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Protein

General transcription and DNA repair factor IIH helicase subunit XPB

Gene

SSL2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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 TFIIK, 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/SSL2, 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/SSL2 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 TFIIK controls the initiation of transcription (PubMed:8269516, PubMed:7693549, PubMed:7961739, PubMed:8202161, PubMed:7813015, PubMed:8631896). XPB/SSL2 acts as a double-stranded DNA translocase promoting DNA opening by tracking along the nontemplate promoter strand, rotating and inserting DNA into the Pol II active site cleft, leading to DNA unwinding. May also use this translocase mechanism during DNA repair rather than physically wedging open damaged DNA (PubMed:25775526).7 Publications

Miscellaneous

A C-terminal deletion renders yeast hypersensitive to UV light.
Present with 825 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi386 – 393ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • 3'-5' DNA helicase activity Source: GO_Central
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent DNA helicase activity Source: SGD
  • DNA binding Source: UniProtKB-KW
  • DNA translocase activity Source: SGD
  • transcription factor binding Source: GO_Central

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

BioCyciYEAST:G3O-31393-MONOMER
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-72086 mRNA Capping
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-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 XPB (EC:3.6.4.12)
Short name:
TFIIH subunit XPB
Alternative name(s):
DNA repair helicase RAD25
RNA polymerase II transcription factor B subunit SSL2
Short name:
TFB subunit SSL2
Suppressor of stem-loop mutation 2
Gene namesi
Name:SSL2
Synonyms:LOM3, RAD25, UVS112
Ordered Locus Names:YIL143C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

SGDiS000001405 SSL2

Subcellular locationi

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001019941 – 843General transcription and DNA repair factor IIH helicase subunit XPBAdd BLAST843

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei752PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ00578
PaxDbiQ00578
PRIDEiQ00578
TopDownProteomicsiQ00578

PTM databases

iPTMnetiQ00578

Interactioni

Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB/SSL2, XPD/RAD3, SSL1, TFB1, TFB2, TFB4 and TFB5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of CCL1, KIN28 and TFB3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.3 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi34849, 126 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-731N
IntActiQ00578, 23 interactors
MINTiQ00578
STRINGi4932.YIL143C

Structurei

3D structure databases

ProteinModelPortaliQ00578
SMRiQ00578
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini373 – 535Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST163
Domaini589 – 743Helicase C-terminalPROSITE-ProRule annotationAdd BLAST155

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi64 – 75Nuclear localization signalSequence analysisAdd BLAST12
Motifi487 – 491DEVH box5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi302 – 309Asp/Glu-rich (acidic)8

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00390000002204
HOGENOMiHOG000160172
InParanoidiQ00578
KOiK10843
OMAiTKHVHPL
OrthoDBiEOG092C0I1P

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, 2 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.

Q00578-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG
60 70 80 90 100
RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI
110 120 130 140 150
PADFVPDSVS GMFRSHDFSY LRLRPDHASR PLWISPSDGR IILESFSPLA
160 170 180 190 200
EQAQDFLVTI AEPISRPSHI HEYKITAYSL YAAVSVGLET DDIISVLDRL
210 220 230 240 250
SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD ILQMLLNDSV
260 270 280 290 300
IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD
310 320 330 340 350
NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP
360 370 380 390 400
DLDIDLKPST QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA
410 420 430 440 450
CTIKKSVIVL CTSSVSVMQW RQQFLQWCTL QPENCAVFTS DNKEMFQTES
460 470 480 490 500
GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR EWGFIILDEV HVVPAAMFRR
510 520 530 540 550
VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW MELSQKGHIA
560 570 580 590 600
NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER
610 620 630 640 650
RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN
660 670 680 690 700
TIFLSKVGDT SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG
710 720 730 740 750
FNAFFYSLVS KDTQEMYYST KRQAFLVDQG YAFKVITHLH GMENIPNLAY
760 770 780 790 800
ASPRERRELL QEVLLKNEEA AGIEVGDDAD NSVGRGSNGH KRFKSKAVRG
810 820 830 840
EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK
Length:843
Mass (Da):95,341
Last modified:April 1, 1993 - v1
Checksum:iFA4013E8156FE1C5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti9P → S in AAA34942 (PubMed:1333609).Curated1
Sequence conflicti48S → L in AAA34942 (PubMed:1333609).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti427W → L in suppressor mutant. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38059 Genomic DNA Translation: CAA86135.1
M94176 Genomic DNA Translation: AAA35102.1
L01414 Genomic DNA Translation: AAA34942.1
AY692883 Genomic DNA Translation: AAT92902.1
BK006942 Genomic DNA Translation: DAA08410.1
PIRiS31272
RefSeqiNP_012123.1, NM_001179491.1

Genome annotation databases

EnsemblFungiiYIL143C; YIL143C; YIL143C
GeneIDi854663
KEGGisce:YIL143C

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38059 Genomic DNA Translation: CAA86135.1
M94176 Genomic DNA Translation: AAA35102.1
L01414 Genomic DNA Translation: AAA34942.1
AY692883 Genomic DNA Translation: AAT92902.1
BK006942 Genomic DNA Translation: DAA08410.1
PIRiS31272
RefSeqiNP_012123.1, NM_001179491.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.001294-785[»]
5OQJelectron microscopy4.7071-843[»]
5OQMelectron microscopy5.8071-843[»]
5SVAelectron microscopy15.30Z1-843[»]
ProteinModelPortaliQ00578
SMRiQ00578
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34849, 126 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-731N
IntActiQ00578, 23 interactors
MINTiQ00578
STRINGi4932.YIL143C

PTM databases

iPTMnetiQ00578

Proteomic databases

MaxQBiQ00578
PaxDbiQ00578
PRIDEiQ00578
TopDownProteomicsiQ00578

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYIL143C; YIL143C; YIL143C
GeneIDi854663
KEGGisce:YIL143C

Organism-specific databases

SGDiS000001405 SSL2

Phylogenomic databases

GeneTreeiENSGT00390000002204
HOGENOMiHOG000160172
InParanoidiQ00578
KOiK10843
OMAiTKHVHPL
OrthoDBiEOG092C0I1P

Enzyme and pathway databases

BioCyciYEAST:G3O-31393-MONOMER
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-72086 mRNA Capping
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-77075 RNA Pol II CTD phosphorylation and interaction with CE

Miscellaneous databases

PROiPR:Q00578

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, 2 hits
TIGRFAMsiTIGR00603 rad25, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRAD25_YEAST
AccessioniPrimary (citable) accession number: Q00578
Secondary accession number(s): D6VVE4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: November 7, 2018
This is version 181 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names
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Main funding by: National Institutes of Health

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