Protein Family Models

Date:

2024-08-14

This family includes Schizosaccharomyces specific SAP domain containing proteins such as gene product new25 [1] . SAP ( SAF-A/B, Acinus and PIAS) motif is a DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. For instance, the SAP domain of SUMO E3 ligase PIAS1 from human is shown to bind an A/T-rich DNA [2]. [1]. 21270388. Augmented annotation of the Schizosaccharomyces pombe genome. reveals additional genes required for growth and viability.. Bitton DA, Wood V, Scutt PJ, Grallert A, Yates T, Smith DL,. Hagan IM, Miller CJ;. Genetics. 2011;187:1207-1217.. [2]. 18831036. Solution structures and DNA binding properties of the N-terminal. SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and. Oryza sativa.. Suzuki R, Shindo H, Tase A, Kikuchi Y, Shimizu M, Yamazaki T;. Proteins. 2009;75:336-347. (from Pfam)

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2024-08-14

Staphylococcal Cassette Chromosome, or SCC elements, are a family of genomic islands found in S. aureus and closely related species. SCC elements that carry the mecA gene are called SCCmec and render S. aureus methicillin-resistant, creating the MRSA strains. Cch, the self-loading helicase encoded by SCCmec type IV, belongs to the pre-sensor II insert clade of AAA+ ATPases, as do the archaeal and eukaryotic MCM-family replicative helicases. The N-terminal domain carries Pfam:PF06048. The central domain (residues 157-438) contains an AAA+ ATPase fold. This domain is found at the C-terminal region, it is a winged helix-turn-helix (WH) domain typical of many dsDNA-binding proteins [1]. [1]. 27571176. Staphylococcal SCCmec elements encode an active MCM-like. helicase and thus may be replicative.. Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S,. Rice PA;. Nat Struct Mol Biol. 2016; [Epub ahead of print] (from Pfam)

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2024-08-14

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001749) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the epipyriculol biosynthetic gene cluster from Pyricularia oryzae 70-15 [1]. This family appears to be predominantly found in fungi. [1]. 27902426. Unravelling the biosynthesis of pyriculol in the rice blast. fungus Magnaporthe oryzae.. Jacob S, Grotsch T, Foster AJ, Schuffler A, Rieger PH, Sandjo. LP, Liermann JC, Opatz T, Thines E;. Microbiology (Reading). 2017;163:541-553. (from Pfam)

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2024-08-14

This is a domain of unknown function found in Phytoreovirus. Family members include the Rice dwarf virus Pns11 and Pns12. Rice dwarf virus (RDV) is an icosahedral, double-layered particle. The viral genome consists of 12 segmented dsRNAs that encode seven structural (P1, P2, P3, P5, P7, P8 and P9) and five non-structural (Pns4, Pns6, Pns10, Pns11 and Pns12) proteins. Pns11 is known to bind nucleic acids and Pns12 is a phosphorylated protein. The non-structural proteins Pns6, Pns11 and Pns12 of RDV are the major constituents of the matrix of viral inclusions in which the assembly of progeny virions and the synthesis of viral RNA are thought to occur [1]. [1]. 16432031. Pns12 protein of Rice dwarf virus is essential for formation of. viroplasms and nucleation of viral-assembly complexes.. Wei T, Shimizu T, Hagiwara K, Kikuchi A, Moriyasu Y, Suzuki N,. Chen H, Omura T;. J Gen Virol. 2006;87:429-438. (from Pfam)

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2024-08-14

MCAfunc domain (MCAfunc) is located in the N-terminal region of a mechanosensitive channel protein MID1-COMPLEMENTING ACTIVITY (MCA). MCAfunc represents the provisionally advocated ARPK domain (Amino-terminal domain of Rice putative Protein Kinases), overlapping with the EF hand-like region at the N-terminus [1]. In MCA proteins, MCAfunc has Ca2+ influx activity and is proposed to be a functional domain of MCAs [2]. MCAfunc is exclusively observed in streptophytes and exists not only in MCA but also in E3 ubiquitin ligase-like proteins, ARO3 like proteins and and protein kinases. In the most basal plant lineage, charophytes, MCAfunc is only found in E3 ubiquitin ligase-like proteins and protein of presently unknown function, while MCA proteins are exclusively found in land plants, from bryophytes to angiosperms [3]. [1]. 17360695. Arabidopsis plasma membrane protein crucial for Ca2+ influx and. touch sensing in roots.. Nakagawa Y, Katagiri T, Shinozaki K, Qi Z, Tatsumi H, Furuichi. T, Kishigami A, Sokabe M, Kojima I, Sato S, Kato T, Tabata S,. Iida K, Terashima A, Nakano M, Ikeda M, Yamanaka T, Iida H;. Proc Natl Acad Sci U S A. 2007;104:3639-3644.. [2]. 21949028. Determination of structural regions important for Ca(2+) uptake. activity in Arabidopsis MCA1 and MCA2 expressed in yeast.. Nakano M, Iida K, Nyunoya H, Iida H;. Plant Cell Physiol. 2011;52:1915-1930.. [3]. 33857196. Mix and match: Patchwork domain evolution of the land. plant-specific Ca2+-permeable mechanosensitive channel MCA.. Nishii K, Moller M, Iida H;. PLoS One. 2021;16:e0249735. (from Pfam)

