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Protein CHROMATIN REMODELING 25 (AtCHR25) (EC 3.6.4.-) (DNA repair and recombination protein RAD54) (AtRAD54)

 CHR25_ARATH             Reviewed;         910 AA.
Q0PCS3; F4JB43; Q9LJK7;
29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
19-SEP-2006, sequence version 1.
29-SEP-2021, entry version 119.
RecName: Full=Protein CHROMATIN REMODELING 25;
Short=AtCHR25;
EC=3.6.4.-;
AltName: Full=DNA repair and recombination protein RAD54 {ECO:0000303|PubMed:17227544};
Short=AtRAD54 {ECO:0000303|PubMed:17227544};
Name=CHR25; Synonyms=RAD54 {ECO:0000303|PubMed:17227544};
OrderedLocusNames=At3g19210 {ECO:0000312|Araport:AT3G19210};
ORFNames=MVI11.13 {ECO:0000312|EMBL:BAB02963.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
NCBI_TaxID=3702 {ECO:0000312|EMBL:BAF03042.1};
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, DISRUPTION PHENOTYPE,
INTERACTION WITH RAD51, TISSUE SPECIFICITY, AND INDUCTION BY
GAMMA-IRRADIATION.
STRAIN=cv. Columbia; TISSUE=Flower bud;
PubMed=17227544; DOI=10.1111/j.1365-313x.2006.02927.x;
Osakabe K., Abe K., Yoshioka T., Osakabe Y., Todoriki S., Ichikawa H.,
Hohn B., Toki S.;
"Isolation and characterization of the RAD54 gene from Arabidopsis
thaliana.";
Plant J. 48:827-842(2006).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND INTERACTION WITH
RAD51.
PubMed=18430956; DOI=10.1534/genetics.108.086777;
Klutstein M., Shaked H., Sherman A., Avivi-Ragolsky N., Shema E.,
Zenvirth D., Levy A.A., Simchen G.;
"Functional conservation of the yeast and Arabidopsis RAD54-like genes.";
Genetics 178:2389-2397(2008).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10907853; DOI=10.1093/dnares/7.3.217;
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
clones.";
DNA Res. 7:217-221(2000).
[4]
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).
[5]
FUNCTION, DISRUPTION PHENOTYPE, GENE FAMILY, AND NOMENCLATURE.
PubMed=16547115; DOI=10.1534/genetics.105.051664;
Shaked H., Avivi-Ragolsky N., Levy A.A.;
"Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family
in DNA damage response and recombination.";
Genetics 173:985-994(2006).
[6]
INDUCTION BY FORMALDEHYDE.
PubMed=20399886; DOI=10.1016/j.mrgentox.2010.04.009;
Li F., Liu P., Wang T., Bian P., Wu Y., Wu L., Yu Z.;
"Genotoxicity/mutagenicity of formaldehyde revealed by the Arabidopsis
thaliana plants transgenic for homologous recombination substrates.";
Mutat. Res. 699:35-43(2010).
[7]
INDUCTION BY LOW-ENERGY-ION IRRADIATION.
PubMed=21557702; DOI=10.3109/09553002.2011.574780;
Li F., Wang T., Xu S., Yuan H., Bian P., Wu Y., Wu L., Yu Z.;
"Abscopal mutagenic effect of low-energy-ions in Arabidopsis thaliana
seeds.";
Int. J. Radiat. Biol. 87:984-992(2011).
[8]
FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH THE GEMINIVIRUS MUNGBEAN
YELLOW MOSAIC VIRUS (MYMV) AND TOMATO LEAF CURL VIRUS (TOLCV)
REPLICATION-ASSOCIATED PROTEIN, AND IDENTIFICATION BY MASS SPECTROMETRY.
STRAIN=cv. Columbia;
PubMed=22171001; DOI=10.1096/fj.11-188508;
Kaliappan K., Choudhury N.R., Suyal G., Mukherjee S.K.;
"A novel role for RAD54: this host protein modulates geminiviral DNA
replication.";
FASEB J. 26:1142-1160(2012).
[9]
INDUCTION BY HEAVY ION IRRADIATION.
