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Hbl, cytotoxin K (CytK) and Nhe are all putative causes. Both Hbl and Nhe are three-component cytotoxins composed of a binding component, B, and two lytic components, L1 and L2. All three subunits act synergically to cause hemolysis. | https://en.wikipedia.org/wiki/Bacillus_haemolytic_enterotoxin |
Maximal cytotoxicity of Nhe against epithelia is dependent on all three components. Nhe has haemolytic activity against erythrocytes from a variety of species. | https://en.wikipedia.org/wiki/Bacillus_haemolytic_enterotoxin |
It is possible that the common structural and functional properties of these toxins indicate that the Hbl/Nhe and ClyA families of toxins constitute a superfamily of pore-forming cytotoxins. Haemolysin BL and non-haemolytic enterotoxin production are both influenced by pH and micro. == References == | https://en.wikipedia.org/wiki/Bacillus_haemolytic_enterotoxin |
In molecular biology, the Bcl-x interacting domain is a protein domain found in BAM, Bim and Bcl2-like protein 11. It is a long alpha helix, which is required for interaction with Bcl-x. == References == | https://en.wikipedia.org/wiki/Bcl-x_interacting_domain |
In molecular biology, the BmKK2 toxins are a family of scorpion toxins. They belong to the scorpion toxin subfamily alpha-KTx 14. They include a novel short-chain peptide from the Asian scorpion Mesobuthus martensii Karsch, a potassium channel blocker composed of 31 amino acid residues. The peptide adopts a classical alpha/beta-scaffold for alpha-KTxs. | https://en.wikipedia.org/wiki/BmKK2_toxin |
BmKK2 selectively inhibits the delayed rectifier K+ current, but does not affect the fast transient K+ current.In comparison with typical short-chain scorpion toxins (e.g., CTX and NTX), the alpha helix is shorter and the beta-sheet element is smaller (each strand consists of only two residues). There is an alpha-mode binding between the toxin and the channels. It has a lower activity towards Kv channels and it is predicted that it may prefer a type of SK channel with a narrower entryway as a specific receptor. == References == | https://en.wikipedia.org/wiki/BmKK2_toxin |
In molecular biology, the BolA-like protein family consists of the morpho-protein BolA from Escherichia coli, the Fra2 protein from Saccharomyces cerevisiae, and various homologs. The BolA protein is a DNA-binding regulator; the Fra2 protein is an iron sulfur cluster protein that binds Grx3/4 and is involved in regulating iron levels .In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the stationary phase. | https://en.wikipedia.org/wiki/BolA-like_protein_family |
BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5. == References == | https://en.wikipedia.org/wiki/BolA-like_protein_family |
In molecular biology, the Bowman–Birk protease inhibitor family of proteins consists of eukaryotic proteinase inhibitors, belonging to MEROPS inhibitor family I12, clan IF. They mainly inhibit serine peptidases of the S1 family, but also inhibit S3 peptidases.Members of this family have a duplicated structure and generally possess two distinct inhibitory sites. These inhibitors are primarily found in plants and in particular in the seeds of legumes, as well as in cereal grains. In cereals, they exist in two forms, one of which is a duplication of the basic structure. | https://en.wikipedia.org/wiki/Bowman–Birk_protease_inhibitor |
Proteins of the Bowman–Birk inhibitor family of serine proteinase inhibitors interact with the enzymes they inhibit via an exposed surface loop that adopts the canonical proteinase inhibitory conformation. The resulting noncovalent complex renders the proteinase inactive. This inhibition mechanism is common for the majority of serine proteinase inhibitor proteins, and many analogous examples are known. A particular feature of the Bowman–Birk inhibitor protein, however, is that the interacting loop is a particularly well-defined, disulfide-linked, short beta-sheet region. | https://en.wikipedia.org/wiki/Bowman–Birk_protease_inhibitor |
In molecular biology, the BsuBI/PstI restriction endonuclease family is a family of type II restriction endonucleases. It includes BsuBI and PstI. The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system. == References == | https://en.wikipedia.org/wiki/BsuBI/PstI_restriction_endonuclease |
In molecular biology, the Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain and the Src homology 3 (SH3) domain. | https://en.wikipedia.org/wiki/Btk-type_zinc_finger |