Date:

2024-08-14

This entry represents a group of plant meiosis-specific proteins, such as AtASY3 from Arabidopsis and PAIR3 from rice. They are coiled-coil domain proteins required for normal meiosis [1]. PAIR3 is an axial element and part of the synaptonemal complex (SC) that forms between homologous chromosomes during meiosis [2]. Members of this family are homologues of SCYP2 from vertebrates and fungal Red1/Rec10 [3]. [1]. 22319460. Inter-homolog crossing-over and synapsis in Arabidopsis meiosis. are dependent on the chromosome axis protein AtASY3.. Ferdous M, Higgins JD, Osman K, Lambing C, Roitinger E, Mechtler. K, Armstrong SJ, Perry R, Pradillo M, Cunado N, Franklin FC;. PLoS Genet. 2012;8:e1002507.. [2]. 28369589. Bivalent Formation 1, a plant-conserved gene, encodes an. OmpH/coiled-coil motif-containing protein required for meiotic. recombination in rice.. Zhou L, Han J, Chen Y, Wang Y, Liu YG;. J Exp Bot. 2017;68:2163-2174.. [3]. 34006126. Repurposing of synaptonemal complex proteins for kinetochores in. Kinetoplastida.. Tromer EC, Wemyss TA, Ludzia P, Waller RF, Akiyoshi B;. Open Biol. 2021;11:210049. (from Pfam)

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2024-08-14

This is the N-terminal domain of ToxB found in Pyrenophora tritici-repentis. This domain is crucial for toxin activity. There are only two amino acid differences between ToxB and toxb, an inactive homolog of ToxB. These two differences are a Val at position 3 in ToxB compared to a Thr in toxb, and an Ala at position 12 in ToxB compared to a Val in toxb. AvrPiz-t, a secreted avirulence protein produced by the rice blast fungus, is a structural homolog to ToxB [1]. [1]. 25063993. Solution NMR structures of Pyrenophora tritici-repentis ToxB and. its inactive homolog reveal potential determinants of toxin. activity.. Nyarko A, Singarapu KK, Figueroa M, Manning VA, Pandelova I,. Wolpert TJ, Ciuffetti LM, Barbar E;. J Biol Chem. 2014;289:25946-25956. (from Pfam)

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2024-08-14

This family includes the PgaD protein from E. coli Swiss:P69432. The homopolymer poly-beta-1,6-N-acetyl-D-glucosamine (beta-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in eubacteria. The pgaABCD operon is required for its synthesis and export. It has been shown that PgaD is essential for this process [2]. [1]. 15090514. The pgaABCD locus of Escherichia coli promotes the synthesis of. a polysaccharide adhesin required for biofilm formation.. Wang X, Preston JF 3rd, Romeo T;. J Bacteriol. 2004;186:2724-2734.. [2]. 18359807. Roles of pgaABCD genes in synthesis, modification, and export of. the Escherichia coli biofilm adhesin. poly-beta-1,6-N-acetyl-D-glucosamine.. Itoh Y, Rice JD, Goller C, Pannuri A, Taylor J, Meisner J,. Beveridge TJ, Preston JF 3rd, Romeo T;. J Bacteriol. 2008;190:3670-3680. (from Pfam)

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2024-08-14

Complex I of the respiratory chain is a proton-pumping, NADH ubiquinone oxidoreductase that oxidises NADH in the electron transport pathway. Plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes [1]. [1]. 12837548. Mitochondrial complex I from Arabidopsis and rice: orthologs of. mammalian and fungal components coupled with plant-specific. subunits.. Heazlewood JL, Howell KA, Millar AH;. Biochim Biophys Acta. 2003;1604:159-169. (from Pfam)

