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Protein

General transcription and DNA repair factor IIH helicase subunit XPB1

Gene

XPB1

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

Functioni

ATP-dependent 3'-5' DNA helicase, component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. The ATPase activity of XPB, but not its helicase activity, is required for DNA opening. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. The ATP-dependent helicase activity of XPB is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription (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)DescriptionActionsGraphical viewLength
Nucleotide bindingi306 – 313ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Helicase, Hydrolase
Biological processDNA damage, DNA repair, Transcription, Transcription regulation
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

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:
General transcription and DNA repair factor IIH helicase subunit XPB1 (EC:3.6.4.12)
Short name:
TFIIH subunit XPB
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

Organism-specific databases

AraportiAT5G41370
TAIRilocus:2177901 AT5G41370

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001019911 – 767General transcription and DNA repair factor IIH helicase subunit XPB1Add BLAST767

Proteomic databases

PaxDbiQ38861
PRIDEiQ38861

PTM databases

iPTMnetiQ38861

Expressioni

Tissue specificityi

Expressed ubiquitously.1 Publication

Gene expression databases

ExpressionAtlasiQ38861 baseline and differential
GenevisibleiQ38861 AT

Interactioni

Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB, XPD, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5, which is active in NER. The core complex associates with the 3-subunit CDK-activating kinase (CAK) module composed of CYCH1/cyclin H1, CDKD and MAT1/At4g30820 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.By similarity1 Publication

Protein-protein interaction databases

BioGridi19390, 1 interactor
IntActiQ38861, 1 interactor
STRINGi3702.AT5G41370.1

Structurei

3D structure databases

ProteinModelPortaliQ38861
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini293 – 455Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST163
Domaini510 – 676Helicase C-terminalPROSITE-ProRule annotationAdd BLAST167

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi408 – 411DEVH box4
Motifi750 – 766Nuclear localization signalSequence analysisAdd BLAST17

Sequence similaritiesi

Belongs to the helicase family. RAD25/XPB subfamily.Curated

Phylogenomic databases

eggNOGiKOG1123 Eukaryota
COG1061 LUCA
HOGENOMiHOG000160172
InParanoidiQ38861
KOiK10843
OMAiTKHVHPL
OrthoDBiEOG0936038E
PhylomeDBiQ38861

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR032438 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
PfamiView protein in Pfam
PF16203 ERCC3_RAD25_C, 1 hit
PF13625 Helicase_C_3, 1 hit
PF04851 ResIII, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 3 hits
TIGRFAMsiTIGR00603 rad25, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit

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 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_123502.3
UniGeneiAt.6482

Genome annotation databases

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

Entry informationi

Entry nameiXPB1_ARATH
AccessioniPrimary (citable) accession number: Q38861
Secondary accession number(s): O04171, Q6JA92, Q9FN63
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: March 1, 2001
Last modified: April 25, 2018
This is version 141 of the entry and version 3 of the sequence. See 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

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