The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger (although these differ from known zinc finger topologies), while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins. The TH domain may be of functional importance in various signalling pathways in different species. | https://en.wikipedia.org/wiki/Btk-type_zinc_finger |
A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain (note that although a Btk motif always occurs C-terminal to a PH domain, not all PH domains are followed by a Btk motif). The crystal structures of Btk show that the Btk-type zinc finger has a globular core, formed by a long loop which is held together by a zinc ion, and that the Btk motif is packed against the PH domain. The zinc-binding residues are a histidine and three cysteines, which are fully conserved in the Btk motif.Proteins known to contain a Btk-type zinc finger include: Mammalian Bruton's tyrosine kinase (Btk), a protein tyrosine kinase involved in modulation of diverse cellular processes. | https://en.wikipedia.org/wiki/Btk-type_zinc_finger |
Mutations affecting Btk are the cause of X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice. Mammalian Tec, Bmx, and Itk proteins, which are tyrosine protein kinases of the Tec subfamily. | https://en.wikipedia.org/wiki/Btk-type_zinc_finger |
Drosophila tyrosine-protein kinase Btk29A, which is required for the development of proper ring canals and of male genitalia and required for adult survival. Mammalian Ras GTPase-activating proteins (RasGAP), which regulate the activation of inactive GDP-bound Ras by converting GDP to GTP. == References == | https://en.wikipedia.org/wiki/Btk-type_zinc_finger |
In molecular biology, the BtpA protein family is a family of proteins which includes BtpA. BtpA appears to play a role in the stabilisation of photosystem I . It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane. Homologs of BtpA are found in the Thermoproteota and "Euryarchaeota", where their function remains unknown. | https://en.wikipedia.org/wiki/BtpA_protein |
The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. | https://en.wikipedia.org/wiki/BtpA_protein |
This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners. Ycf3 contains a number of tetratricopeptide repeats (TPR); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions. == References == | https://en.wikipedia.org/wiki/BtpA_protein |
In molecular biology, the Btz domain (CASC3/Barentsz eIF4AIII binding domain) is a protein domain found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide. == References == | https://en.wikipedia.org/wiki/Btz_domain |
In molecular biology, the CAS/CSE protein family is a family of proteins which includes mammalian cellular apoptosis susceptibility (CAS) proteins and yeast chromosome-segregation protein, CSE1. CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. | https://en.wikipedia.org/wiki/CAS/CSE_protein_family |
In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. | https://en.wikipedia.org/wiki/CAS/CSE_protein_family |
Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.Members of the CAS/CSE family of proteins have two domains. An N-terminal Cse1 domain, which contains HEAT repeats, and a C-terminal domain. == References == | https://en.wikipedia.org/wiki/CAS/CSE_protein_family |
In molecular biology, the CAT RNA-binding domain (Co-AntiTerminator RNA-binding domain) is a protein domain found at the amino terminus of a family of transcriptional antiterminator proteins. This domain forms a dimer in the crystal structure. Transcriptional antiterminators of the BglG/SacY family are regulatory proteins that mediate the induction of sugar metabolizing operons in Gram-positive and Gram-negative bacteria. Upon activation, these proteins bind to specific targets in nascent mRNAs, thereby preventing abortive dissociation of the RNA polymerase from the DNA template. == References == | https://en.wikipedia.org/wiki/CAT_RNA-binding_domain |
In molecular biology, the CBS domain is a protein domain found in a range of proteins in all species from bacteria to humans. It was first identified as a conserved sequence region in 1997 and named after cystathionine beta synthase, one of the proteins it is found in. CBS domains are also found in a wide variety of other proteins such as inosine monophosphate dehydrogenase, voltage gated chloride channels and AMP-activated protein kinase (AMPK). CBS domains regulate the activity of associated enzymatic and transporter domains in response to binding molecules with adenosyl groups such as AMP and ATP, or s-adenosylmethionine. | https://en.wikipedia.org/wiki/CBS_domain |