PubMed=22683605; DOI=10.1016/j.mrfmmm.2012.05.006;
Wang T., Li F., Liu Q., Bian P., Wang J., Wu Y., Wu L., Li W.;
"Homologous recombination in Arabidopsis seeds along the track of energetic
carbon ions.";
Mutat. Res. 737:51-57(2012).
[10]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=22860689; DOI=10.1111/j.1365-313x.2012.05119.x;
Roth N., Klimesch J., Dukowic-Schulze S., Pacher M., Mannuss A., Puchta H.;
"The requirement for recombination factors differs considerably between
different pathways of homologous double-strand break repair in somatic
plant cells.";
Plant J. 72:781-790(2012).
[11]
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).
-!- FUNCTION: Dissociates RAD51 from nucleoprotein filaments formed on
dsDNA. Could be involved in the turnover of RAD51 protein-dsDNA
filaments. Addition of RAD54 overcomes inhibition of DNA strand
exchange by RAD51 bound to substrate dsDNA. Species preference in the
RAD51 dissociation and DNA strand exchange assays underlines the
importance of specific RAD54-RAD51 interactions. RAD51 is unable to
release dsDNA upon ATP hydrolysis, leaving it stuck on the heteroduplex
DNA product after DNA strand exchange (By similarity). Involved in DNA
repair and mitotic recombination (PubMed:17227544, PubMed:16547115,
PubMed:18430956). Functions in the homologous recombinational DNA
repair (RAD52) pathway (PubMed:17227544, PubMed:16547115,
PubMed:18430956). Required for synthesis-dependent strand annealing
(SDSA) during double-strand break repair (PubMed:22860689).
{ECO:0000250|UniProtKB:P32863, ECO:0000269|PubMed:16547115,
ECO:0000269|PubMed:17227544, ECO:0000269|PubMed:18430956,
ECO:0000269|PubMed:22860689}.
-!- FUNCTION: Facilitates geminiviral replication (e.g. geminivirus
mungbean yellow mosaic virus (MYMV) and tomato leaf curl virus
(ToLCV)). {ECO:0000269|PubMed:22171001}.
-!- SUBUNIT: Interacts with RAD51 (PubMed:17227544, PubMed:18430956). Binds
to the geminivirus mungbean yellow mosaic virus (MYMV) and to the
tomato leaf curl virus (ToLCV) replication-associated proteins
(PubMed:22171001). {ECO:0000269|PubMed:17227544,
ECO:0000269|PubMed:18430956, ECO:0000269|PubMed:22171001}.
-!- INTERACTION:
Q0PCS3; P94102: RAD51; NbExp=3; IntAct=EBI-1768899, EBI-307687;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P32863}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q0PCS3-1; Sequence=Displayed;
Name=2;
IsoId=Q0PCS3-2; Sequence=VSP_057104;
-!- TISSUE SPECIFICITY: Expressed ubiquitously, with the highest levels of
expression in flower buds. Present in flower buds (at protein level).
{ECO:0000269|PubMed:17227544}.
-!- INDUCTION: Induced by gamma-irradiation and by heavy ion irradiation
(PubMed:17227544, PubMed:22683605). Induced by the genotoxic
formaldehyde (FA) (PubMed:20399886). Accumulates in aerial part of low-
energy-ion irradiated dormant plant seeds, thus revealing an abscopal
mutagenic effect (PubMed:21557702). {ECO:0000269|PubMed:17227544,
ECO:0000269|PubMed:20399886, ECO:0000269|PubMed:21557702,
ECO:0000269|PubMed:22683605}.
-!- DISRUPTION PHENOTYPE: Increased sensitivity to gamma-irradiation and to
the cross-linking reagent cisplatin (PubMed:17227544). Reduced
efficiency of somatic homologous recombination (HR) (PubMed:17227544,
PubMed:16547115). Reduced synthesis-dependent strand annealing (SDSA)
frequency (PubMed:22860689). Impaired geminiviral replication (e.g.
tomato leaf curl virus (ToLCV)) (PubMed:22171001).
{ECO:0000269|PubMed:16547115, ECO:0000269|PubMed:17227544,
ECO:0000269|PubMed:22171001, ECO:0000269|PubMed:22860689}.
