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ISWI chromatin-remodeling complex ATPase CHR11 (EC 3.6.4.-) (ISW2-like) (Protein CHROMATIN REMODELING 11) (Sucrose nonfermenting protein 2 homolog)

 ISW2_ARATH              Reviewed;        1056 AA.
Q8RWY3; F4JAW0; F4JAW1; Q9SQU3;
25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
09-DEC-2015, sequence version 4.
25-APR-2018, entry version 120.
RecName: Full=ISWI chromatin-remodeling complex ATPase CHR11 {ECO:0000305};
EC=3.6.4.- {ECO:0000305};
AltName: Full=ISW2-like {ECO:0000305};
AltName: Full=Protein CHROMATIN REMODELING 11 {ECO:0000303|PubMed:16286646};
AltName: Full=Sucrose nonfermenting protein 2 homolog {ECO:0000305};
Name=CHR11 {ECO:0000303|PubMed:16286646};
OrderedLocusNames=At3g06400 {ECO:0000312|Araport:AT3G06400};
ORFNames=F24P17.13 {ECO:0000312|EMBL:AAF08585.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130713; DOI=10.1038/35048706;
Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M.,
Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
Monfort A., Argiriou A., Flores M., Liguori R., Vitale D.,
Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Tabata S.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
FUNCTION, AND DEVELOPMENTAL STAGE.
PubMed=16286646; DOI=10.1073/pnas.0508186102;
Huanca-Mamani W., Garcia-Aguilar M., Leon-Martinez G.,
Grossniklaus U., Vielle-Calzada J.P.;
"CHR11, a chromatin-remodeling factor essential for nuclear
proliferation during female gametogenesis in Arabidopsis thaliana.";
Proc. Natl. Acad. Sci. U.S.A. 102:17231-17236(2005).
[5]
FUNCTION, INTERACTION WITH RLT1 AND RLT2, SUBCELLULAR LOCATION, TISSUE
SPECIFICITY, AND DISRUPTION PHENOTYPE.
PubMed=22694359; DOI=10.1111/j.1365-313X.2012.05074.x;
Li G., Zhang J., Li J., Yang Z., Huang H., Xu L.;
"Imitation Switch chromatin remodeling factors and their interacting
RINGLET proteins act together in controlling the plant vegetative
phase in Arabidopsis.";
Plant J. 72:261-270(2012).
[6]
INTERACTION WITH RLT1; RLT2; PTM AND DDR4.
PubMed=23691993; DOI=10.1111/jipb.12069;
Dong J., Gao Z., Liu S., Li G., Yang Z., Huang H., Xu L.;
"SLIDE, the protein interacting domain of Imitation Switch remodelers,
binds DDT-domain proteins of different subfamilies in chromatin
remodeling complexes.";
J. Integr. Plant Biol. 55:928-937(2013).
[7]
GENE FAMILY.
PubMed=24265739; DOI=10.1371/journal.pone.0078982;
Xu R., Zhang S., Huang J., Zheng C.;
"Genome-wide comparative in silico analysis of the RNA helicase gene
family in Zea mays and Glycine max: a comparison with Arabidopsis and
Oryza sativa.";
PLoS ONE 8:E78982-E78982(2013).
[8]
FUNCTION.
PubMed=24606212; DOI=10.1111/tpj.12499;
Li G., Liu S., Wang J., He J., Huang H., Zhang Y., Xu L.;
"ISWI proteins participate in the genome-wide nucleosome distribution
in Arabidopsis.";
Plant J. 78:706-714(2014).
[9]
FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH FGT1.
STRAIN=cv. Columbia;
PubMed=27680998; DOI=10.7554/eLife.17061;
Brzezinka K., Altmann S., Czesnick H., Nicolas P., Gorka M., Benke E.,
Kabelitz T., Jaehne F., Graf A., Kappel C., Baeurle I.;
"Arabidopsis FORGETTER1 mediates stress-induced chromatin memory
through nucleosome remodeling.";
Elife 5:0-0(2016).
-!- FUNCTION: Possesses intrinsic ATP-dependent nucleosome-remodeling
activity. Constitutes the catalytic subunit of several complexes
capable of forming ordered nucleosome arrays on chromatin (By
similarity). Involved in the formation of nucleosome distribution
patterns (PubMed:24606212). Involved in nuclear proliferation
during megagametogenesis and cell expansion in the sporophyte
(PubMed:16286646). Required for the maintenance of the plant
vegetative phase. In association with RLT1 or RLT2 may prevent the
early activation of the vegetative-to-reproductive transition by
regulating key genes that contribute to flower timing, such as FT,
SEP1, SEP3, AGL8/FUL, SOC1 and FLC (PubMed:22694359). Necessary to
acquire heat stress (HS) memory (PubMed:27680998).
{ECO:0000250|UniProtKB:O60264, ECO:0000269|PubMed:16286646,
ECO:0000269|PubMed:22694359, ECO:0000269|PubMed:24606212,
ECO:0000269|PubMed:27680998}.