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2024-08-14

CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. Mutations in human CTC1 have been recognised as contributing to cerebroretinal microangiopathy. [1]. 19854130. RPA-like mammalian Ctc1-Stn1-Ten1 complex binds to. single-stranded DNA and protects telomeres independently of the. Pot1 pathway.. Miyake Y, Nakamura M, Nabetani A, Shimamura S, Tamura M,. Yonehara S, Saito M, Ishikawa F;. Mol Cell. 2009;36:193-206.. [2]. 22267198. Mutations in CTC1, encoding conserved telomere maintenance. component 1, cause Coats plus.. Anderson BH, Kasher PR, Mayer J, Szynkiewicz M, Jenkinson EM,. Bhaskar SS, Urquhart JE, Daly SB, Dickerson JE, O'Sullivan J,. Leibundgut EO, Muter J, Abdel-Salem GM, Babul-Hirji R, Baxter P,. Berger A, Bonafe L, Brunstom-Hernandez JE, Buckard JA, Chitayat. D, Chong WK, Cordelli DM, Ferreira P, Fluss J, Forrest EH,. Franzoni E, Garone C, Hammans SR, Houge G, Hughes I, Jacquemont. S, Jeannet PY, Jefferson RJ, Kumar R, Kutschke G, Lundberg S,. Lourenco CM, Mehta R, Naidu S, Nischal KK, Nunes L, Ounap K,. Philippart M, Prabhakar P, Risen SR, Schiffmann R, Soh C,. Stephenson JB, Stewart H, Stone J, Tolmie JL, van der Knaap MS,. Vieira JP, Vilain CN, Wakeling EL, Wermenbol V, Whitney A,. Lovell SC, Meyer S, Livingston JH, Baerlocher GM, Black GC, Rice. GI, Crow YJ;. Nat Genet. 2012;44:338-342.. [3]. 22387016. Mutations in CTC1, encoding the CTS telomere maintenance complex. component 1, cause cerebroretinal microangiopathy with. calcifications and cysts.. Polvi A, Linnankivi T, Kivela T, Herva R, Keating JP, Makitie O,. P. TRUNCATED at 1650 bytes (from Pfam)

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2024-08-14

The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus [1]. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor) [2]. They are structurally similar to TPR repeats [2]. [1]. 8455721. SNAP family of NSF attachment proteins includes a brain-specific. isoform.. Whiteheart SW, Griff IC, Brunner M, Clary DO, Mayer T, Buhrow. SA, Rothman JE;. Nature. 1993;362:353-355.. [2]. 10445030. Crystal structure of the vesicular transport protein Sec17:. implications for SNAP function in SNARE complex disassembly.. Rice LM, Brunger AT;. Mol Cell. 1999;4:85-95. (from Pfam)

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2024-08-14

The rice tungro spherical waikavirus polyprotein is cleaved into 7 proteins, including three capsid proteins, by the tungro spherical virus-type peptidase Pfam:PF12381. This family represents the capsid protein 1 [1,2]. [1]. 8460478. Nucleotide sequence and genomic organization of rice tungro. spherical virus.. Shen P, Kaniewska M, Smith C, Beachy RN;. Virology. 1993;193:621-630.. [2]. 9683576. Rice tungro spherical virus polyprotein processing:. identification of a virus-encoded protease and mutational. analysis of putative cleavage sites.. Thole V, Hull R;. Virology. 1998;247:106-114. (from Pfam)

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2024-08-14

This is a family of eukaryotic nucleoporins of several different sizes. All of them are long and form the scaffold of the nuclear pore complex. Nup192 in particular modulates the permeability of the central channel of the NPC central or nuclear pore complex [1]. [1]. 23499021. Structure, dynamics, evolution, and function of a major scaffold. component in the nuclear pore complex.. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL,. Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z,. Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK,. Sali A, Rout MP, Almo SC;. Structure. 2013;21:560-571. (from Pfam)

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2024-08-14

GPAT_N is the N-terminal domain of glycerol-3-phosphate acyltransferases, and it forms a four-helix bundle [1]. Glycerol-3-phosphate (1)-acyltransferase(G3PAT) catalyses the incorporation of an acyl group from either acyl-acyl carrier proteins or acyl-CoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol-3-phosphate. G3PATs can either be selective, preferentially using the unsaturated fatty acid, oleate (C18:1), as the acyl donor, or non-selective, using either oleate or the saturated fatty acid, palmitate (C16:0), at comparable rates. The differential substrate-specificity for saturated versus unsaturated fatty acids seen within this enzyme family has been implicated in the sensitivity of plants to chilling temperatures [2]. The exact function of this domain is not known. it lies upstream of family Acyltransferase, Pfam:PF01553. [1]. 14684887. Substrate recognition and selectivity of plant. glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita. moscata and Spinacea oleracea.. Tamada T, Feese MD, Ferri SR, Kato Y, Yajima R, Toguri T, Kuroki. R;. Acta Crystallogr D Biol Crystallogr. 2004;60:13-21.. [2]. 11377195. Analysis of the structure, substrate specificity, and mechanism. of squash glycerol-3-phosphate (1)-acyltransferase.. Turnbull AP, Rafferty JB, Sedelnikova SE, Slabas AR, Schierer. TP, Kroon JT, Simon JW, Fawcett T, Nishida I, Murata N, Rice DW;. Structure. 2001;9:347-353. (from Pfam)

