INO80_ARATH
ID INO80_ARATH Reviewed; 1507 AA.
AC Q8RXS6; Q9M2L7;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Chromatin-remodeling ATPase INO80 {ECO:0000303|PubMed:15525519};
DE Short=AtINO80 {ECO:0000303|PubMed:15525519};
DE EC=3.6.4.- {ECO:0000250|UniProtKB:Q9ULG1};
DE AltName: Full=DNA helicase-related INO80 complex homolog 1 {ECO:0000305};
GN Name=INO80 {ECO:0000303|PubMed:15525519};
GN OrderedLocusNames=At3g57300 {ECO:0000312|Araport:AT3G57300};
GN ORFNames=F28O9.150 {ECO:0000312|EMBL:CAB68136.1};
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=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 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 FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=15525519; DOI=10.1016/j.molcel.2004.09.034;
RA Fritsch O., Benvenuto G., Bowler C., Molinier J., Hohn B.;
RT "The INO80 protein controls homologous recombination in Arabidopsis
RT thaliana.";
RL Mol. Cell 16:479-485(2004).
RN [5]
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 [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH EIN6.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=31418686; DOI=10.7554/elife.47835;
RA Zander M., Willige B.C., He Y., Nguyen T.A., Langford A.E., Nehring R.,
RA Howell E., McGrath R., Bartlett A., Castanon R., Nery J.R., Chen H.,
RA Zhang Z., Jupe F., Stepanova A., Schmitz R.J., Lewsey M.G., Chory J.,
RA Ecker J.R.;
RT "Epigenetic silencing of a multifunctional plant stress regulator.";
RL Elife 8:0-0(2019).
CC -!- FUNCTION: ATPase component of the chromatin remodeling INO80 complex
CC which is involved in transcriptional regulation, DNA replication and
CC DNA repair (By similarity). Binds DNA (By similarity). As part of the
CC INO80 complex, remodels chromatin by shifting nucleosomes (By
CC similarity). The INO80 complex controls ethylene-induced H2A.Z eviction
CC dynamics (PubMed:31418686). Positive regulator of homologous
CC recombination, but not an essential component of homologous
CC recombination (PubMed:15525519). Not involved in the illegitimate
CC repair pathway (PubMed:15525519). {ECO:0000250|UniProtKB:Q9ULG1,
CC ECO:0000269|PubMed:15525519, ECO:0000269|PubMed:31418686}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000250|UniProtKB:Q9ULG1};
CC -!- SUBUNIT: Component of the INO80 chromatin-remodeling complex (By
CC similarity). Associates with REF6/EIN6 (PubMed:31418686).
CC {ECO:0000255|PROSITE-ProRule:PRU00746, ECO:0000303|PubMed:31418686}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00746}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q8RXS6-1; Sequence=Displayed;
CC -!- INDUCTION: Not induced by methyl methanesulfonate (MMS) treatment.
CC {ECO:0000269|PubMed:15525519}.
CC -!- DOMAIN: The DBINO region is involved in binding to DNA.
CC {ECO:0000250|UniProtKB:Q9ULG1}.
CC -!- DISRUPTION PHENOTYPE: Decreased homologous recombination frequency, but
CC unchanged sensitivity to genotoxic agents and efficiency of T-DNA
CC integration (PubMed:15525519). Differential expression of several genes
CC (PubMed:31418686). Compromised ethylene-induced H2A.Z eviction dynamics
CC (PubMed:31418686). The double mutant ref6-1 ino80-1 is insensitive to
CC ethylene (ET) and exhibits reduced levels of EIN2 associated with a
CC shift of the chromatin landscape to a repressive state at its locus
CC (e.g. H3K27me3 and H2A.Z) (PubMed:31418686).
CC {ECO:0000269|PubMed:15525519, ECO:0000269|PubMed:31418686}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB68136.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL137080; CAB68136.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE79637.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65731.1; -; Genomic_DNA.
DR EMBL; AY080695; AAL86315.1; -; mRNA.
DR PIR; T45808; T45808.
DR RefSeq; NP_001319776.1; NM_001339850.1. [Q8RXS6-1]
DR RefSeq; NP_191289.2; NM_115590.4. [Q8RXS6-1]
DR AlphaFoldDB; Q8RXS6; -.
DR SMR; Q8RXS6; -.
DR BioGRID; 10213; 7.
DR STRING; 3702.AT3G57300.2; -.
DR iPTMnet; Q8RXS6; -.
DR PaxDb; Q8RXS6; -.
DR PRIDE; Q8RXS6; -.
DR ProteomicsDB; 248460; -. [Q8RXS6-1]
DR EnsemblPlants; AT3G57300.1; AT3G57300.1; AT3G57300. [Q8RXS6-1]
DR EnsemblPlants; AT3G57300.4; AT3G57300.4; AT3G57300. [Q8RXS6-1]
DR GeneID; 824897; -.
DR Gramene; AT3G57300.1; AT3G57300.1; AT3G57300. [Q8RXS6-1]
DR Gramene; AT3G57300.4; AT3G57300.4; AT3G57300. [Q8RXS6-1]
DR KEGG; ath:AT3G57300; -.
DR Araport; AT3G57300; -.