In molecular biology, the CD20-like family of proteins includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc, MS4A2. MS4A2 has a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. It has four putative transmembrane segments and a probable topology where both amino- and carboxy termini protrude into the cytoplasm. | https://en.wikipedia.org/wiki/CD20-like_family |
This family also includes LR8 like proteins from humans (TMEM176B), mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan, a transmembrane component of dystrophin-associated glycoprotein. | https://en.wikipedia.org/wiki/CD20-like_family |
Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton. == References == | https://en.wikipedia.org/wiki/CD20-like_family |
In molecular biology, the CDC48 N-terminal domain is a protein domain found in AAA ATPases including cell division protein 48 (CDC48), VCP-like ATPase and N-ethylmaleimide sensitive fusion protein. It is a substrate recognition domain which binds polypeptides, prevents protein aggregation, and catalyses refolding of permissive substrates. It is composed of two equally sized subdomains. The amino-terminal subdomain (CDC48_N) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. | https://en.wikipedia.org/wiki/CDC48_N-terminal_domain |
The carboxy-terminal subdomain (CDC48_2) forms a novel six-stranded beta-clam fold. Together these subdomains form a kidney-shaped structure, in close agreement with results from electron microscopy. CDC48_N is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. == References == | https://en.wikipedia.org/wiki/CDC48_N-terminal_domain |
In molecular biology, the CFC domain (Cripto_Frl-1_Cryptic domain) is a protein domain found at the C-terminus of a number of proteins including Cripto (or teratocarcinoma-derived growth factor). It is structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2. CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain.The CFC domain appears to play a crucial role in the tumourigenic activity of Cripto proteins, as it is through the CFC domain that Cripto interferes with the onco-suppressive activity of Activins, either by blocking the Activin receptor ALK4 or by antagonising proteins of the TGF-beta family. == References == | https://en.wikipedia.org/wiki/CFC_domain |
In molecular biology, the CHAP domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the family Trypanosomidae. The domain is named after the acronym cysteine, histidine-dependent amidohydrolases/peptidases. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. | https://en.wikipedia.org/wiki/CHAP_domain |
It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism.The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands.Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. | https://en.wikipedia.org/wiki/CHAP_domain |
A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. | https://en.wikipedia.org/wiki/CHAP_domain |
Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). == References == | https://en.wikipedia.org/wiki/CHAP_domain |
In molecular biology, the CHB HEX N-terminal domain represents the N-terminal domain in chitobiases and beta-hexosaminidases. Chitobiases degrade chitin, which forms the exoskeleton in insects and crustaceans, and which is one of the most abundant polysaccharides on earth. Beta-hexosaminidases are composed of either a HexA/HexB heterodimer or a HexB homodimer, and can hydrolyse diverse substrates, including GM(2)-gangliosides; mutations in this enzyme are associated with Tay–Sachs disease. | https://en.wikipedia.org/wiki/CHB_HEX_N-terminal_domain |
HexB is structurally similar to chitobiase, consisting of a beta sandwich structure; this structure is similar to that found in the cellulose-binding domain of cellulase from Cellulomonas fimi. This domain may function as a carbohydrate binding module. == References == | https://en.wikipedia.org/wiki/CHB_HEX_N-terminal_domain |
In molecular biology, the CLP protease family is a family of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP, although the P subunit alone does possess some catalytic activity. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, in the mitochondria of metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. Mutations in mitochondrial CLPP are associated with Perrault syndrome and cause a variety of molecular defects, from the loss of ATPase docking, to the activation or inhibition of peptidase activity. | https://en.wikipedia.org/wiki/CLP_protease_family |