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2024-08-14

This is the C-terminal domain of Beta-carotene isomerase D27 that may contain an iron binding domain [1]. Beta-carotene isomerase D27 (also known as Protein DWARF-27) from plants is involved in strigolactones biosynthesis. It is a beta-carotene isomerase that converts all-trans-beta-carotene into 9-cis-beta-carotene, which is cleaved by CCD7 into a 9-cis-configured aldehyde [2,3]. This is an iron-containing protein that localises in chloroplasts and is expressed mainly in vascular cells of shoots and roots [1]. [1]. 19470589. DWARF27, an iron-containing protein required for the. biosynthesis of strigolactones, regulates rice tiller bud. outgrowth.. Lin H, Wang R, Qian Q, Yan M, Meng X, Fu Z, Yan C, Jiang B, Su. Z, Li J, Wang Y;. Plant Cell. 2009;21:1512-1525.. [2]. 22422982. The path from beta-carotene to carlactone, a strigolactone-like. plant hormone.. Alder A, Jamil M, Marzorati M, Bruno M, Vermathen M, Bigler P,. Ghisla S, Bouwmeester H, Beyer P, Al-Babili S;. Science. 2012;335:1348-1351.. [3]. 22623516. The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1. in the control of plant development by strigolactones.. Waters MT, Brewer PB, Bussell JD, Smith SM, Beveridge CA;. Plant Physiol. 2012;159:1073-1085. (from Pfam)

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2024-08-14

This eukaryotic family of proteins includes a group of fungal proteins, including Egh16 from Erysiphe graminis f.sp. hordei and its homologues [1, 2]. They are found in pathogenic fungi and may play important roles during the early infection stage in fungal pathogens [3]. [1]. 8621073. Isolation and characterization of two novel genes expressed in. germinating conidia of the obligate biotroph Erysiphe graminis. f.sp. hordei.. Justesen A, Somerville S, Christiansen S, Giese H;. Gene. 1996;170:131-135.. [2]. 12853153. A Blumeria graminis gene family encoding proteins with a. C-terminal variable region with homologues in pathogenic fungi.. Grell MN, Mouritzen P, Giese H;. Gene. 2003;311:181-192.. [3]. 12215509. Two novel fungal virulence genes specifically expressed in. appressoria of the rice blast fungus.. Xue C, Park G, Choi W, Zheng L, Dean RA, Xu JR;. Plant Cell. 2002;14:2107-2119. (from Pfam)

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2024-08-14

This is the protease for self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The protease activity of the polyprotein is at the C-terminal end, adjacent to the putative RNA polymerase. [1]. 9683576. Rice tungro spherical virus polyprotein processing:. identification of a virus-encoded protease and mutational. analysis of putative cleavage sites.. Thole V, Hull R;. Virology. 1998;247:106-114.. [2]. 15503215. 3C-like protease encoded by Rice tungro spherical virus is. autocatalytically processed.. Sekiguchi H, Isogai M, Masuta C, Uyeda I;. Arch Virol. 2005;150:595-601. (from Pfam)

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2024-08-14

This entry represents the SiaC family regulatory phosphoprotein which undergoes a regulatory phosphorylation at Thr-68 of founder protein PA0170 from Pseudomonas aeruginosa, but in more distant homologs, T can be S. Also, it is part of motif NTSS, so may contain more than one phosphorylation site. Phosphorylation causes regulatory change to protein-protein interaction, in a pathway that seems broadly distributed, involves a diguanylate cyclase, and in the case of Pseudomonas aeruginosa affects aggregation and biofilm formation responses. [1]. 33156827. The SiaABC threonine phosphorylation pathway controls biofilm. formation in response to carbon availability in Pseudomonas. aeruginosa.. Poh WH, Lin J, Colley B, Muller N, Goh BC, Schleheck D, El. Sahili A, Marquardt A, Liang Y, Kjelleberg S, Lescar J, Rice SA,. Klebensberger J;. PLoS One. 2020;15:e0241019. (from Pfam)

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2024-08-14

This family of proteins is found in eukaryotes. Proteins in this family are typically between 174 and 411 amino acids in length. The family is found in association with Pfam:PF00170. There is a conserved KVK sequence motif. There is a single completely conserved residue K that may be functionally important. Various bZIP proteins have been found and shown to play a role in seed-specific gene expression. bZIP binds to the alpha-globulin gene promoter, but not to promoters of other major storage genes such as glutelin, prolamin and albumin. [1]. 9049271. Characterization of a novel rice bZIP protein which binds to the. alpha-globulin promoter.. Nakase M, Aoki N, Matsuda T, Adachi T;. Plant Mol Biol. 1997;33:513-522. (from Pfam)

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2024-08-14