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 27-MAR-2024, entry version 130.
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.Q9M297; -.
DR PaxDb; 3702-AT3G42670-1; -.
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; AT3G42670; CHR38.
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:0003682; F:chromatin binding; 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: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 GO; GO:0031047; P:regulatory ncRNA-mediated gene silencing; IMP:TAIR.
DR CDD; cd18007; DEXHc_ATRX-like; 1.
DR CDD; cd18793; SF2_C_SNF; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 3.40.50.10810; Tandem AAA-ATPase domain; 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; IPR032001; SAWADEE_dom.
DR InterPro; IPR038718; SNF2-like_sf.
DR InterPro; IPR049730; SNF2/RAD54-like_C.
DR InterPro; IPR000330; SNF2_N.
DR PANTHER; PTHR45821:SF8; SNF2 DOMAIN-CONTAINING PROTEIN CLASSY 1; 1.
DR PANTHER; PTHR45821; SNF2 DOMAIN-CONTAINING PROTEIN CLASSY 2-RELATED; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF16719; SAWADEE; 1.
DR Pfam; PF00176; SNF2-rel_dom; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 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
//
