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

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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

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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

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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

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2024-02-09

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2024-08-14

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2024-08-14

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2024-08-14

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2024-08-14

This is the endonuclease domain of Terminase large subunit TerL [1,2], a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (Pfam:PF03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full [1,2]. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly [2]. This nuclease domain has a RNAse H-like fold and it has been proposed to utilise a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases [1]. [1]. 28100693. Viral genome packaging terminase cleaves DNA using the canonical. RuvC-like two-metal catalysis mechanism.. Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E,. Minakhin L, Severinov K, Greive SJ, Antson AA;. Nucleic Acids Res. 2017;45:3580-3590.. [2]. 26150523. Structure and mechanism of the ATPase that powers viral genome. packaging.. Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA;. Proc Natl Acad Sci U S A. 2015;112:E3792-E3799. (from Pfam)

Date:

2024-08-14

TMEM127 modulates mTOR function in the endolysosome. Its interaction with early endosomal GTPase Rab5 to inhibit mTOR signalling seems to be related with its tumour-suppressing properties [1,2]. [1]. 24334765. The tumor susceptibility gene TMEM127 is mutated in renal cell. carcinomas and modulates endolysosomal function.. Qin Y, Deng Y, Ricketts CJ, Srikantan S, Wang E, Maher ER, Dahia. PL;. Hum Mol Genet. 2014;23:2428-2439.. [2]. 20154675. Germline mutations in TMEM127 confer susceptibility to. pheochromocytoma.. Qin Y, Yao L, King EE, Buddavarapu K, Lenci RE, Chocron ES,. Lechleiter JD, Sass M, Aronin N, Schiavi F, Boaretto F, Opocher. G, Toledo RA, Toledo SP, Stiles C, Aguiar RC, Dahia PL;. Nat Genet. 2010;42:229-233. (from Pfam)

Date:

2024-08-14

Astrotactin-1 and 2 (ASTN1/2) are integral membrane proteins with a large C-terminal domain, extracellular for ASTN1 and endosome luminal for ASTN-2 [1,2]. They play critical roles in neurodevelopment, and ASTN-2 is also involved in the planar cell polarity pathway in hair cells. This is a domain found in the middle of the C-terminal of ASTN-1 and 2, which comprises a fibronectin type III (Fn(III)) domain [1]. This domain located between the MACPF and annexin domains. The structure of Fn(III) from ASTN2 revealed an unexpected feature which has two additional beta strands folded across the core. The junction between EGF-4 and Fn(III) domains in ASTN2 (but not in ASTN1) is thought to be an inositol triphosphate binding site [1]. Paper describing PDB structure 5j67. [1]. 27249642. Structure of astrotactin-2: a conserved vertebrate-specific and. perforin-like membrane protein involved in neuronal development.. Ni T, Harlos K, Gilbert R;. Open Biol. 2016; [Epub ahead of print]. [2]. 20573900. Astn2, a novel member of the astrotactin gene family, regulates. the trafficking of ASTN1 during glial-guided neuronal migration.. Wilson PM, Fryer RH, Fang Y, Hatten ME;. J Neurosci. 2010;30:8529-8540. (from Pfam)

Date:

2024-08-14

This is the BAR (Bin/amphiphysin/Rvs) domain of Sortin nexin 8 (Snx8), which can sense, stabilise and induce membrane curvature [1]. These proteins are involved in intracellular protein transport from early endosomes to the trans-Golgi network [1]. Its yeast counterpart, Mvp1 is required for sorting proteins to the vacuole [2]. [1]. 19782049. Sorting nexin 8 regulates endosome-to-Golgi transport.. Dyve AB, Bergan J, Utskarpen A, Sandvig K;. Biochem Biophys Res Commun. 2009;390:109-114.. [2]. 24567361. Fission of SNX-BAR-coated endosomal retrograde transport. carriers is promoted by the dynamin-related protein Vps1.. Chi RJ, Liu J, West M, Wang J, Odorizzi G, Burd CG;. J Cell Biol. 2014;204:793-806. (from Pfam)

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2024-08-14

This is the C-terminal domain of Furry (Fry) protein. Fry plays a crucial role in the structural integrity of mitotic centrosomes and in the maintenance of spindle bipolarity. This domain binds to polo-like kinase 1 (Plk1) through the polo-box domain (PBD) of Plk1 in a manner dependent on the cyclin-dependent kinase 1-mediated Fry phosphorylation, promoting Plk1 activity during early mitosis. Fry also binds to Aurora A and may function as a scaffold promoting the interaction between AURKA and PLK1, thereby enhancing AURKA-mediated PLK1 phosphorylation [1]. [1]. 22753416. Furry protein promotes aurora A-mediated Polo-like kinase 1. activation.. Ikeda M, Chiba S, Ohashi K, Mizuno K;. J Biol Chem. 2012;287:27670-27681. (from Pfam)

