CHR28_ARATH
ID CHR28_ARATH Reviewed; 981 AA.
AC Q94BR5; Q9LPR7; Q9SX56;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Helicase-like transcription factor CHR28 {ECO:0000305};
DE EC=3.6.4.- {ECO:0000305};
DE AltName: Full=Protein CHROMATIN REMODELING 28 {ECO:0000305};
DE AltName: Full=Protein SNF2-RING-HELICASE-LIKE 2 {ECO:0000303|PubMed:25425661};
GN Name=CHR28 {ECO:0000303|PubMed:25420628};
GN Synonyms=FRG2 {ECO:0000303|PubMed:25420628};
GN OrderedLocusNames=At1g50410 {ECO:0000312|Araport:AT1G50410};
GN ORFNames=F11F12.23 {ECO:0000312|EMBL:AAF87890.1},
GN F14I3.1 {ECO:0000312|EMBL:AAD50036.1};
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;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, AND INTERACTION WITH SUVR2.
RX PubMed=25420628; DOI=10.1038/cr.2014.156;
RA Han Y.F., Dou K., Ma Z.Y., Zhang S.W., Huang H.W., Li L., Cai T., Chen S.,
RA Zhu J.K., He X.J.;
RT "SUVR2 is involved in transcriptional gene silencing by associating with
RT SNF2-related chromatin-remodeling proteins in Arabidopsis.";
RL Cell Res. 24:1445-1465(2014).
RN [5]
RP FUNCTION.
RX PubMed=25425661; DOI=10.1073/pnas.1420515111;
RA Groth M., Stroud H., Feng S., Greenberg M.V., Vashisht A.A.,
RA Wohlschlegel J.A., Jacobsen S.E., Ausin I.;
RT "SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-
RT directed DNA methylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:17666-17671(2014).
CC -!- FUNCTION: Probable helicase-like transcription factor involved in
CC transcriptional gene silencing. Associates with SUVR2 and contributes
CC to transcriptional gene silencing at RNA-directed DNA methylation
CC (RdDM) target loci but also at RdDM-independent target loci. May be
CC involved in nucleosome positioning to form ordered nucleosome arrays on
CC chromatin (PubMed:25420628). Associates with SUVR2 and functions
CC redundantly with FRG1. Required for the efficient methylation of a
CC broad range of RdDM target loci (PubMed:25425661).
CC {ECO:0000269|PubMed:25420628, ECO:0000269|PubMed:25425661}.
CC -!- SUBUNIT: Interacts with SUVR2. {ECO:0000269|PubMed:25420628}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9ZUL5}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. RAD16 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD50036.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAF87890.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007980; AAD50036.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC012561; AAF87890.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32545.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM61085.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM61086.1; -; Genomic_DNA.
DR EMBL; AY039939; AAK64043.1; -; mRNA.
DR EMBL; AY142669; AAN13207.1; -; mRNA.
DR PIR; D96540; D96540.
DR RefSeq; NP_001323325.1; NM_001333433.1.
DR RefSeq; NP_001323326.1; NM_001333434.1.
DR RefSeq; NP_564568.1; NM_103924.2.
DR AlphaFoldDB; Q94BR5; -.
DR SMR; Q94BR5; -.
DR IntAct; Q94BR5; 1.
DR STRING; 3702.AT1G50410.1; -.
DR PaxDb; Q94BR5; -.
DR PRIDE; Q94BR5; -.
DR ProteomicsDB; 246786; -.
DR EnsemblPlants; AT1G50410.1; AT1G50410.1; AT1G50410.
DR EnsemblPlants; AT1G50410.2; AT1G50410.2; AT1G50410.
DR EnsemblPlants; AT1G50410.3; AT1G50410.3; AT1G50410.
DR GeneID; 841463; -.
DR Gramene; AT1G50410.1; AT1G50410.1; AT1G50410.
DR Gramene; AT1G50410.2; AT1G50410.2; AT1G50410.
DR Gramene; AT1G50410.3; AT1G50410.3; AT1G50410.
