CLSY3_ARATH
ID CLSY3_ARATH Reviewed; 1410 AA.
AC F4I8S3; Q0WWJ9; Q9ZVY9;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=SNF2 domain-containing protein CLASSY 3;
DE EC=3.6.4.-;
DE AltName: Full=Protein CHROMATIN REMODELING 31 {ECO:0000303|PubMed:16547115};
DE Short=AtCHR31;
GN Name=CLSY3; Synonyms=CHR31 {ECO:0000303|PubMed:16547115};
GN OrderedLocusNames=At1g05490; ORFNames=T25N20.14;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16547115; DOI=10.1534/genetics.105.051664;
RA Shaked H., Avivi-Ragolsky N., Levy A.A.;
RT "Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family
RT in DNA damage response and recombination.";
RL Genetics 173:985-994(2006).
RN [5]
RP IDENTIFICATION, AND GENE FAMILY.
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 [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH NRPD1, AND
RP NOMENCLATURE.
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 [7]
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).
CC -!- FUNCTION: Probable chromatin remodeling factor.
CC {ECO:0000303|PubMed:16547115}.
CC -!- SUBUNIT: Interacts with NRPD1. {ECO:0000269|PubMed:21811420}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250, ECO:0000255|PROSITE-
CC ProRule:PRU00768}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79734.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC005106; AAF79734.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27845.1; -; Genomic_DNA.
DR EMBL; AK226351; BAE98499.1; -; mRNA.
DR RefSeq; NP_172040.2; NM_100428.4.
DR AlphaFoldDB; F4I8S3; -.
DR SMR; F4I8S3; -.
DR BioGRID; 22293; 1.
DR STRING; 3702.AT1G05490.1; -.
DR iPTMnet; F4I8S3; -.
DR PaxDb; F4I8S3; -.
DR PRIDE; F4I8S3; -.
DR ProteomicsDB; 241043; -.
DR EnsemblPlants; AT1G05490.1; AT1G05490.1; AT1G05490.
DR GeneID; 837051; -.
DR Gramene; AT1G05490.1; AT1G05490.1; AT1G05490.
DR KEGG; ath:AT1G05490; -.
DR Araport; AT1G05490; -.
DR TAIR; locus:2201006; AT1G05490.
DR eggNOG; KOG0390; Eukaryota.
DR HOGENOM; CLU_244196_0_0_1; -.
DR InParanoid; F4I8S3; -.
DR OMA; WEELAFF; -.
DR OrthoDB; 100510at2759; -.
DR PRO; PR:F4I8S3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; F4I8S3; baseline and differential.
DR Genevisible; F4I8S3; AT.
DR GO; GO:0005634; C:nucleus; 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:0003677; F:DNA binding; IEA:UniProtKB-KW.
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 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; Coiled coil; DNA-binding; Helicase; Hydrolase;
KW Nucleotide-binding; Nucleus; Reference proteome; Repeat.
FT CHAIN 1..1410
FT /note="SNF2 domain-containing protein CLASSY 3"
FT /id="PRO_0000423315"
FT DOMAIN 850..1060
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 1206..1359
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 87..108
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 209..330
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 344..376
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 428..593
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 632..654
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 248..278
FT /evidence="ECO:0000255"
FT COILED 356..377
FT /evidence="ECO:0000255"
FT MOTIF 22..29
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 328..335
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 1011..1014
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOTIF 1132..1139
FT /note="Nuclear localization signal 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 51..74
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 92..108
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 217..243
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 248..265
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 271..306
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 307..330
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 428..447
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 492..506
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 537..551
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 863..870
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 640
FT /note="S -> P (in Ref. 3; BAE98499)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1410 AA; 158723 MW; 14859DB2524169B8 CRC64;
MECIGKRVKS RSWQRLQAVN KRKKMETVAP VTSPPKKRRQ KKPKNYDSDI EDITPTCNDS
VPPPQVSNMY SVPNNSVKES FSRIMRDLNV EKKSGPSSSR LTDGSEQNPC LKERSFRVSD
LGVEKKCSPE ITDLDVGIPV PRFSKLKDVS EQKNTCLMQK SSPEIADLDL VISVPSSSVL
KDVSEEIRFL KDKCSPEIRG LVLEKSVPGE IEILSDSESE TEARRRASAK KKLFEESSRI
VESISDGEDS SSETDEEEEE NQDSEDNNTK DNVTVESLSS EDPSSSSSSS SSSSSSSSSS
SSDDESYVKE VVGDNRDDDD LRKASSPIKR VSLVERKALV RYKRSGSSLT KPRERDNKIQ
KLNHREEEKK ERQREVVRVV TKQPSNVVYT CAHCGKENTG NPESHSSFIR PHSIRDEIED
VNNFASTNVS KYEDSVSINS GKTTGAPSRP EVENPETGKE LNTPEKPSIS RPEIFTTEKA
IDVQVPEEPS RPEIYSSEKA KEVQAPEMPS RPEVFSSEKA KEIQVPEMPS IPEIQNSEKA
KEVQANNRMG LTTPAVAEGL NKSVVTNEHI EDDSDSSISS GDGYESDPTL KDKEVKINNH
SDWRILNGNN KEVDLFRLLV NSVWEKGQLG EEDEADELVS SAEDQSQEQA REDHRKYDDA
GLLIIRPPPL IEKFGVEEPQ SPPVVSEIDS EEDRLWEELA FFTKSNDIGG NELFSNVEKN
ISANETPAAQ CKKGKHDLCI DLEVGLKCMH CGFVEREIRS MDVSEWGEKT TRERRKFDRF
EEEEGSSFIG KLGFDAPNNS LNEGCVSSEG TVWDKIPGVK SQMYPHQQEG FEFIWKNLAG
TIMLNELKDF ENSDETGGCI MSHAPGTGKT RLTIIFLQAY LQCFPDCKPV IIAPASLLLT
WAEEFKKWNI SIPFHNLSSL DFTGKENSAA LGLLMQKNAT ARSNNEIRMV KIYSWIKSKS
ILGISYNLYE KLAGVKDEDK KTKMVREVKP DKELDDIREI LMGRPGLLVL DEAHTPRNQR
SCIWKTLSKV ETQKRILLSG TPFQNNFLEL CNVLGLARPK YLERLTSTLK KSGMTVTKRG
KKNLGNEINN RGIEELKAVM LPFVHVHKGS ILQSSLPGLR ECVVVLNPPE LQRRVLESIE
VTHNRKTKNV FETEHKLSLV SVHPSLVSRC KISEKERLSI DEALLAQLKK VRLDPNQSVK
TRFLMEFVEL CEVIKEKVLV FSQYIDPLKL IMKHLVSRFK WNPGEEVLYM HGKLEQKQRQ
TLINEFNDPK SKAKVFLAST KACSEGISLV GASRVILLDV VWNPAVERQA ISRAYRIGQK
RIVYTYHLVA KGTPEGPKYC KQAQKDRISE LVFACSSRHD KGKEKIAEAV TEDKVLDTMV
EHSKLGDMFD NLIVQPKEAD LVEGFSILMP