Date:

2024-08-14

This entry represents the C-terminal domain (CTD) (residues 1,291-1,603) of the DEPDC5 protein [1]. It contains two structurally similar lobes and has a pseudo-2-fold rotational symmetry. Each half consists of a five-stranded beta-sheet, with an alpha-helix covering one side. The CTD is located in the core of DEPDC5 and contacts all the other domains of DEPDC5 except the NTD, making it the central organizer of this multi-domain protein [1]. Paper describing PDB structure 6ces. [1]. 29590090. Architecture of the human GATOR1 and GATOR1-Rag GTPases. complexes.. Shen K, Huang RK, Brignole EJ, Condon KJ, Valenstein ML,. Chantranupong L, Bomaliyamu A, Choe A, Hong C, Yu Z, Sabatini. DM;. Nature. 2018;556:64-69. (from Pfam)

Date:

2024-08-14

This is the N-terminal matrix-like domain (MA) of Activity-Regulated Cytoskeleton-Associated protein (Arc). This domain might be involved in stabilising the relative domain orientations of the capside-like domain (CA) upon capsid assembly. Arc is a regulator of synaptic scaling and dendrite remodelling [1]. [1]. 31080121. The Capsid Domain of Arc Changes Its Oligomerization Propensity. through Direct Interaction with the NMDA Receptor.. Nielsen LD, Pedersen CP, Erlendsson S, Teilum K;. Structure. 2019;27:1071-1081. (from Pfam)

Date:

2024-08-14

This is the C-terminal domain mainly found in E3 ubiquitin ligases. Proteolysis 6 (PRT6) encodes a ubiquitin E3 ligase belonging to the N-end rule pathway of targeted protein degradation, which is a specialised subset of the ubiquitin proteasome system [1]. In Arabidopsis, at least two N-recognins (E3 ubiquitin ligases) with different substrate specificities exist, namely PROTEOLYSIS1 (PRT1) and PRT6 [2]. [1]. 30117535. Distinct branches of the N-end rule pathway modulate the plant. immune response.. Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y,. Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A,. Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K,. Holdsworth MJ;. New Phytol. 2019;221:988-1000.. [2]. 27173012. The N-end rule pathway regulates pathogen responses in plants.. de Marchi R, Sorel M, Mooney B, Fudal I, Goslin K, Kwasniewska. K, Ryan PT, Pfalz M, Kroymann J, Pollmann S, Feechan A, Wellmer. F, Rivas S, Graciet E;. Sci Rep. 2016;6:26020. (from Pfam)

Date:

2024-08-14

This entry represents part of the Tra1 protein composed of alpha solenoid repeats that form a ring region [1]. Paper describing PDB structure 5oej. [1]. 29146944. Structure of the transcription activator target Tra1 within the. chromatin modifying complex SAGA.. Sharov G, Voltz K, Durand A, Kolesnikova O, Papai G, Myasnikov. AG, Dejaegere A, Ben Shem A, Schultz P;. Nat Commun. 2017;8:1556.. Paper describing PDB structure 5ojs. [2]. 28767037. Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1. at 3.7 angstrom resolution.. Diaz-Santin LM, Lukoyanova N, Aciyan E, Cheung AC;. Elife. 2017; [Epub ahead of print]. Paper describing PDB structure 5y81. [3]. 29559617. Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex.. Wang X, Ahmad S, Zhang Z, Cote J, Cai G;. Nat Commun. 2018;9:1147.. Paper describing PDB structure 6ig9. [4]. 31069110. Architecture of Saccharomyces cerevisiae SAGA complex.. Liu G, Zheng X, Guan H, Cao Y, Qu H, Kang J, Ren X, Lei J, Dong. MQ, Li X, Li H;. Cell Discov. 2019;5:25. (from Pfam)

Date:

2024-08-14

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000406) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the phosphinothricintripeptide biosynthetic gene cluster from Streptomyces viridochromogenes [1]. This family appears to be predominantly found in Actinobacteria. [1]. 15574905. Biosynthetic gene cluster of the herbicide phosphinothricin. tripeptide from Streptomyces viridochromogenes Tu494.. Schwartz D, Berger S, Heinzelmann E, Muschko K, Welzel K,. Wohlleben W;. Appl Environ Microbiol. 2004;70:7093-7102. (from Pfam)

Date:

2024-08-14