoters. Transcription is initiated at the TATA box in TATA-containing genes. | https://en.wikipedia.org/wiki/Hogness_box |
The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic genes. Gene transcription by RNA polymerase II depends on the regulation of the core promoter by long-range regulatory elements such as enhancers and silencers. Without proper regulation of transcription, eukaryotic organisms would not be able to properly respond to their environment. | https://en.wikipedia.org/wiki/Hogness_box |
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