In molecular biology, the CRM domain is an approximately 100-amino acid RNA-binding domain. The name CRM (chloroplast RNA splicing and ribosome maturation) has been suggested to reflect the functions established for four characterised members of the family: Zea mays (Maize) CRS1, CAF1 and CAF2 proteins and the Escherichia coli protein YhbY. Proteins containing the CRM domain are found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. | https://en.wikipedia.org/wiki/CRM_domain |
It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets.The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. | https://en.wikipedia.org/wiki/CRM_domain |
The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue.Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. | https://en.wikipedia.org/wiki/CRM_domain |
GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. | https://en.wikipedia.org/wiki/CRM_domain |
These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. == References == | https://en.wikipedia.org/wiki/CRM_domain |
In molecular biology, the CRP domain is a protein domain consisting of a helix-turn-helix (HTH) motif. It is found at the C-terminus of numerous bacterial transcription regulatory proteins. These proteins bind DNA via the CRP domain. | https://en.wikipedia.org/wiki/Crp_domain |
These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including ANR, CRP, CLP, CysR, FixK, Flp, FNR, FnrN, HlyX and NtcA. == References == | https://en.wikipedia.org/wiki/Crp_domain |
In molecular biology, the CUT domain (also known as ONECUT) is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, which is often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the CUT domain, and two modes of transcriptional stimulation, which hinge on the homeodomain. == References == | https://en.wikipedia.org/wiki/CUT_domain |
In molecular biology, the CVNH domain (CyanoVirin-N Homology domain) is a conserved protein domain. It is found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as proteins from filamentous ascomycetes and in the fern Ceratopteris richardii.Cyanovirin-N (CV-N) is an 11-kDa protein from the cyanobacterium Nostoc ellipsosporum that displays virucidal activity against several viruses, including human immunodeficiency virus (AIDS). The virucidal activity of CV-N is mediated through specific high-affinity interactions with the viral surface envelope glycoproteins gp120 and gp41, as well as to high-mannose oligosaccharides found on the HIV envelope. In addition, CV-N is active against rhinoviruses, human parainfluenza virus, respiratory syncytial virus, and enteric viruses. | https://en.wikipedia.org/wiki/CVNH_domain |
The virucidal activity of CV-N against influenza virus is directed towards viral haemagglutinin. CV-N has a complex fold composed of a duplication of a tandem repeat of two homologous motifs comprising three-stranded beta sheet and beta hairpins. == References == | https://en.wikipedia.org/wiki/CVNH_domain |
In molecular biology, the Cbl TKB domain (tyrosine kinase binding domain), also known as the phosphotyrosine binding (PTB) domain is a conserved region found at the N-terminus of Cbl adaptor proteins. This N-terminal region is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle domain, an EF hand-like domain and a SH2-like domain, which together are known to bind to phosphorylated tyrosine residues. == References == | https://en.wikipedia.org/wiki/Cbl_TKB_domain |
In molecular biology, the Cfr10I/Bse634I family of restriction endonucleases includes the type II restriction endonucleases Cfr10I and Bse634I. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. | https://en.wikipedia.org/wiki/Cfr10I/Bse634I |
Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R. Recognition sequence Cut 5' RCCGGY 5' ---R CCGGY--- 3' 3' YGGCCR 3' ---YGGCC R--- 5' == References == | https://en.wikipedia.org/wiki/Cfr10I/Bse634I |
In molecular biology, the CodY protein family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk. == References == | https://en.wikipedia.org/wiki/CodY_protein_family |
In molecular biology, the Cofactor transferase family is a family of protein domains that includes biotin protein ligases, lipoate-protein ligases A, octanoyl-(acyl carrier protein):protein N-octanoyltransferases, and lipoyl-protein:protein N-lipoyltransferases. The metabolism of the cofactors Biotin and lipoic acid share this family. They also share the target modification domain (Pfam PF00364), and the sulfur insertion enzyme (Pfam PF04055). Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the biotin carboxyl carrier protein. | https://en.wikipedia.org/wiki/Cofactor_transferase_family |
