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CLSY1_ARATH
ID   CLSY1_ARATH             Reviewed;        1256 AA.
AC   Q9M297;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   03-AUG-2022, entry version 123.
DE   RecName: Full=SNF2 domain-containing protein CLASSY 1;
DE   AltName: Full=Protein CHROMATIN REMODELING 38;
GN   Name=CLSY1; Synonyms=CHR38; OrderedLocusNames=At3g42670;
GN   ORFNames=T12K4.120;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130713; DOI=10.1038/35048706;
RA   Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA   Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA   Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA   Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA   Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA   Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA   Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA   Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA   Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA   Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA   Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA   de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA   Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA   Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA   Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA   Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA   Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA   Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA   Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA   Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA   Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA   Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL   Nature 408:820-822(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   FUNCTION, 3D-STRUCTURE MODELING, SUBCELLULAR LOCATION, MUTAGENESIS OF
RP   GLY-592, GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=17526749; DOI=10.1105/tpc.107.051540;
RA   Smith L.M., Pontes O., Searle I., Yelina N., Yousafzai F.K., Herr A.J.,
RA   Pikaard C.S., Baulcombe D.C.;
RT   "An SNF2 protein associated with nuclear RNA silencing and the spread of a
RT   silencing signal between cells in Arabidopsis.";
RL   Plant Cell 19:1507-1521(2007).
RN   [4]
RP   FUNCTION, MUTAGENESIS OF PRO-738, AND DISRUPTION PHENOTYPE.
RX   PubMed=21150311; DOI=10.4161/epi.6.3.14242;
RA   Greenberg M.V., Ausin I., Chan S.W., Cokus S.J., Cuperus J.T., Feng S.,
RA   Law J.A., Chu C., Pellegrini M., Carrington J.C., Jacobsen S.E.;
RT   "Identification of genes required for de novo DNA methylation in
RT   Arabidopsis.";
RL   Epigenetics 6:344-354(2011).
RN   [5]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH NRPD1.
RX   PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA   Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT   "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT   RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL   PLoS Genet. 7:E1002195-E1002195(2011).
RN   [6]
RP   GENE FAMILY.
RX   PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA   Xu R., Zhang S., Huang J., Zheng C.;
RT   "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT   in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT   sativa.";
RL   PLoS ONE 8:E78982-E78982(2013).
RN   [7]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH SHH1; NRPD1 AND
RP   NRPD3.
RX   PubMed=23637343; DOI=10.1073/pnas.1300585110;
RA   Zhang H., Ma Z.Y., Zeng L., Tanaka K., Zhang C.J., Ma J., Bai G., Wang P.,
RA   Zhang S.W., Liu Z.W., Cai T., Tang K., Liu R., Shi X., He X.J., Zhu J.K.;
RT   "DTF1 is a core component of RNA-directed DNA methylation and may assist in
RT   the recruitment of Pol IV.";
RL   Proc. Natl. Acad. Sci. U.S.A. 110:8290-8295(2013).
CC   -!- FUNCTION: Probable chromatin remodeling factor. Required for the
CC       initial establishment of DNA methylation and for accumulation of 24-nt
CC       siRNAs. May act on RNA templates by remodeling ribonucleoprotein
CC       structures and thereby influencing the availability of the RNA to
CC       polymerases. {ECO:0000269|PubMed:17526749,
CC       ECO:0000269|PubMed:21150311}.
CC   -!- SUBUNIT: Interacts with NRPD1, NRPD3 and SHH1.
CC       {ECO:0000269|PubMed:21811420, ECO:0000269|PubMed:23637343}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC       {ECO:0000269|PubMed:17526749}. Nucleus, nucleolus
CC       {ECO:0000269|PubMed:17526749}. Note=In the nucleolus, localized in a
CC       ring around the inner periphery.
CC   -!- DISRUPTION PHENOTYPE: Decreased, but not completely blocked de novo
CC       methylation. Probably due to a partial redundancy with CLSY2.
CC       {ECO:0000269|PubMed:21150311}.
CC   -!- MISCELLANEOUS: Associates in vivo with Pol IV but not with Pol V.
CC       {ECO:0000305|PubMed:23637343}.
CC   -!- SIMILARITY: Belongs to the helicase family. {ECO:0000305}.
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DR   EMBL; AL138640; CAB86450.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE77745.1; -; Genomic_DNA.
DR   EMBL; CP002686; ANM65979.1; -; Genomic_DNA.
DR   EMBL; CP002686; ANM65981.1; -; Genomic_DNA.
DR   PIR; T47325; T47325.
DR   RefSeq; NP_001327910.1; NM_001339087.1.
DR   RefSeq; NP_001327912.1; NM_001339086.1.
DR   RefSeq; NP_189853.1; NM_114134.2.
DR   AlphaFoldDB; Q9M297; -.
DR   BioGRID; 8612; 5.
DR   STRING; 3702.AT3G42670.1; -.
DR   PaxDb; Q9M297; -.
DR   PRIDE; Q9M297; -.
DR   ProteomicsDB; 240892; -.
DR   EnsemblPlants; AT3G42670.1; AT3G42670.1; AT3G42670.
DR   EnsemblPlants; AT3G42670.2; AT3G42670.2; AT3G42670.
DR   EnsemblPlants; AT3G42670.3; AT3G42670.3; AT3G42670.
