Protein Family Models

This roughly 80-amino acid domain belongs to the clan of ATP-binding domains with the Walker A motif (P-loop). It starts and ends with well-conserved alpha-helical regions, interrupted by a region of beta-strands that are prone to insertions of additional sequence. In a large fraction of members, the critical lysine (K) of the P-loop motif GxxGxGK[ST] is replaced by phenylalanine (F), making the function of the motif in those family members unclear. This domain tends to occur as a N-terminal domain of proteins that average over 1000 amino acids in length, such as the human protein sacsin.

Date:

2024-07-26

YjbH domain-containing protein, similar to Escherichia coli K-12 YjbH which is a putative lipoprotein and/or porin involved in exopolysaccharide production

Date:

2024-02-09

protease modulator HflK (high frequency of lysogenization K) is an inner membrane protein and is part of the HflCK complex that modulates FtsH protease

Date:

2024-02-09

protease modulator HflK (high frequency of lysogenization K) is an inner membrane protein and is part of the HflCK complex that modulates FtsH protease

Date:

2024-02-09

photosystem I (PSI) protein PsaX is a component of the cyanobacterial PSI reaction center that is composed of one copy each of PsaA, B, C, D, E, F, I, J, K, L, M and X

Date:

2024-02-09

protease modulator HflK family protein with a cation efflux domain; HflK (high frequency of lysogenization K) is part of the HflCK complex that modulates FtsH protease

Date:

2024-02-09

Members of this family average about 145 amino acids in length, with a signal peptide, a variable length low-complexity region rich in N, D, Q, E, K, and R, and the roughly 80 amino acid C-terminal region described by this HMM. A few members of the family have candidate lipoprotein signal peptides. The family is named for member protein MHO_1590 from Mycoplasma hominis.

Date:

2024-05-14

The multidrug resistance outer membrane protein MdtQ occurs in Klebsiella pneumoniae, Salmonella enterica, and Escherichia coli, but notably is a pseudogene in E. coli K-12.

Gene:

mdtQ

Date:

2024-03-21

GPI-anchor transamidase is a component of the GPI transamidase complex, necessary for transfer of GPI to proteins

Date:

2023-12-27

ligand-gated ion channel (LIC or LGIC) is a member of a family of neurotransmitter receptors vital for communication throughout the nervous system

Date:

2023-12-19

photosystem II protein K is one of the components of the core complex of photosystem II (PSII), which is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation

Date:

2023-12-13

kinesin/myosin motor domain-containing protein may have ATPase activity and function as a molecular motor, such as kinesins and myosins

Date:

2023-12-06

This presumed domain is found in bacteria, and is approximately 60 amino acids in length. Structure prediction suggests that it has a ribbon-helix-helix motif, a DNA-binding motif commonly found in antitoxin families [1,2]. Members containing this domain may be related to CopG antitoxin family. [1]. 9857196. The structure of plasmid-encoded transcriptional repressor CopG. unliganded and bound to its operator.. Gomis-R th FX, Sol M, Acebo P, Parraga A, Guasch A, Eritja R,. Gonzalez A, Espinosa M, del Solar G, Coll M. EMBO J 1998;17:7404-7415.. [2]. 15864262. Prokaryotic toxin-antitoxin stress response loci.. Gerdes K, Christensen SK, Lobner-Olesen A;. Nat Rev Microbiol. 2005;3:371-382. (from Pfam)

Date:

2024-07-16

This entry represents the C-terminal alpha-helical domain of Integrator complex subunit 14 (IntS14) [1], a component of the integrator complex which is involved in the transcription of small nuclear RNAs (snRNA) and their 3'-box dependent processing. This complex is also involved in the 3'-end processing of the U7 snRNA, and the spliceosomal snRNAs U1 and U5 [2]. IntS14 interacts with IntS13; both of them consist of an N-terminal VWA domain followed by a central beta-barrel domain and a C-terminal alpha-helical domain, which are connected through a linker devoid of secondary structure elements. This domain contribute to binding by packing against the beta-barrel of IntS13 [1]. [1]. 32647223. INTS10-INTS13-INTS14 form a functional module of Integrator that. binds nucleic acids and the cleavage module.. Sabath K, Staubli ML, Marti S, Leitner A, Moes M, Jonas S;. Nat Commun. 2020;11:3422.. [2]. 23097424. An RNAi screen identifies additional members of the Drosophila. Integrator complex and a requirement for cyclin C/Cdk8 in snRNA. 3'-end formation.. Chen J, Ezzeddine N, Waltenspiel B, Albrecht TR, Warren WD,. Marzluff WF, Wagner EJ;. RNA. 2012;18:2148-2156. (from Pfam)

Date:

