Protein Family Models

This domain is found at the C-terminus of proteins belonging to the JAKMIP family (Janus kinase and microtubule-interacting proteins) and is predicted to be a coiled coil. It interacts with the Janus family kinases Tyk2 and Jak1 [1-3]. [1]. 15277531. Jamip1 (marlin-1) defines a family of proteins interacting with. janus kinases and microtubules.. Steindler C, Li Z, Algarte M, Alcover A, Libri V, Ragimbeau J,. Pellegrini S;. J Biol Chem. 2004;279:43168-43177.. [2]. 17532644. Marlin-1 and conventional kinesin link GABAB receptors to the. cytoskeleton and regulate receptor transport.. Vidal RL, Ramirez OA, Sandoval L, Koenig-Robert R, Hartel S,. Couve A;. Mol Cell Neurosci. 2007;35:501-512.. [3]. 14718537. Marlin-1, a novel RNA-binding protein associates with GABA. receptors.. Couve A, Restituito S, Brandon JM, Charles KJ, Bawagan H,. Freeman KB, Pangalos MN, Calver AR, Moss SJ;. J Biol Chem. 2004;279:13934-13943. (from Pfam)

Date:

2024-08-14

This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilisation of gamma-aminobutyric acid [1]. [1]. 11910018. Structural genomics: a pipeline for providing structures for the. biologist.. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A,. Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He. G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang. LK;. Protein Sci. 2002;11:723-738. (from Pfam)

Date:

2024-08-14

The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (Pfam:PF02501) and T2SK (Pfam:PF03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteristics [1]. [1]. 18438417. Structure of the GspK-GspI-GspJ complex from the enterotoxigenic. Escherichia coli type 2 secretion system.. Korotkov KV, Hol WG;. Nat Struct Mol Biol. 2008;15:462-468.. [2]. 15533433. The structure of the cytoplasmic domain of EpsL, an inner. membrane component of the type II secretion system of Vibrio. cholerae: an unusual member of the actin-like ATPase. superfamily.. Abendroth J, Bagdasarian M, Sandkvist M, Hol WG;. J Mol Biol 2004;344:619-633.. [2]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [3]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Date:

2024-08-14

This is a highly conserved family of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N-terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein I3 (Bri3) [1]. Their function is unknown but they appear to play a role in TNF-induced cell death [2]. [1]. 11290423. Sequence, genomic structure and tissue expression of Human BRI3,. a member of the BRI gene family.. Vidal R, Calero M, Revesz T, Plant G, Ghiso J, Frangione B;. Gene. 2001;266:95-102.. [2]. 14592447. bri3, a novel gene, participates in tumor necrosis. factor-alpha-induced cell death.. Wu H, Liu G, Li C, Zhao S;. Biochem Biophys Res Commun. 2003;311:518-524. (from Pfam)

Date:

2024-08-14

Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX. They consist of two tandem SAM-like domains, this entry represents the second one. [1]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [2]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [3]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Date:

2024-08-14

This family of membrane proteins consists of Type II secretion system protein M sequences from several Gram-negative (diderm) bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the T2SM (EpsM) protein interacts with the T2SL (EpsL) protein, and also forms homodimers [1]. [1]. 10322014. Direct interaction of the EpsL and EpsM proteins of the general. secretion apparatus in Vibrio cholerae.. Sandkvist M, Hough LP, Bagdasarian MM, Bagdasarian M;. J Bacteriol 1999;181:3129-3135.. [2]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [3]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Gene:

gspM

Date:

2024-08-14

This domain is found at the N-terminus of the Type II secretion secretion system protein E (GspE) and type IV pilus extensin ATPase PilB and near the C-terminus of the glycosyltransferase NfrB. A variant of this domain, called MshEN, binds cyclic di-GMP [4,6,7], which modulates the activity of the respective protein. The structure of this domain is now known [1,2,4]. [1]. 15843017. The X-ray structure of the type II secretion system complex. formed by the N-terminal domain of EpsE and the cytoplasmic. domain of EpsL of Vibrio cholerae.. Abendroth J, Murphy P, Sandkvist M, Bagdasarian M, Hol WG;. J Mol Biol. 2005;348:845-855.. Paper describing PDB structure 2d27. [2]. 16162504. Structure and function of the XpsE N-terminal domain, an. essential component of the Xanthomonas campestris type II. secretion system.. Chen Y, Shiue SJ, Huang CW, Chang JL, Chien YL, Hu NT, Chan NL;. J Biol Chem. 2005;280:42356-42363.. [3]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. Paper describing PDB structure 5htl. [4]. 27578558. Nucleotide binding by the widespread high-affinity cyclic di-GMP. receptor MshEN domain.. Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH,. Galperin MY, Chou SH;. Nat Commun. 2016;7:12481.. Paper describing PDB structure 6ejf. [5]. 30232337. Structural cycle of the Thermus thermophilus PilF ATPase: the. powering of type IVa pilus assembly.. Collins R, Karuppiah V, Siebert CA, Dajani R, Thistlethwaite A,. Derrick JP;. Sci Rep. 2018. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences [1]. [1]. 8407845. Isolation and analysis of eight exe genes and their involvement. in extracellular protein secretion and outer membrane assembly. in Aeromonas hydrophila.. Howard SP, Critch J, Bedi A;. J Bacteriol 1993;175:6695-6703.. [2]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [3]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Date:

2024-08-14

The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions [2,3]. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation [4]. [1]. 1861988. Conserved KRAB protein domain identified upstream from the zinc. finger region of Kox 8.. Thiesen HJ, Bellefroid E, Revelant O, Martial JA;. Nucleic Acids Res 1991;19:3996-3996.. [2]. 8986806. A novel member of the RING finger family, KRIP-1, associates. with the KRAB-A transcriptional repressor domain of zinc finger. proteins.. Kim SS, Chen YM, O'Leary E, Witzgall R, Vidal M, Bonventre JV;. Proc Natl Acad Sci U S A 1996;93:15299-15304.. [3]. 8769649. KAP-1, a novel corepressor for the highly conserved KRAB. repression domain.. Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP,. Neilson EG, Rauscher FJ;. Genes Dev 1996;10:2067-2078.. [4]. 14519192. KRAB-containing zinc-finger repressor proteins.. Urrutia R;. Genome Biol 2003;4:231. (from Pfam)

Date:

2024-08-14

Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown. [1]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [2]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [3]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Gene:

gspN

Date:

2024-08-14

The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella [1]. This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats). [1]. 11266368. An inner membrane platform in the type II secretion machinery of. Gram-negative bacteria.. Py B, Loiseau L, Barras F;. EMBO Rep 2001;2:244-248.. [2]. 15223057. The general secretory pathway: a general misnomer?.. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309.. [3]. 14600218. Type II protein secretion and its relationship to bacterial type. IV pili and archaeal flagella.. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP,. Saier MH Jr;. Microbiology. 2003;149:3051-3072.. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a. semantic awareness issue.. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam)

Date:

2024-08-14