Each organism likely has only one BPL protein. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Biotin attachment is required for biotin biosynthesis and utilization of free biotin.Lipoate-protein ligase catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue of the lipoyl domain of lipoate dependent enzymes. | https://en.wikipedia.org/wiki/Cofactor_transferase_family |
They are required for the utilization of free lipoic acid.Octanoyl-(acyl carrier protein):protein N-octanoyltransferases, or octanoyltransferases, are required for lipoic acid biosynthesis. They transfer octanoate from the acyl carrier protein (ACP), part of fatty acid biosynthesis, to the specific lysine residue of lipoyl domains. Two octanoyltransferase isozymes exist in this superfamily.Lipoyl-protein:protein N-lipoyltransferases, or lipoylamidotransferases, are required for lipoic acid metabolism in some organisms. | https://en.wikipedia.org/wiki/Cofactor_transferase_family |
They transfer lipoic acid or octanoate from lipoyl domains and transfer to other lipoyl domains. In Bacillus subtilis, the transfer is from the glycine cleavage system H protein, GcvH, to other lipoyl domains. This is because the octanoyltransferase of B. subtilis is specific for GcvH. | https://en.wikipedia.org/wiki/Cofactor_transferase_family |
In molecular biology, the Cro repressor family is a family of repressor proteins in bacteriophage lambda that includes the Cro repressor. Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. | https://en.wikipedia.org/wiki/Cro_repressor_family |
The crystal structure of the lambda Cro repressor reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement. == References == | https://en.wikipedia.org/wiki/Cro_repressor_family |
In molecular biology, the Cys/Met metabolism PLP-dependent enzyme family is a family of proteins including enzymes involved in cysteine and methionine metabolism which use PLP (pyridoxal-5'-phosphate) as a cofactor. | https://en.wikipedia.org/wiki/Cys/Met_metabolism_PLP-dependent_enzyme_family |
In molecular biology, the DEP domain (Dishevelled, Egl-10 and Pleckstrin domain) is a globular protein domain of about 80 amino acids that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which plays a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarised cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system in RGS9.Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain.Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. | https://en.wikipedia.org/wiki/DEP_domain |
It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region. == References == | https://en.wikipedia.org/wiki/DEP_domain |
In molecular biology, the DHH phosphatase family is a family of putative phosphoesterases. The family includes Drosophila prune protein and bacterial RecJ exonuclease. The RecJ protein of Escherichia coli plays an important role in a number of DNA repair and recombination pathways. | https://en.wikipedia.org/wiki/DHH_phosphatase_family |
RecJ catalyses processive degradation of single-stranded DNA in a 5'-to-3' direction. Sequences highly related to those encoding RecJ can be found in many of the eubacterial genomes sequenced to date. == References == | https://en.wikipedia.org/wiki/DHH_phosphatase_family |
In molecular biology, the DSS1/SEM1 protein family is a family of short acidic proteins which includes the 26S proteasome complex subunits SEM1 from Saccharomyces cerevisiae and Drosophila and DSS1 (SHFM1) in mammals. In Saccharomyces cerevisiae, SEM1 is a regulator of both exocyst function and pseudohyphal differentiation. Loss of DSS1 in Homo sapiens (human) has been associated with split hand/split foot malformations. DSS1 is playing role as a modifier in a novel protein posttranslational modification, referred to as DSSylation, which is probably targeting oxidized proteins and guiding them to proteasomal degradation. == References == | https://en.wikipedia.org/wiki/DSS1/SEM1_protein_family |
In molecular biology, the DinI-like protein family is a family of short proteins. The family includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co-protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. | https://en.wikipedia.org/wiki/DinI-like_protein_family |
Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known. == References == | https://en.wikipedia.org/wiki/DinI-like_protein_family |
