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Protein

DNA repair helicase XPB1

Gene

XPB1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Putative ATP-dependent 3'-5' DNA helicase involved in nucleotide excision repair (NER) of DNA. May be involved in RNA transcription by RNA polymerase II. Acts by opening DNA around either the RNA transcription start site or the DNA damage (By similarity). Required during the early stages of development, including seed germination (PubMed:11737776).By similarity1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi306 – 3138ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:GQT-1908-MONOMER.
ReactomeiR-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-5696395. Formation of Incision Complex in GG-NER.
R-ATH-5696400. Dual Incision in GG-NER.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair helicase XPB1 (EC:3.6.4.12)
Alternative name(s):
ERCC3 homolog 1
Protein araXPB
RAD25 homolog 1
Short name:
AtXPB1
XPB homolog 1
Gene namesi
Name:XPB1
Synonyms:XPB
Ordered Locus Names:At5g41370
ORF Names:MYC6.8
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G41370.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 767767DNA repair helicase XPB1PRO_0000101991Add
BLAST

Proteomic databases

PaxDbiQ38861.
PRIDEiQ38861.

PTM databases

iPTMnetiQ38861.

Expressioni

Tissue specificityi

Expressed ubiquitously.1 Publication

Gene expression databases

GenevisibleiQ38861. AT.

Interactioni

Subunit structurei

Component of the TFIIH core complex, which is composed of 7 subunits, XPD, XPB, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5.1 Publication

Protein-protein interaction databases

BioGridi19390. 1 interaction.
IntActiQ38861. 1 interaction.
MINTiMINT-8070993.
STRINGi3702.AT5G41370.1.

Structurei

3D structure databases

ProteinModelPortaliQ38861.
SMRiQ38861. Positions 283-697.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini293 – 455163Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini510 – 676167Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi408 – 4114DEVH box
Motifi750 – 76617Nuclear localization signalSequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the helicase family. RAD25/XPB subfamily.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1123. Eukaryota.
COG1061. LUCA.
HOGENOMiHOG000160172.
InParanoidiQ38861.
KOiK10843.
OMAiREREWGL.
PhylomeDBiQ38861.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR032438. ERCC3_RAD25_C.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001161. XPB/Ssl2.
IPR032830. XPB/Ssl2_N.
[Graphical view]
PfamiPF16203. ERCC3_RAD25_C. 1 hit.
PF13625. Helicase_C_3. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR00603. rad25. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q38861-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGNGERGRPN KKMKYGGKDD QKMKNIQNAE DYYDDADEDS RDGEGEEKKR
60 70 80 90 100
DFTKLELKPD HGNRPLWACA DGRIFLETFS PLYKQAYDFL IAIAEPVCRP
110 120 130 140 150
ESMHEYNLTP HSLYAAVSVG LETETIISVL NKLSKTKLPK EMIEFIHAST
160 170 180 190 200
ANYGKVKLVL KKNRYFIESP FPEVLKRLLS DDVINRARFS SEPYYGGDGF
210 220 230 240 250
SVGRTCGELE AGPGELLNEA EFAAAAEEKE THSFEIDPAQ VENVKQRCLP
260 270 280 290 300
NALNYPMLEE YDFRNDNVNP DLDMELKPHA QPRPYQEKSL SKMFGNGRAR
310 320 330 340 350
SGIIVLPCGA GKSLVGVSAA ARIKKSCLCL ATNAVSVDQW AFQFKLWSTI
360 370 380 390 400
RDDQICRFTS DSKERFRGNA GVVVTTYNMV AFGGKRSEES EKIIEEMRNR
410 420 430 440 450
EWGLLLMDEV HVVPAHMFRK VISITKSHCK LGLTATLVRE DERITDLNFL
460 470 480 490 500
IGPKLYEANW LDLVKGGFIA NVQCAEVWCP MTKEFFAEYL KKENSKKKQA
510 520 530 540 550
LYVMNPNKFR ACEFLIRFHE QQRGDKIIVF ADNLFALTEY AMKLRKPMIY
560 570 580 590 600
GATSHIERTK ILEAFKTSKD VNTVFLSKVG DNSIDIPEAN VIIQISSHAG
610 620 630 640 650
SRRQEAQRLG RILRAKGKLE DRMAGGKEEY NAFFYSLVST DTQEMYYSTK
660 670 680 690 700
RQQFLIDQGY SFKVITSLPP PDAGSSLSYH SQEEQLSLLG KVMNAGDDLV
710 720 730 740 750
GLEQLEEDTD GMALQKARRS MGSMSVMSGS KGMVYMEYNS GRHKSGQQFK
760
KPKDPTKRHN LFKKRYV
Length:767
Mass (Da):87,062
Last modified:March 1, 2001 - v3
Checksum:i4F7464797F66CCBC
GO

