CLSY4_ARATH
ID CLSY4_ARATH Reviewed; 1132 AA.
AC Q9LK10;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=SNF2 domain-containing protein CLASSY 4;
DE EC=3.6.4.-;
DE AltName: Full=Protein CHROMATIN REMODELING 40 {ECO:0000303|PubMed:16547115};
DE Short=AtCHR40;
GN Name=CLSY4; Synonyms=CHR40 {ECO:0000303|PubMed:16547115};
GN OrderedLocusNames=At3g24340; ORFNames=K7M2.11;
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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 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 [4]
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 [5]
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 [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).
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}.
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DR EMBL; AP000382; BAB02934.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76891.1; -; Genomic_DNA.
DR RefSeq; NP_189077.1; NM_113341.2.
DR AlphaFoldDB; Q9LK10; -.
DR SMR; Q9LK10; -.
DR BioGRID; 7355; 1.
DR STRING; 3702.AT3G24340.1; -.
DR PaxDb; Q9LK10; -.
DR PRIDE; Q9LK10; -.
DR ProteomicsDB; 240983; -.
DR EnsemblPlants; AT3G24340.1; AT3G24340.1; AT3G24340.
DR GeneID; 822023; -.
DR Gramene; AT3G24340.1; AT3G24340.1; AT3G24340.
DR KEGG; ath:AT3G24340; -.
DR Araport; AT3G24340; -.
DR TAIR; locus:2087223; AT3G24340.
DR eggNOG; KOG0390; Eukaryota.
DR HOGENOM; CLU_302146_0_0_1; -.
DR InParanoid; Q9LK10; -.
DR OMA; LWSEMEI; -.
DR OrthoDB; 142408at2759; -.
DR PhylomeDB; Q9LK10; -.
DR PRO; PR:Q9LK10; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LK10; baseline and differential.
DR Genevisible; Q9LK10; 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; DNA-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..1132
FT /note="SNF2 domain-containing protein CLASSY 4"
FT /id="PRO_0000423316"
FT DOMAIN 603..796
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 934..1087
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 24..104
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 224..331
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 376..396
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 525..544
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 47..54
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 747..750
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 39..58
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 66..91
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 240..254
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 266..282
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 283..299
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 306..328
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 376..395
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 616..623
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 1132 AA; 128343 MW; AE40911268F2C917 CRC64;
MDMTSCVARR TRSRTESYLN SILNKSKGIS GEEEDQSLGC VNSRTEKRRV NMRDACSPSP
RKKKRRRRKD DDDDVVFVRT EYPEGKRDDE NVGSTSGNLQ SKSFDFGDRV CDFDADDRNL
GCEEKASNFN PIDDDDDVVF VGTVQRENDH VEDDDNVGSA SVISPRVCDF DEDDAKVSGK
ENPLSPDDDD DVVFLGTIAG ENQHVEDVNA GSEVCDILLD DANLRGEEKT YVSDEVVSLS
SSSDDEEDPL EELGTDSREE VSGEDRDSGE SDMDEDANDS DSSDYVGESS DSSDVESSDS
DFVCSEDEEG GTRDDATCEK NPSEKVYHHK KSRTFRRKHN FDVINLLAKS MLESKDVFKE
DIFSWDKIAE VDSREDPVVR ESSSEKVNEH GKPRERRSFH RVREKNHLNG ESFYGGEKLC
DGEETINYST EDSPPLNLRF GCEEPVLIEK TEEEKELDSL WEDMNVALTL EGMHSSTPDK
NGDMLCSKGT HDFVLDDEIG LKCVHCAYVA VEIKDISPAM DKYRPSVNDN KKCSDRKGDP
LPNRLEFDAS DPSSFVAPLD NIEGTVWQYV PGIKDTLYPH QQEGFEFIWK NLAGTTKINE
LNSVGVKGSG GCIISHKAGT GKTRLTVVFL QSYLKRFPNS HPMVIAPATL MRTWEDEVRK
WNVNIPFYNM NSLQLSGYED AEAVSRLEGN RHHNSIRMVK LVSWWKQKSI LGISYPLYEK
LAANKNTEGM QVFRRMLVEL PGLLVLDEGH TPRNQSSLIW KVLTEVRTEK RIFLSGTLFQ
NNFKELSNVL CLARPADKDT ISSRIHELSK CSQEGEHGRV NEENRIVDLK AMIAHFVHVH
EGTILQESLP GLRDCVVVLN PPFQQKKILD RIDTSQNTFE FEHKLSAVSV HPSLYLCCNP
TKKEDLVIGP ATLGTLKRLR LKYEEGVKTK FLIDFIRISG TVKEKVLVYS QYIDTLKLIM
EQLIAECDWT EGEQILLMHG KVEQRDRQHM IDNFNKPDSG SKVLLASTKA CSEGISLVGA
SRVVILDVVW NPSVESQAIS RAFRIGQKRA VFIYHLMVKD TSEWNKYCKQ SEKHRISELV
FSSTNEKDKP INNEVVSKDR ILDEMVRHEK LKHIFEKILY HPKKSDMNTS FF