2024-07-16

This family includes secretoglobin family 3A member 1 (SCGB3A1) and member 2 (SCGB3A2), also known as uteroglobin-related proteins [1]. They are a small secreted proteins expressed in airway epithelial cells. SCGB3A2, also known as UGRP1, has an important anti-inflammatory activity and is involved in asthma [2,3,4]. SCGB3A2 mediates its anti-inflammatory action through inhibition of ERK and JNK activation [5]. It is also involved in lung development [6] and has anti-fibrotic activity in lung [7]. [1]. 12406855. Secretoglobins SCGB3A1 and SCGB3A2 define secretory cell subsets. in mouse and human airways.. Reynolds SD, Reynolds PR, Pryhuber GS, Finder JD, Stripp BR;. Am J Respir Crit Care Med. 2002;166:1498-1509.. [2]. 18089940. Plasma UGRP1 levels associate with promoter G-112A polymorphism. and the severity of asthma.. Inoue K, Wang X, Saito J, Tanino Y, Ishida T, Iwaki D, Fujita T,. Kimura S, Munakata M;. Allergol Int. 2008;57:57-64.. [3]. 11813133. A polymorphism in the human UGRP1 gene promoter that regulates. transcription is associated with an increased risk of asthma.. Niimi T, Munakata M, Keck-Waggoner CL, Popescu NC, Levitt RC,. Hisada M, Kimura S;. Am J Hum Genet. 2002;70:718-725.. [4]. 16456148. Uteroglobin-related protein 1 expression suppresses allergic. airway inflammation in mice.. Chiba Y, Kurotani R, Kusakabe T, Miura T, Link BW, Misawa M,. Kimura S;. Am J Respir Crit Care Med. 2006;173:958-964.. [5]. 25117566. Secretoglobin 3A2 attenuates lipopolysaccharide-induced. inflammation through inhibition of ERK and JNK pathways in. bronchial epithelial cells.. Wang X, Tanino Y, Sato S, Nikaido T, Misa K, Fukuha. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-07-16

This is the N-terminal regulatory domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116) [1,2]. It has an alpha-helical fold, with two long, parallel alpha-helices that form a large hairpin structure followed by two short, parallel alpha-helices forming a small hairpin segment. This domain is linked to the C-terminal kinase domain by a short (27 residues) alpha-helix [2]. [1]. 9409817. Size and sequence polymorphism in the isocitrate dehydrogenase. kinase/phosphatase gene (aceK) and flanking regions in. Salmonella enterica and Escherichia coli.. Nelson K, Wang FS, Boyd EF, Selander RK;. Genetics 1997;147:1509-1520.. [2]. 20505668. Structure of the bifunctional isocitrate dehydrogenase. kinase/phosphatase.. Zheng J, Jia Z;. Nature. 2010;465:961-965. (from Pfam)

Date:

2024-07-17

DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organised into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe B which adopts an unusual architecture of two antiparallel beta sheets disposed in a loosely packed orthogonal arrangement. This lobe changes its position relative to lobe C and the bound GTPase, which suggests that lobe B distinguishes between the switch 1 conformations of Rac1 and Cdc42 [2]. [1]. 32651375. Structure of the DOCK2-ELMO1 complex provides insights into. regulation of the auto-inhibited state.. Chang L, Yang J, Jo CH, Boland A, Zhang Z, McLaughlin SH,. Abu-Thuraia A, Killoran RC, Smith MJ, Cote JF, Barford D;. Nat Commun. 2020;11:3464.. [2]. 30853411. Structural Basis for the Dual Substrate Specificity of DOCK7. Guanine Nucleotide Exchange Factor.. Kukimoto-Niino M, Tsuda K, Ihara K, Mishima-Tsumagari C, Honda. K, Ohsawa N, Shirouzu M;. Structure. 2019;27:741-748. (from Pfam)

Date:

2024-07-17

DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organised into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe C which form an antiparallel four alpha-helical bundle [1,2] and contains a loop known as the nucleotide sensor characterised by a conserved valine residue essential for catalytic activity [2]. [1]. 32651375. Structure of the DOCK2-ELMO1 complex provides insights into. regulation of the auto-inhibited state.. Chang L, Yang J, Jo CH, Boland A, Zhang Z, McLaughlin SH,. Abu-Thuraia A, Killoran RC, Smith MJ, Cote JF, Barford D;. Nat Commun. 2020;11:3464.. [2]. 30853411. Structural Basis for the Dual Substrate Specificity of DOCK7. Guanine Nucleotide Exchange Factor.. Kukimoto-Niino M, Tsuda K, Ihara K, Mishima-Tsumagari C, Honda. K, Ohsawa N, Shirouzu M;. Structure. 2019;27:741-748. (from Pfam)

Date:

2024-07-16

This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer. RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from. Escherichia coli K-12 has two enzymatic activities.. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. (from Pfam)

Date:

2024-07-16

N-terminal Sel1-like repeats found in the wolframin protein. This region has been linked to calmodulin-binding, suggesting these repeats may mediate a protein interaction. [1]. 32117448. Functional Innovation in the Evolution of the Calcium-Dependent. System of the Eukaryotic Endoplasmic Reticulum.. Schaffer DE, Iyer LM, Burroughs AM, Aravind L;. Front Genet. 2020;11:34.. [2]. 19292454. Identification and characterization of wolframin, the product of. the wolfram syndrome gene (WFS1), as a novel calmodulin-binding. protein.. Yurimoto S, Hatano N, Tsuchiya M, Kato K, Fujimoto T, Masaki T,. Kobayashi R, Tokumitsu H;. Biochemistry. 2009;48:3946-3955. (from Pfam)

Date:

2024-07-17