-!- SUBUNIT: Interacts with RLT1 and RLT2 (PubMed:22694359). Interacts
(via C-terminus) with RLT1 (via the DDT domain), RLT2 (via the DDT
domain), PTM (via the DDT domain) and DDR4 (via the DDT domain)
(PubMed:23691993). Binds to FGT1 (PubMed:27680998).
{ECO:0000269|PubMed:22694359, ECO:0000269|PubMed:23691993,
ECO:0000269|PubMed:27680998}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00624, ECO:0000269|PubMed:22694359}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8RWY3-1; Sequence=Displayed;
Name=2;
IsoId=Q8RWY3-2; Sequence=VSP_058012;
Note=No experimental confirmation available. {ECO:0000305};
-!- TISSUE SPECIFICITY: Highly expressed in growing tissues such as
inflorescence and flower meristems, young leaves and floral
organs. Expressed in roots, rosette and cauline leaves, stems,
flowers, inflorescences and siliques.
{ECO:0000269|PubMed:22694359}.
-!- DEVELOPMENTAL STAGE: In developing ovule, expressed in all cells
of the young nucellus, including the functional megaspore. After
the initiation of megagametogenesis, expressed in most cells of
the ovule, including the integuments, the developing
megagametophyte, and the funiculus. In mature ovules, strongly
expressed in the cellularized megagametophyte. After double
fertilization, expressed in the developing embryo and the free
nuclear endosperm until seed maturity. Expressed in developing
male gametophytes and mature pollen grains.
{ECO:0000269|PubMed:16286646}.
-!- DISRUPTION PHENOTYPE: Reduced heat stress (HS) memory. Premature
decline of expression of HSA32, HSP18.2, HSP21, HSP22 and HSP101
after HS in the double mutant plants chr11-1 and chr17-1
(PubMed:27680998). No visible phenotype under normal growth
conditions, but the double mutant plants chr11-1 and chr17-1 are
very small and display early flowering and sterility
(PubMed:22694359). {ECO:0000269|PubMed:22694359,
ECO:0000269|PubMed:27680998}.
-!- MISCELLANEOUS: Plants silencing CHR11 display reduced plant height
and small cotyledonary embryos with limited cell expansion. Plants
silencing CHR11 specifically at the onset of female gametogenesis
(megagametogenesis) have defective female gametophytes arrested
before the completion of the mitotic haploid nuclear divisions.
{ECO:0000269|PubMed:16286646}.
-!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. ISWI
subfamily. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAF08585.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AC011623; AAF08585.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002686; AEE74386.1; -; Genomic_DNA.
EMBL; CP002686; AEE74388.1; -; Genomic_DNA.
EMBL; AY091030; AAM13851.1; -; mRNA.
RefSeq; NP_001189827.1; NM_001202898.2. [Q8RWY3-1]
RefSeq; NP_187291.2; NM_111515.5. [Q8RWY3-2]
UniGene; At.28209; -.
UniGene; At.67057; -.
ProteinModelPortal; Q8RWY3; -.
SMR; Q8RWY3; -.
BioGrid; 5149; 10.
STRING; 3702.AT3G06400.3; -.
iPTMnet; Q8RWY3; -.
PaxDb; Q8RWY3; -.
PRIDE; Q8RWY3; -.
EnsemblPlants; AT3G06400.1; AT3G06400.1; AT3G06400. [Q8RWY3-2]
EnsemblPlants; AT3G06400.2; AT3G06400.2; AT3G06400. [Q8RWY3-1]
GeneID; 819814; -.
Gramene; AT3G06400.1; AT3G06400.1; AT3G06400. [Q8RWY3-2]
Gramene; AT3G06400.2; AT3G06400.2; AT3G06400. [Q8RWY3-1]
KEGG; ath:AT3G06400; -.
Araport; AT3G06400; -.
eggNOG; KOG0385; Eukaryota.
eggNOG; COG0553; LUCA.
HOGENOM; HOG000192862; -.
InParanoid; Q8RWY3; -.
KO; K11654; -.
Reactome; R-ATH-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
PRO; PR:Q8RWY3; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q8RWY3; baseline and differential.
Genevisible; Q8RWY3; AT.
GO; GO:0005634; C:nucleus; IMP:UniProtKB.
GO; GO:0016589; C:NURF complex; IEA:InterPro.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0016887; F:ATPase activity; IEA:InterPro.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
GO; GO:0031491; F:nucleosome binding; IEA:InterPro.
GO; GO:0043044; P:ATP-dependent chromatin remodeling; IEA:InterPro.
GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
GO; GO:0009561; P:megagametogenesis; IMP:UniProtKB.
GO; GO:0034728; P:nucleosome organization; IMP:UniProtKB.
GO; GO:1900036; P:positive regulation of cellular response to heat; IMP:UniProtKB.
