XPB2_ARATH
ID XPB2_ARATH Reviewed; 766 AA.
AC Q9FUG4; Q9FN64;
DT 04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB2;
DE Short=TFIIH subunit XPB;
DE EC=3.6.4.12;
DE AltName: Full=ERCC3 homolog 2;
DE AltName: Full=RAD25 homolog 2;
DE Short=AtXPB2;
DE AltName: Full=XPB homolog 2;
GN Name=XPB2; OrderedLocusNames=At5g41360; ORFNames=MYC6.7;
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 [MRNA].
RX PubMed=11737776; DOI=10.1046/j.1365-313x.2001.01162.x;
RA Costa R.M.A., Morgante P.G., Berra C.M., Nakabashi M., Bruneau D.,
RA Bouchez D., Sweder K.S., Van Sluys M.-A., Menck C.F.M.;
RT "The participation of AtXPB1, the XPB/RAD25 homologue gene from Arabidopsis
RT thaliana, in DNA repair and plant development.";
RL Plant J. 28:385-395(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=15656976; DOI=10.1016/j.gene.2004.10.006;
RA Morgante P.G., Berra C.M., Nakabashi M., Costa R.M.A., Menck C.F.M.,
RA Van Sluys M.-A.;
RT "Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of
RT AtXPB2 and expression analysis.";
RL Gene 344:93-103(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
RN [4]
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 [5]
RP COMPONENT OF TFIIH CORE COMPLEX, AND NOMENCLATURE.
RX PubMed=15645454; DOI=10.1002/em.20094;
RA Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.;
RT "Components of nucleotide excision repair and DNA damage tolerance in
RT Arabidopsis thaliana.";
RL Environ. Mol. Mutagen. 45:115-127(2005).
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: ATP-dependent 3'-5' DNA helicase, component of the general
CC transcription and DNA repair factor IIH (TFIIH) core complex, which is
CC involved in general and transcription-coupled nucleotide excision
CC repair (NER) of damaged DNA and, when complexed to CAK, in RNA
CC transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA
CC around the lesion to allow the excision of the damaged oligonucleotide
CC and its replacement by a new DNA fragment. The ATPase activity of XPB,
CC but not its helicase activity, is required for DNA opening. In
CC transcription, TFIIH has an essential role in transcription initiation.
CC When the pre-initiation complex (PIC) has been established, TFIIH is
CC required for promoter opening and promoter escape. The ATP-dependent
CC helicase activity of XPB is required for promoter opening and promoter
CC escape. Phosphorylation of the C-terminal tail (CTD) of the largest
CC subunit of RNA polymerase II by the kinase module CAK controls the
CC initiation of transcription. {ECO:0000250|UniProtKB:P19447}.
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; EC=3.6.4.12;
CC -!- SUBUNIT: Component of the 7-subunit TFIIH core complex composed of XPB,
CC XPD, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5,
CC which is active in NER. The core complex associates with the 3-subunit
CC CDK-activating kinase (CAK) module composed of CYCH1/cyclin H1, CDKD
CC and MAT1/At4g30820 to form the 10-subunit holoenzyme (holo-TFIIH)
CC active in transcription. {ECO:0000250|UniProtKB:P19447,
CC ECO:0000305|PubMed:15645454}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the helicase family. RAD25/XPB subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08508.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF308595; AAG27465.1; -; mRNA.
DR EMBL; AY550923; AAT36214.1; -; Genomic_DNA.
DR EMBL; AB006707; BAB08508.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED94669.1; -; Genomic_DNA.
DR PIR; S71206; S71206.
DR RefSeq; NP_568591.1; NM_123501.3.
DR AlphaFoldDB; Q9FUG4; -.
DR SMR; Q9FUG4; -.
DR BioGRID; 19389; 1.
DR STRING; 3702.AT5G41360.1; -.
DR PaxDb; Q9FUG4; -.
DR PRIDE; Q9FUG4; -.
DR ProteomicsDB; 242792; -.
DR EnsemblPlants; AT5G41360.1; AT5G41360.1; AT5G41360.