In molecular biology, the DmpG-like communication domain is a protein domain found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain. The communication domain is thought to play an important role in the heterodimerisation of the enzyme.This domain heterodimerises with acetaldehyde dehydrogenases to form a bifunctional aldolase-dehydrogenase. == References == | https://en.wikipedia.org/wiki/DmpG-like_communication_domain |
In molecular biology, the DpnII restriction endonuclease family is a family of restriction endonucleases which includes DpnII from Diplococcus pneumoniae. These enzymes recognise the double-stranded DNA unmethylated sequence GATC and cleave before G-1, where it encompasses the full length of the protein. == References == | https://en.wikipedia.org/wiki/DpnII_restriction_endonuclease_family |
In molecular biology, the DyP-type peroxidase family is a family of haem peroxidase enzymes. Haem peroxidases were originally divided into two superfamilies, namely, the animal peroxidases and the plant peroxidases (which are subdivided into class I, II and III), which include fungal (class II) and bacterial peroxidases. The DyP (for dye de-colourising peroxidase) family constitutes a novel class of haem peroxidase. Because these enzymes were derived from fungal sources, the DyP family was thought to be structurally related to the class II secretory fungal peroxidases. | https://en.wikipedia.org/wiki/DyP-type_peroxidase_family |
However, the DyP family exhibits only low sequence similarity to classical fungal peroxidases, such as LiP and MnP, and does not contain the conserved proximal and distal histidines and an essential arginine found in other plant peroxidase superfamily members. DyP proteins have several characteristics that distinguish them from all other peroxidases, including a particularly wide substrate specificity, a lack of homology to most other peroxidases, and the ability to function well under much lower pH conditions compared with the other plant peroxidases. In terms of substrate specificity, DyP degrades the typical peroxidase substrates, but also degrades hydroxyl-free anthraquinone (many dyes are derived from anthraquinone compounds). | https://en.wikipedia.org/wiki/DyP-type_peroxidase_family |
Crystal structures of DyP family members reveal two domains, each one adopting a ferredoxin-like fold. The proteins consist of an N-terminal domain and a C-terminal domain likely to be related by a duplication of an ancestral gene, as inferred from the conserved topology of the domains. The haem iron is penta-coordinated, with the protein contributing a conserved histidine ligand to the iron centre. | https://en.wikipedia.org/wiki/DyP-type_peroxidase_family |
A conserved Asp most likely acts as a proton donor/acceptor and takes the place of the catalytic histidine used by plant peroxidases. This Asp substitution helps explain why the DyP family is active at low pH. == References == | https://en.wikipedia.org/wiki/DyP-type_peroxidase_family |
In molecular biology, the Dymeclin protein family is a family of proteins which includes human Dymeclin. Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 amino acids long and present in plants and animals. In humans, mutations in the gene coding for this protein give rise to a disorder called Dyggve-Melchior-Clausen syndrome, which is an autosomal-recessive disorder characterised by the association of spondylo-epi-metaphyseal dysplasia, postnatal onset microcephaly and intellectual disability.This family of proteins also includes Hid1 (high-temperature-induced dauer-formation protein 1) from Caenorhabditis elegans which encodes a novel highly conserved putative transmembrane protein expressed in neurons. | https://en.wikipedia.org/wiki/Dymeclin_protein_family |
It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally this protein might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor. == References == | https://en.wikipedia.org/wiki/Dymeclin_protein_family |
In molecular biology, the EAL domain is a conserved protein domain. It is found in diverse bacterial signalling proteins. It is named EAL after its conserved residues. | https://en.wikipedia.org/wiki/EAL_domain |
The EAL domain may function as a diguanylate phosphodiesterase. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site. == References == | https://en.wikipedia.org/wiki/EAL_domain |
In molecular biology, the EF1 guanine nucleotide exchange domain is a protein domain found in the beta and delta chains of elongation factors from eukaryotes and archaea. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta).The EF1 guanine nucleotide exchange domain is found in the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. | https://en.wikipedia.org/wiki/EF1_guanine_nucleotide_exchange_domain |
