XPB1_ARATH
ID XPB1_ARATH Reviewed; 767 AA.
AC Q38861; O04171; Q6JA92; Q9FN63;
DT 04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 3.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB1;
DE Short=TFIIH subunit XPB;
DE EC=3.6.4.12;
DE AltName: Full=ERCC3 homolog 1;
DE AltName: Full=Protein araXPB;
DE AltName: Full=RAD25 homolog 1;
DE Short=AtXPB1;
DE AltName: Full=XPB homolog 1;
GN Name=XPB1; Synonyms=XPB; OrderedLocusNames=At5g41370; ORFNames=MYC6.8;
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], AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=9524267; DOI=10.1016/s0378-1119(97)00656-2;
RA Ribeiro D.T., Machado C.R., Costa R.M.A., Praekelt U.M., Van Sluys M.-A.,
RA Menck C.F.M.;
RT "Cloning of a cDNA from Arabidopsis thaliana homologous to the human XPB
RT gene.";
RL Gene 208:207-213(1998).
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 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 [6]
RP FUNCTION.
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 [7]
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 [8]
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 (By similarity). Required during the early
CC stages of development, including seed germination (PubMed:11737776).
CC {ECO:0000250|UniProtKB:P19447, ECO:0000269|PubMed:11737776}.
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 -!- TISSUE SPECIFICITY: Expressed ubiquitously.
CC {ECO:0000269|PubMed:9524267}.
CC -!- SIMILARITY: Belongs to the helicase family. RAD25/XPB subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08509.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; U29168; AAC49987.2; -; mRNA.
DR EMBL; AY550923; AAT36215.1; -; Genomic_DNA.
DR EMBL; AB006707; BAB08509.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED94670.1; -; Genomic_DNA.
DR EMBL; AY039547; AAK62602.1; -; mRNA.
DR EMBL; AY113008; AAM47316.1; -; mRNA.
DR PIR; S71206; S71206.
DR RefSeq; NP_568592.1; NM_123502.3.
DR AlphaFoldDB; Q38861; -.
DR SMR; Q38861; -.
DR BioGRID; 19390; 1.
DR IntAct; Q38861; 1.
DR STRING; 3702.AT5G41370.1; -.
DR iPTMnet; Q38861; -.
DR PaxDb; Q38861; -.
DR PRIDE; Q38861; -.
DR ProteomicsDB; 242578; -.
DR EnsemblPlants; AT5G41370.1; AT5G41370.1; AT5G41370.
DR GeneID; 834139; -.
DR Gramene; AT5G41370.1; AT5G41370.1; AT5G41370.
DR KEGG; ath:AT5G41370; -.
DR Araport; AT5G41370; -.
DR TAIR; locus:2177901; AT5G41370.
DR eggNOG; KOG1123; Eukaryota.
DR HOGENOM; CLU_008213_0_0_1; -.
DR InParanoid; Q38861; -.
DR OMA; PTHIHEY; -.
DR OrthoDB; 100698at2759; -.
DR PhylomeDB; Q38861; -.
DR PRO; PR:Q38861; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q38861; baseline and differential.
DR Genevisible; Q38861; AT.
DR GO; GO:0005737; C:cytoplasm; HDA:TAIR.
DR GO; GO:0000112; C:nucleotide-excision repair factor 3 complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
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:0009411; P:response to UV; 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..767
FT /note="General transcription and DNA repair factor IIH
FT helicase subunit XPB1"
FT /id="PRO_0000101991"
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..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 742..767
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 408..411
FT /note="DEVH box"
FT MOTIF 750..766
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 BINDING 306..313
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ SEQUENCE 767 AA; 87062 MW; 4F7464797F66CCBC CRC64;
MGNGERGRPN KKMKYGGKDD QKMKNIQNAE DYYDDADEDS RDGEGEEKKR DFTKLELKPD
HGNRPLWACA DGRIFLETFS PLYKQAYDFL IAIAEPVCRP ESMHEYNLTP HSLYAAVSVG
LETETIISVL NKLSKTKLPK EMIEFIHAST ANYGKVKLVL KKNRYFIESP FPEVLKRLLS
DDVINRARFS SEPYYGGDGF SVGRTCGELE AGPGELLNEA EFAAAAEEKE THSFEIDPAQ
VENVKQRCLP NALNYPMLEE YDFRNDNVNP DLDMELKPHA QPRPYQEKSL SKMFGNGRAR
SGIIVLPCGA GKSLVGVSAA ARIKKSCLCL ATNAVSVDQW AFQFKLWSTI RDDQICRFTS
DSKERFRGNA GVVVTTYNMV AFGGKRSEES EKIIEEMRNR EWGLLLMDEV HVVPAHMFRK
VISITKSHCK LGLTATLVRE DERITDLNFL IGPKLYEANW LDLVKGGFIA NVQCAEVWCP
MTKEFFAEYL KKENSKKKQA LYVMNPNKFR ACEFLIRFHE QQRGDKIIVF ADNLFALTEY
AMKLRKPMIY GATSHIERTK ILEAFKTSKD VNTVFLSKVG DNSIDIPEAN VIIQISSHAG
SRRQEAQRLG RILRAKGKLE DRMAGGKEEY NAFFYSLVST DTQEMYYSTK RQQFLIDQGY
SFKVITSLPP PDAGSSLSYH SQEEQLSLLG KVMNAGDDLV GLEQLEEDTD GMALQKARRS
MGSMSVMSGS KGMVYMEYNS GRHKSGQQFK KPKDPTKRHN LFKKRYV