GO; GO:0048510; P:regulation of timing of transition from vegetative to reproductive phase; IMP:UniProtKB.
CDD; cd00079; HELICc; 1.
CDD; cd00167; SANT; 1.
Gene3D; 1.10.1040.30; -; 1.
Gene3D; 3.40.50.10810; -; 1.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR009057; Homeobox-like_sf.
InterPro; IPR029915; ISWI.
InterPro; IPR015194; ISWI_HAND-dom.
InterPro; IPR036306; ISWI_HAND-dom_sf.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR001005; SANT/Myb.
InterPro; IPR017884; SANT_dom.
InterPro; IPR015195; SLIDE.
InterPro; IPR038718; SNF2-like_sf.
InterPro; IPR000330; SNF2_N.
PANTHER; PTHR10799:SF887; PTHR10799:SF887; 1.
Pfam; PF09110; HAND; 1.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF09111; SLIDE; 1.
Pfam; PF00176; SNF2_N; 1.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SMART; SM00717; SANT; 2.
SUPFAM; SSF101224; SSF101224; 1.
SUPFAM; SSF46689; SSF46689; 2.
SUPFAM; SSF52540; SSF52540; 2.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
PROSITE; PS51293; SANT; 1.
1: Evidence at protein level;
Alternative splicing; ATP-binding; Chromatin regulator; Coiled coil;
Complete proteome; Flowering; Helicase; Hydrolase; Nucleotide-binding;
Nucleus; Reference proteome; Repeat.
CHAIN 1 1056 ISWI chromatin-remodeling complex ATPase
CHR11.
/FTId=PRO_0000074331.
DOMAIN 201 366 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 494 645 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 840 892 SANT 1. {ECO:0000255|PROSITE-
ProRule:PRU00624}.
DOMAIN 941 1002 SANT 2. {ECO:0000255|PROSITE-
ProRule:PRU00624}.
NP_BIND 214 221 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
COILED 12 105 {ECO:0000255}.
MOTIF 317 320 DEAH box. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
COMPBIAS 155 161 Poly-Glu.
COMPBIAS 165 168 Poly-Glu.
COMPBIAS 708 738 Asp-rich.
VAR_SEQ 820 820 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_058012.
CONFLICT 168 168 D -> E (in Ref. 3; AAM13851).
{ECO:0000305}.
SEQUENCE 1056 AA; 122558 MW; 28770AB52EBE9936 CRC64;
MARNSNSDEA FSSEEEEERV KDNEEEDEEE LEAVARSSGS DDDEVAAADE SPVSDGEAAP
VEDDYEDEED EEKAEISKRE KARLKEMQKL KKQKIQEMLE SQNASIDADM NNKGKGRLKY
LLQQTELFAH FAKSDGSSSQ KKAKGRGRHA SKITEEEEDE EYLKEEEDGL TGSGNTRLLT
QPSCIQGKMR DYQLAGLNWL IRLYENGING ILADEMGLGK TLQTISLLAY LHEYRGINGP
HMVVAPKSTL GNWMNEIRRF CPVLRAVKFL GNPEERRHIR EDLLVAGKFD ICVTSFEMAI
KEKTALRRFS WRYIIIDEAH RIKNENSLLS KTMRLFSTNY RLLITGTPLQ NNLHELWALL
NFLLPEIFSS AETFDEWFQI SGENDQQEVV QQLHKVLRPF LLRRLKSDVE KGLPPKKETI
LKVGMSQMQK QYYKALLQKD LEAVNAGGER KRLLNIAMQL RKCCNHPYLF QGAEPGPPYT
TGDHLITNAG KMVLLDKLLP KLKERDSRVL IFSQMTRLLD ILEDYLMYRG YLYCRIDGNT
GGDERDASIE AYNKPGSEKF VFLLSTRAGG LGINLATADV VILYDSDWNP QVDLQAQDRA
HRIGQKKEVQ VFRFCTESAI EEKVIERAYK KLALDALVIQ QGRLAEQKTV NKDELLQMVR
YGAEMVFSSK DSTITDEDID RIIAKGEEAT AELDAKMKKF TEDAIQFKMD DSADFYDFDD
DNKDENKLDF KKIVSDNWND PPKRERKRNY SESEYFKQTL RQGAPAKPKE PRIPRMPQLH
DFQFFNIQRL TELYEKEVRY LMQTHQKNQL KDTIDVEEPE EGGDPLTTEE VEEKEGLLEE
GFSTWSRRDF NTFLRACEKY GRNDIKSIAS EMEGKTEEEV ERYAKVFKER YKELNDYDRI
IKNIERGEAR ISRKDEIMKA IGKKLDRYRN PWLELKIQYG QNKGKLYNEE CDRFMICMIH
KLGYGNWDEL KAAFRTSSVF RFDWFVKSRT SQELARRCDT LIRLIEKENQ EFDERERQAR
KEKKLAKSAT PSKRPLGRQA SESPSSTKKR KHLSMR


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