-!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAB02963.1; Type=Erroneous gene model prediction;
---------------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
---------------------------------------------------------------------------
EMBL; AB250666; BAF03042.1; -; mRNA.
EMBL; DQ912973; ABJ99465.1; -; mRNA.
EMBL; AP000419; BAB02963.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002686; AEE76208.1; -; Genomic_DNA.
EMBL; CP002686; AEE76209.1; -; Genomic_DNA.
RefSeq; NP_001189933.1; NM_001203004.1. [Q0PCS3-2]
RefSeq; NP_188552.3; NM_112808.4. [Q0PCS3-1]
SMR; Q0PCS3; -.
BioGRID; 6788; 5.
IntAct; Q0PCS3; 4.
STRING; 3702.AT3G19210.1; -.
iPTMnet; Q0PCS3; -.
PaxDb; Q0PCS3; -.
PRIDE; Q0PCS3; -.
ProteomicsDB; 247002; -. [Q0PCS3-1]
EnsemblPlants; AT3G19210.1; AT3G19210.1; AT3G19210. [Q0PCS3-1]
EnsemblPlants; AT3G19210.2; AT3G19210.2; AT3G19210. [Q0PCS3-2]
GeneID; 821455; -.
Gramene; AT3G19210.1; AT3G19210.1; AT3G19210. [Q0PCS3-1]
Gramene; AT3G19210.2; AT3G19210.2; AT3G19210. [Q0PCS3-2]
KEGG; ath:AT3G19210; -.
Araport; AT3G19210; -.
TAIR; locus:2094083; AT3G19210.
eggNOG; KOG0390; Eukaryota.
HOGENOM; CLU_000315_10_4_1; -.
InParanoid; Q0PCS3; -.
PhylomeDB; Q0PCS3; -.
PRO; PR:Q0PCS3; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q0PCS3; baseline and differential.
Genevisible; Q0PCS3; AT.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0015616; F:DNA translocase activity; IBA:GO_Central.
GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
GO; GO:0070615; F:nucleosome-dependent ATPase activity; IEA:InterPro.
GO; GO:0051701; P:biological process involved in interaction with host; IPI:UniProtKB.
GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
GO; GO:0071480; P:cellular response to gamma radiation; IEP:UniProtKB.
GO; GO:0071248; P:cellular response to metal ion; IEP:UniProtKB.
GO; GO:0000724; P:double-strand break repair via homologous recombination; IMP:TAIR.
GO; GO:0045003; P:double-strand break repair via synthesis-dependent strand annealing; IDA:TAIR.
GO; GO:0007131; P:reciprocal meiotic recombination; IBA:GO_Central.
GO; GO:0010332; P:response to gamma radiation; IEP:TAIR.
Gene3D; 3.40.50.10810; -; 1.
Gene3D; 3.40.50.300; -; 1.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR038718; SNF2-like_sf.
InterPro; IPR000330; SNF2_N.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF00176; SNF2_N; 1.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF52540; SSF52540; 2.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
1: Evidence at protein level;
Alternative splicing; ATP-binding; Cell cycle; Cell division; Coiled coil;
DNA damage; DNA repair; DNA-binding; Helicase; Host-virus interaction;
Hydrolase; Mitosis; Nucleotide-binding; Nucleus; Reference proteome.