Sequence cautioni

The sequence BAB08509.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29168 mRNA. Translation: AAC49987.2.
AY550923 Genomic DNA. Translation: AAT36215.1.
AB006707 Genomic DNA. Translation: BAB08509.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED94670.1.
AY039547 mRNA. Translation: AAK62602.1.
AY113008 mRNA. Translation: AAM47316.1.
PIRiS71206.
RefSeqiNP_568592.1. NM_123502.2.
UniGeneiAt.6482.

Genome annotation databases

EnsemblPlantsiAT5G41370.1; AT5G41370.1; AT5G41370.
GeneIDi834139.
GrameneiAT5G41370.1; AT5G41370.1; AT5G41370.
KEGGiath:AT5G41370.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29168 mRNA. Translation: AAC49987.2.
AY550923 Genomic DNA. Translation: AAT36215.1.
AB006707 Genomic DNA. Translation: BAB08509.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED94670.1.
AY039547 mRNA. Translation: AAK62602.1.
AY113008 mRNA. Translation: AAM47316.1.
PIRiS71206.
RefSeqiNP_568592.1. NM_123502.2.
UniGeneiAt.6482.

3D structure databases

ProteinModelPortaliQ38861.
SMRiQ38861. Positions 283-697.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19390. 1 interaction.
IntActiQ38861. 1 interaction.
MINTiMINT-8070993.
STRINGi3702.AT5G41370.1.

PTM databases

iPTMnetiQ38861.

Proteomic databases

PaxDbiQ38861.
PRIDEiQ38861.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G41370.1; AT5G41370.1; AT5G41370.
GeneIDi834139.
GrameneiAT5G41370.1; AT5G41370.1; AT5G41370.
KEGGiath:AT5G41370.

Organism-specific databases

TAIRiAT5G41370.

Phylogenomic databases

eggNOGiKOG1123. Eukaryota.
COG1061. LUCA.
HOGENOMiHOG000160172.
InParanoidiQ38861.
KOiK10843.
OMAiREREWGL.
PhylomeDBiQ38861.

Enzyme and pathway databases

BioCyciARA:GQT-1908-MONOMER.
ReactomeiR-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-5696395. Formation of Incision Complex in GG-NER.
R-ATH-5696400. Dual Incision in GG-NER.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PROiQ38861.

Gene expression databases

GenevisibleiQ38861. AT.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR032438. ERCC3_RAD25_C.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001161. XPB/Ssl2.
IPR032830. XPB/Ssl2_N.
[Graphical view]
PfamiPF16203. ERCC3_RAD25_C. 1 hit.
PF13625. Helicase_C_3. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR00603. rad25. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning of a cDNA from Arabidopsis thaliana homologous to the human XPB gene."
    Ribeiro D.T., Machado C.R., Costa R.M.A., Praekelt U.M., Van Sluys M.-A., Menck C.F.M.
    Gene 208:207-213(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  2. "Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of AtXPB2 and expression analysis."
    Morgante P.G., Berra C.M., Nakabashi M., Costa R.M.A., Menck C.F.M., Van Sluys M.-A.
    Gene 344:93-103(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Landsberg erecta.
  3. "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones."
    Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N., Tabata S.
    DNA Res. 4:291-300(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "The participation of AtXPB1, the XPB/RAD25 homologue gene from Arabidopsis thaliana, in DNA repair and plant development."
    Costa R.M.A., Morgante P.G., Berra C.M., Nakabashi M., Bruneau D., Bouchez D., Sweder K.S., Van Sluys M.-A., Menck C.F.M.
    Plant J. 28:385-395(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Components of nucleotide excision repair and DNA damage tolerance in Arabidopsis thaliana."
    Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.
    Environ. Mol. Mutagen. 45:115-127(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: COMPONENT OF TFIIH CORE COMPLEX, NOMENCLATURE.
  8. "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."
    Xu R., Zhang S., Huang J., Zheng C.
    PLoS ONE 8:E78982-E78982(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.

Entry informationi

Entry nameiXPB1_ARATH
AccessioniPrimary (citable) accession number: Q38861
Secondary accession number(s): O04171, Q6JA92, Q9FN63
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: March 1, 2001
Last modified: June 8, 2016
This is version 128 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.