DR GeneID; 834138; -.
DR Gramene; AT5G41360.1; AT5G41360.1; AT5G41360.
DR KEGG; ath:AT5G41360; -.
DR Araport; AT5G41360; -.
DR TAIR; locus:2177891; AT5G41360.
DR eggNOG; KOG1123; Eukaryota.
DR HOGENOM; CLU_008213_0_0_1; -.
DR InParanoid; Q9FUG4; -.
DR OrthoDB; 100698at2759; -.
DR PhylomeDB; Q9FUG4; -.
DR PRO; PR:Q9FUG4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FUG4; baseline and differential.
DR Genevisible; Q9FUG4; AT.
DR GO; GO:0000112; C:nucleotide-excision repair factor 3 complex; IBA:GO_Central.
DR GO; GO:0005675; C:transcription factor TFIIH holo complex; IBA:GO_Central.
DR GO; GO:0097550; C:transcription preinitiation complex; IBA:GO_Central.
DR GO; GO:0043138; F:3'-5' DNA helicase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0033683; P:nucleotide-excision repair, DNA incision; IBA:GO_Central.
DR GO; GO:0010224; P:response to UV-B; IEP:TAIR.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR032438; ERCC3_RAD25_C.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR001161; XPB/Ssl2.
DR InterPro; IPR032830; XPB/Ssl2_N.
DR Pfam; PF16203; ERCC3_RAD25_C; 1.
DR Pfam; PF13625; Helicase_C_3; 1.
DR Pfam; PF04851; ResIII; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR TIGRFAMs; TIGR00603; rad25; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; DNA damage; DNA repair; DNA-binding; Helicase; Hydrolase;
KW Nucleotide-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..766
FT /note="General transcription and DNA repair factor IIH
FT helicase subunit XPB2"
FT /id="PRO_0000101992"
FT DOMAIN 293..455
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 510..676
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..56
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 739..766
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 408..411
FT /note="DEVH box"
FT MOTIF 749..765
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 1..31
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 42..56
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 306..313
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 766 AA; 86736 MW; 45F17E5291C0C73A CRC64;
MGNDERKRPT KKMKYGGKDD QKMKNIQNVE DYYDDADEDS RDGEGEEKRR DFTDLELKPD
HGNRPLWACA DGKIFLETFS PLYKQAYDFL IAIAEPVCRP ESMHEYNLTP HSLYAAVSVG
LETETIISVL NKLSKTKLPG EIIDFIHAST ANYGKVKLVL KKNRYFIESP FPEVLKRLLS
DDVINRARFT SEPYYGGDGF TIGKTSGELE AGPGELLNEA ELAAAAEEKE THSFEIDPAL
VENVKQRCLP NALNYPMLEE YDFRNDNVNP DLDMELKPHA QPRPYQEKSL SKMFGNGRAR
SGIIVLPCGA GKSLVGVSAA ARIKKSCLCL ATNAVSVDQW AYQFKLWSTI KDDQICRFTS
DSKERFRGNA GVVVTTYNMI AFGGKRSEEA EKIIEEMRNR EWGLLLMDEV HVVPAHMFRK
VISITKSHCK LGLTATLVRE DEKITDLNFL IGPKLYEANW LDLVKGGFIA NVQCAEVWCP
MTKEFFAEYL KKENSKKKQA LYVMNPNKFR ACEFLIRFHE QQRGDKIIVF ADNLFALTEY
AMKLRKPMIY GATSHIERTK ILEAFKTSKT VNTVFLSKVG DNSIDIPEAN VIIQISSHAG
SRRQEAQRLG RILRAKGKLE DRMAGGKEEY NAFFYSLVST DTQEMYYSTK RQQFLIDQGY
SFKVITSLPP PDAGSSLGYH SQEEQLSLLG KVLNAGDDMV GLEQLEEDTD GKALKTRRSM
GSMSAMSGAN GRVYMEYNSG RQKSGNQSKK PKDPTKRHNI FKKRYV