CHAIN 1..910
/note="Protein CHROMATIN REMODELING 25"
/id="PRO_0000430859"
DOMAIN 198..371
/note="Helicase ATP-binding"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
DOMAIN 538..696
/note="Helicase C-terminal"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
NP_BIND 211..218
/note="ATP"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
REGION 1..39
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
REGION 828..861
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COILED 396..417
/evidence="ECO:0000255"
MOTIF 322..325
/note="DEAH box"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
VAR_SEQ 447..458
/note="STLYNHFISSKN -> TTYNGCLCMQ (in isoform 2)"
/id="VSP_057104"
SEQUENCE 910 AA; 101858 MW; 3423B9EC60C0D8AE CRC64;
MEEEDEEILS SSDCDDSSDS YKDDSQDSEG ENDNPECEDL AVVSLSSDAD RKSKNVKDLL
RGNLVVQRQP LLPRVLSVSD GAAVCRKPFK PPCSHGYDST GQLSRRLSAR KRFVPWGSST
PVVVALPTKL EASTNIERDE EEEVVCLPPD IEPLVLWQSE EDGMSNVTTI MVHSVLVKFL
RPHQREGVQF MFDCVSGLHG SANINGCILA DDMGLGKTLQ SITLLYTLLC QGFDGTPMVK
KAIIVTPTSL VSNWEAEIKK WVGDRIQLIA LCESTRDDVL SGIDSFTRPR SALQVLIISY
ETFRMHSSKF CQSESCDLLI CDEAHRLKND QTLTNRALAS LTCKRRVLLS GTPMQNDLEE
FFAMVNFTNP GSLGDAAHFR HYYEAPIICG REPTATEEEK NLAADRSAEL SSKVNQFILR
RTNALLSNHL PPKIIEVVCC KMTTLQSTLY NHFISSKNLK RALADNAKQT KVLAYITALK
KLCNHPKLIY DTIKSGNPGT VGFENCLEFF PAEMFSGRSG AWTGGDGAWV ELSGKMHVLS
RLLANLRRKT DDRIVLVSNY TQTLDLFAQL CRERRYPFLR LDGSTTISKR QKLVNRLNDP
TKDEFAFLLS SKAGGCGLNL IGANRLVLFD PDWNPANDKQ AAARVWRDGQ KKRVYVYRFL
STGTIEEKVY QRQMSKEGLQ KVIQHEQTDN STRQGNLLST EDLRDLFSFH GDVRSEIHEK
MSCSRCQNDA SGTENIEEGN ENNVDDNACQ IDQEDIGGFA KDAGCFNLLK NSERQVGTPL
EEDLGSWGHH FTSKSVPDAI LQASAGDEVT FVFTNQVDGK LVPIESNVSP KTVESEEHNR
NQPVNKRAFN KPQQRPREPL QPLSLNETTK RVKLSTYKRL HGNSNIDDAQ IKMSLQRPNL
VSVNHDDDFV


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[ERCC6 CSB] DNA excision repair protein ERCC-6 (EC 3.6.4.-) (ATP-dependent helicase ERCC6) (Cockayne syndrome protein CSB)
[Iswi CG8625] Chromatin-remodeling complex ATPase chain Iswi (EC 3.6.4.-) (CHRAC 140 kDa subunit) (Nucleosome-remodeling factor 140 kDa subunit) (NURF-140) (Protein imitation swi)
[mit1 SPBP35G2.10] Chromatin remodeling factor mit1 (EC 3.6.4.-) (Mi2-like interacting with clr3 protein 1) (Snf2/Hdac-containing repressor complex protein mit1) (SHREC protein mit1)
[RDH54 TID1 YBR073W YBR0715] DNA repair and recombination protein RDH54 (RAD homolog 54) (Recombination factor TID1) (Two hybrid interaction with DMC1 protein 1) [Includes: DNA topoisomerase (EC 5.99.1.-); Putative helicase (EC 3.6.4.12)]
[Smarca4 Baf190a Brg1 Snf2b Snf2l4] Transcription activator BRG1 (EC 3.6.4.-) (ATP-dependent helicase SMARCA4) (BRG1-associated factor 190A) (BAF190A) (Protein brahma homolog 1) (SNF2-beta) (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4)
[CHR17 At5g18620] ISWI chromatin-remodeling complex ATPase CHR17 (EC 3.6.4.-) (Protein CHROMATIN REMODELING 17)
[HLTF HIP116A RNF80 SMARCA3 SNF2L3 ZBU1] Helicase-like transcription factor (EC 2.3.2.27) (EC 3.6.4.-) (DNA-binding protein/plasminogen activator inhibitor 1 regulator) (HIP116) (RING finger protein 80) (RING-type E3 ubiquitin transferase HLTF) (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3) (Sucrose nonfermenting protein 2-like 3)
[Hltf Smarca3 Snf2l3 Zbu1] Helicase-like transcription factor (EC 2.3.2.27) (EC 3.6.4.-) (P113) (RING-type E3 ubiquitin transferase HLTF) (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3) (Sucrose nonfermenting protein 2-like 3) (TNF-response element-binding protein)

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