DR eggNOG; KOG0388; Eukaryota.
DR HOGENOM; CLU_000315_20_2_1; -.
DR InParanoid; Q8RXS6; -.
DR PhylomeDB; Q8RXS6; -.
DR PRO; PR:Q8RXS6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8RXS6; baseline and differential.
DR Genevisible; Q8RXS6; AT.
DR GO; GO:0031011; C:Ino80 complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; 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:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR GO; GO:0043618; P:regulation of transcription from RNA polymerase II promoter in response to stress; IBA:GO_Central.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 3.40.50.10810; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR020838; DBINO.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR031047; Ino80.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR038718; SNF2-like_sf.
DR InterPro; IPR000330; SNF2_N.
DR PANTHER; PTHR45685:SF2; PTHR45685:SF2; 1.
DR Pfam; PF13892; DBINO; 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; PS51413; DBINO; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; ATP-binding; DNA damage; DNA repair;
KW DNA-binding; Hydrolase; Nucleotide-binding; Nucleus; Reference proteome;
KW Transcription; Transcription regulation.
FT CHAIN 1..1507
FT /note="Chromatin-remodeling ATPase INO80"
FT /id="PRO_0000375865"
FT DOMAIN 350..475
FT /note="DBINO"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00746"
FT DOMAIN 598..769
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 1210..1360
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 30..82
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 428..452
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1415..1507
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 40..64
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1420..1442
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1454..1480
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1481..1507
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 611..618
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 1507 AA; 172172 MW; B64F7CCF96452E6B CRC64;
MDPSRRPPKD SPYANLFDLE PLMKFRIPKP EDEVDYYGSS SQDESRSTQG GVVANYSNGS
KSRMNASSKK RKRWTEAEDA EDDDDLYNQH VTEEHYRSML GEHVQKFKNR SKETQGNPPH
LMGFPVLKSN VGSYRGRKPG NDYHGRFYDM DNSPNFAADV TPHRRGSYHD RDITPKIAYE
PSYLDIGDGV IYKIPPSYDK LVASLNLPSF SDIHVEEFYL KGTLDLRSLA ELMASDKRSG
VRSRNGMGEP RPQYESLQAR MKALSPSNST PNFSLKVSEA AMNSAIPEGS AGSTARTILS
EGGVLQVHYV KILEKGDTYE IVKRSLPKKL KAKNDPAVIE KTERDKIRKA WINIVRRDIA
KHHRIFTTFH RKLSIDAKRF ADGCQREVRM KVGRSYKIPR TAPIRTRKIS RDMLLFWKRY
DKQMAEERKK QEKEAAEAFK REQEQRESKR QQQRLNFLIK QTELYSHFMQ NKTDSNPSEA
LPIGDENPID EVLPETSAAE PSEVEDPEEA ELKEKVLRAA QDAVSKQKQI TDAFDTEYMK
LRQTSEMEGP LNDISVSGSS NIDLHNPSTM PVTSTVQTPE LFKGTLKEYQ MKGLQWLVNC
YEQGLNGILA DEMGLGKTIQ AMAFLAHLAE EKNIWGPFLV VAPASVLNNW ADEISRFCPD
LKTLPYWGGL QERTILRKNI NPKRMYRRDA GFHILITSYQ LLVTDEKYFR RVKWQYMVLD
EAQAIKSSSS IRWKTLLSFN CRNRLLLTGT PIQNNMAELW ALLHFIMPML FDNHDQFNEW
FSKGIENHAE HGGTLNEHQL NRLHAILKPF MLRRVKKDVV SELTTKTEVT VHCKLSSRQQ
AFYQAIKNKI SLAELFDSNR GQFTDKKVLN LMNIVIQLRK VCNHPELFER NEGSSYLYFG
VTSNSLLPHP FGELEDVHYS GGQNPIIYKI PKLLHQEVLQ NSETFCSSVG RGISRESFLK
HFNIYSPEYI LKSIFPSDSG VDQVVSGSGA FGFSRLMDLS PSEVGYLALC SVAERLLFSI
LRWERQFLDE LVNSLMESKD GDLSDNNIER VKTKAVTRML LMPSKVETNF QKRRLSTGPT
RPSFEALVIS HQDRFLSSIK LLHSAYTYIP KARAPPVSIH CSDRNSAYRV TEELHQPWLK
RLLIGFARTS EANGPRKPNS FPHPLIQEID SELPVVQPAL QLTHRIFGSC PPMQSFDPAK
LLTDSGKLQT LDILLKRLRA GNHRVLLFAQ MTKMLNILED YMNYRKYKYL RLDGSSTIMD
RRDMVRDFQH RSDIFVFLLS TRAGGLGINL TAADTVIFYE SDWNPTLDLQ AMDRAHRLGQ
TKDVTVYRLI CKETVEEKIL HRASQKNTVQ QLVMTGGHVQ GDDFLGAADV VSLLMDDAEA
AQLEQKFREL PLQVKDRQKK KTKRIRIDAE GDATLEELED VDRQDNGQEP LEEPEKPKSS
NKKRRAASNP KARAPQKAKE EANGEDTPQR TKRVKRQTKS INESLEPVFS ASVTESNKGF
DPSSSAN