DR KEGG; ath:AT1G50410; -.
DR Araport; AT1G50410; -.
DR TAIR; locus:2008096; AT1G50410.
DR eggNOG; KOG1001; Eukaryota.
DR HOGENOM; CLU_000315_2_3_1; -.
DR InParanoid; Q94BR5; -.
DR OMA; ALMRQWE; -.
DR OrthoDB; 132523at2759; -.
DR PhylomeDB; Q94BR5; -.
DR PRO; PR:Q94BR5; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94BR5; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008094; F:ATP-dependent activity, acting on DNA; IBA:GO_Central.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.40.50.10810; -; 3.
DR Gene3D; 3.40.50.300; -; 1.
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 InterPro; IPR018957; Znf_C3HC4_RING-type.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR017907; Znf_RING_CS.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00176; SNF2-rel_dom; 1.
DR Pfam; PF00097; zf-C3HC4; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00184; RING; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS00518; ZF_RING_1; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Chromatin regulator; DNA-binding; Helicase; Hydrolase;
KW Metal-binding; Nucleotide-binding; Nucleus; Reference proteome;
KW RNA-mediated gene silencing; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..981
FT /note="Helicase-like transcription factor CHR28"
FT /id="PRO_0000435118"
FT DOMAIN 241..526
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 804..976
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 679..718
FT /note="RING-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 1..66
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 112..194
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 293..337
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 439..462
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 779..808
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 12..40
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 42..66
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 161..178
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 321..335
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 779..797
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 254..261
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 981 AA; 108111 MW; 2CC49EE1351F544B CRC64;
MDSAIDISSD SDVEIQETRT RPQHPPRIAE GSHRRDLSTL RPHFLSGSSS GANGHTKTGL
TNLDSRNGFE SKPLPRAEHH THIPGNGSIV TSRIPNISVG DYEKFSSQQA FKRTHPPTFS
RPPFPPRPDI GTSNGNASHF RGGAHDDLGM GRVTNGTRIL PPSVAHGTSA SPSHFNGLSD
PMHRNGIGEE RNSENDERLI YQAALQELNQ PKSEVDLPAG LLSVPLMKHQ KIALAWMFQK
ETNSLHCMGG ILADDQGLGK TVSTIALILK QMHEAKLKSK NSGNQEAEAL DLDADDESEN
AFEKPESKAS NGSGVNGDSG IKKAKGEEAS TSTRKFNRKR PAAGTLIVCP ASVVRQWARE
LDEKVTDEAK LSVLIYHGGN RTKDPIELAK YDVVMTTYAI VSNEVPKQPL VDDDENDEKN
SEKYGLASGF SINKKRKNVV GTTKKSKKKK GNNNAGDSSD PDSGTLAKVG WFRVVLDEAQ
TIKNHRTQVA RACCGLRAKR RWCLSGTPIQ NTIDDLYSYF RFLKYDPYAV YKSFCHQIKG
PISRNSLQGY KKLQAVLRAI MLRRTKGTLL DGQPIINLPP KTINLSQVDF SVEERSFYVK
LESDSRSQFK AYAAAGTLNQ NYANILLMLL RLRQACDHPQ LVKRYNSDSV GKVSEEAVKK
LPKEDLVSLL SRLESSPICC VCHDPPEDPV VTLCGHIFCY QCVSDYITGD EDTCPAPRCR
EQLAHDVVFS KSTLRSCVAD DLGCSSSEDN SHDKSVFQNG EFSSSKIKAV LDILQSLSNQ
GTSNSTQNGQ MASSSQQPND DDDDDDDDVT IVEKTSLKST PSNGGPIKTI IFSQWTGMLD
LVELSLIENS IEFRRLDGTM SLIARDRAVK EFSNDPDVKV MIMSLKAGNL GLNMIAACHV
ILLDLWWNPT TEDQAIDRAH RIGQTRPVTV TRITIKNTVE DRILALQEEK RKMVASAFGE
DHGGSSATRL TVDDLKYLFM V