DR   GeneID; 823287; -.
DR   Gramene; AT3G42670.1; AT3G42670.1; AT3G42670.
DR   Gramene; AT3G42670.2; AT3G42670.2; AT3G42670.
DR   Gramene; AT3G42670.3; AT3G42670.3; AT3G42670.
DR   KEGG; ath:AT3G42670; -.
DR   Araport; AT3G42670; -.
DR   TAIR; locus:2096499; AT3G42670.
DR   eggNOG; KOG0390; Eukaryota.
DR   HOGENOM; CLU_002499_0_0_1; -.
DR   InParanoid; Q9M297; -.
DR   PhylomeDB; Q9M297; -.
DR   PRO; PR:Q9M297; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q9M297; baseline and differential.
DR   Genevisible; Q9M297; AT.
DR   GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR   GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0031047; P:gene silencing by RNA; IMP:TAIR.
DR   GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IEA:InterPro.
DR   GO; GO:1900370; P:positive regulation of post-transcriptional gene silencing by RNA; IMP:TAIR.
DR   Gene3D; 3.40.50.10810; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   InterPro; IPR044567; CLSY/DRD1.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR038718; SNF2-like_sf.
DR   InterPro; IPR000330; SNF2_N.
DR   PANTHER; PTHR45821; PTHR45821; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF00176; SNF2-rel_dom; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW   Reference proteome.
FT   CHAIN           1..1256
FT                   /note="SNF2 domain-containing protein CLASSY 1"
FT                   /id="PRO_0000423313"
FT   DOMAIN          699..898
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          1061..1222
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   REGION          269..290
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          448..467
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           849..852
FT                   /note="DEAH box"
FT   BINDING         712..719
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   MUTAGEN         592
FT                   /note="G->E: Loss of endogenous 24-nt siRNAs."
FT                   /evidence="ECO:0000269|PubMed:17526749"
FT   MUTAGEN         738
FT                   /note="P->L: Decreased de novo methylation."
FT                   /evidence="ECO:0000269|PubMed:21150311"
SQ   SEQUENCE   1256 AA;  144574 MW;  3D6D093A8D5AF32C CRC64;
     MKRKHYFEFN HPFNPCPFEV FCWGTWKAVE YLRIENGTMT MRLLENGQVL DDIKPFQRLR
     IRSRKATLID CTSFLRPGID VCVLYQRDEE TPEPVWVDAR VLSIERKPHE SECLCTFHVS
     VYIDQGCIGL EKHRMNKVPV LVGLNEIAIL QKFCKEQSLD RYYRWRYSED CSSLVKTRLN
     LGKFLPDLTW LLVTSVLKNI VFQIRTVHEK MVYQIVTDED CEGSSSSLSA MNITVEDGVV
     MSKVVLFNPA EDTCQDSDVK EEIEEEVMEL RRSKRRSGRP ERYGDSEIQP DSKDGWVRMM
     PYRYNIWNVS SDDDDEEEDC EDDKDTDDDL YLPLSHLLRK KGSKKGFSKD KQREIVLVDK
     TERKKRKKTE GFSRSCELSV IPFTPVFEPI PLEQFGLNAN SLCGGVSGNL MDEIDKYRSK
     AAKYGKKKKK KIEMEEMESD LGWNGPIGNV VHKRNGPHSR IRSVSRETGV SEEPQIYKKR
     TLSAGAYNKL IDSYMSRIDS TIAAKDKATN VVEQWQGLKN PASFSIEAEE RLSEEEEDDG
     ETSENEILWR EMELCLASSY ILDDHEVRVD NEAFHKATCD CEHDYELNEE IGMCCRLCGH
     VGTEIKHVSA PFARHKKWTT ETKQINEDDI NTTIVNQDGV ESHTFTIPVA SSDMPSAEES
     DNVWSLIPQL KRKLHLHQKK AFEFLWKNLA GSVVPAMMDP SSDKIGGCVV SHTPGAGKTF
     LIIAFLASYL KIFPGKRPLV LAPKTTLYTW YKEFIKWEIP VPVHLLHGRR TYCMSKEKTI
     QFEGIPKPSQ DVMHVLDCLD KIQKWHAQPS VLVMGYTSFL TLMREDSKFA HRKYMAKVLR
     ESPGLLVLDE GHNPRSTKSR LRKALMKVDT DLRILLSGTL FQNNFCEYFN TLCLARPKFV
     HEVLVELDKK FQTNQAEQKA PHLLENRARK FFLDIIAKKI DTKVGDERLQ GLNMLRNMTS
     GFIDNYEGSG SGSGDVLPGL QIYTLLMNST DVQHKSLTKL QNIMSTYHGY PLELELLITL
     AAIHPWLVKT TTCCAKFFNP QELLEIEKLK HDAKKGSKVM FVLNLVFRVV KREKILIFCH
     NIAPIRLFLE LFENVFRWKR GRELLTLTGD LELFERGRVI DKFEEPGGQS RVLLASITAC
     AEGISLTAAS RVIMLDSEWN PSKTKQAIAR AFRPGQQKVV YVYQLLSRGT LEEDKYRRTT
     WKEWVSSMIF SEEFVEDPSQ WQAEKIEDDV LREIVEEDKV KSFHMIMKNE KASTGG
 
 
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