The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). == References == | https://en.wikipedia.org/wiki/EF1_guanine_nucleotide_exchange_domain |
In molecular biology, the ELFV dehydrogenase family of enzymes include glutamate, leucine, phenylalanine and valine dehydrogenases. These enzymes are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases EC 1.4.1.2, EC 1.4.1.3 and EC 1.4.1.4 (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate. | https://en.wikipedia.org/wiki/ELFV_dehydrogenase |
GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha-keto acids.Leucine dehydrogenase EC 1.4.1.9 (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. | https://en.wikipedia.org/wiki/ELFV_dehydrogenase |
The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase EC 1.4.1.20 (PheDH) is an NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate.Valine dehydrogenase EC 1.4.1.8 (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate.These enzymes contain two domains, an N-terminal dimerisation domain, and a C-terminal domain. == References == | https://en.wikipedia.org/wiki/ELFV_dehydrogenase |
In molecular biology, the EMI domain, first named after its presence in proteins of the EMILIN family, is a small cysteine-rich protein domain of around 75 amino acids. The EMI domain is most often found at the N terminus of metazoan extracellular proteins that are forming or are compatible with multimer formation. It is found in association with other domains, such as C1q, laminin-type EGF-like, collagen-like, FN3, WAP, ZP or FAS1. It has been suggested that the EMI domain could be a protein-protein interaction module, as the EMI domain of EMILIN-1 was found to interact with the C1q domain of EMILIN-2.The EMI domain possesses six highly conserved cysteine residues, which likely form disulphide bonds. | https://en.wikipedia.org/wiki/EMI_domain |
Other key features of the EMI domain are the C-C-x-G- pattern, a hydrophobic position just preceding the first cysteine (Cys1) of the domain and a cluster of hydrophobic residues between Cys3 and Cys4. The EMI domain could be made of two sub-domains, the fold of the second one sharing similarities with the C-terminal sub-module characteristic of EGF-like domains.Proteins known to contain an EMI domain include: Vertebrate Emilins, extracellular matrix glycoproteins. Vertebrate Multimerins, extracellular matrix glycoproteins. | https://en.wikipedia.org/wiki/EMI_domain |
Vertebrate Emu proteins, which could interact with several different extracellular matrix components and serve to connect and integrate the function of multiple partner molecules. Vertebrate beta-IG-H3. Vertebrate osteoblast-specific factor 2 (OSF-2). | https://en.wikipedia.org/wiki/EMI_domain |
Mammalian NEU1/NG3 proteins. Drosophila midline fasciclin. Caenorhabditis elegans ced-1, a transmembrane receptor that mediates cell corpse engulfment. == References == | https://en.wikipedia.org/wiki/EMI_domain |
In molecular biology, the EcoEI R protein C-terminal domain is a protein domain found at the C-terminus of both the R subunit of type I restriction enzymes and the Res subunit of type III restriction enzymes. The type I enzymes include EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity. == References == | https://en.wikipedia.org/wiki/EcoEI_R_protein_C-terminal_domain |
In molecular biology, the F-actin capping protein is a protein complex which binds in a calcium-independent manner to the fast-growing ends of actin filaments (barbed end), thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta. | https://en.wikipedia.org/wiki/F-actin_capping_protein |
Neither of the subunits shows sequence similarity to other filament-capping proteins. The alpha subunit is a protein of about 268 to 286 amino acid residues and the beta subunit is approximately 280 amino acids, their sequences are well conserved in eukaryotic species.The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis, as well as muscle contraction. == References == | https://en.wikipedia.org/wiki/F-actin_capping_protein |
In molecular biology, the FAD dependent oxidoreductase family of proteins is a family of FAD dependent oxidoreductases. Members of this family include Glycerol-3-phosphate dehydrogenase EC 1.1.99.5, Sarcosine oxidase beta subunit EC 1.5.3.1, D-amino-acid dehydrogenase EC 1.4.99.1, D-aspartate oxidase EC 1.4.3.1. D-amino acid oxidase EC 1.4.3.3 (DAMOX or DAO) is an FAD flavoenzyme that catalyses the oxidation of neutral and basic D-amino acids into their corresponding keto acids. | https://en.wikipedia.org/wiki/FAD_dependent_oxidoreductase_family |
DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase EC 1.4.3.1 (DASOX) is an enzyme, structurally related to DAO, which catalyses the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown to be important for the enzyme's catalytic activity. | https://en.wikipedia.org/wiki/FAD_dependent_oxidoreductase_family |
In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus in the majority of proteins in which it is found. | https://en.wikipedia.org/wiki/FERM_domain |
In molecular biology, the FEZ-like protein family is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic. The Caenorhabditis elegans homologue, UNC-76, may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells) and these roles have also been postulated for other FEZ family proteins. Certain homologues have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells. | https://en.wikipedia.org/wiki/FEZ-like_protein |
The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta. The members of this family are predicted to form coiled-coil structures which may interact with members of the RhoA family of signalling proteins, but are not thought to contain other characteristic protein motifs. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues. == References == | https://en.wikipedia.org/wiki/FEZ-like_protein |
In molecular biology, the FHIPEP protein family (Flagellar/Hr/Invasion Proteins Export Pore family)consists of a number of proteins that constitute the type III secretion (or signal peptide-independent) pathway apparatus. This mechanism translocates proteins lacking an N-terminal signal peptide across the cell membrane in one step, as it does not require an intermediate periplasmic process to cleave the signal peptide. It is a common pathway amongst Gram-negative bacteria for secreting toxic and flagellar proteins. The pathway apparatus comprises three components: two within the inner membrane and one within the outer. | https://en.wikipedia.org/wiki/FHIPEP_protein_family |
An FHIPEP protein is located within the inner membrane, although it is unknown which component it constitutes. FHIPEP proteins have all about 700 amino acid residues. | https://en.wikipedia.org/wiki/FHIPEP_protein_family |
Within the sequence, the N terminus is highly conserved and hydrophobic, suggesting that this terminus is embedded within the membrane, with 6-8 transmembrane (TM) domains, while the C terminus is less conserved and appears to be devoid of TM regions. It is possible that members of the FHIPEP family serve as pores for the export of specific proteins. == References == | https://en.wikipedia.org/wiki/FHIPEP_protein_family |
In molecular biology, the FLYWCH zinc finger is a zinc finger domain. It is found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. | https://en.wikipedia.org/wiki/FLYWCH_zinc_finger |
This domain was first characterised in Drosophila modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione S-transferase (GST) domain. == References == | https://en.wikipedia.org/wiki/FLYWCH_zinc_finger |
In molecular biology, the Fic/DOC protein family is a family of proteins which catalyzes the post-translational modification of proteins using phosphate-containing compound as a substrate. Fic domain proteins typically use ATP as a co-factor, but in some cases GTP or UTP is used. Post-translational modification performed by Fic domains is usually NMPylation (AMPylation, GMPylation or UMPylation), however they also catalyze phosphorylation and phosphocholine transfer. This family contains a central conserved motif HPFXGNGR in most members and it carries the invariant catalytic histidine. Fic domain was found in bacteria, eukaryotes and archaea and can be found organized in almost hundred different multi-domain assemblies. | https://en.wikipedia.org/wiki/Fic/DOC_protein_family |
In molecular biology, the GA module, or protein G-related albumin-binding module, is a protein domain which occurs on the surface of numerous Gram-positive bacterial pathogens. Protein G of group C and G Streptococci interacts with the constant region of IgG and with human serum albumin. The GA module is composed of a left-handed three-helix bundle and is found in a range of bacterial cell surface proteins. GA modules may promote bacterial growth and virulence in mammalian hosts by scavenging albumin-bound nutrients and camouflaging the bacteria. | https://en.wikipedia.org/wiki/GA_module |
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