UniProtKB - Q00578 (RAD25_YEAST)
Protein
General transcription and DNA repair factor IIH helicase subunit XPB
Gene
SSL2
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
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
- EC:3.6.4.12
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 386 – 393 | ATPPROSITE-ProRule annotation | 8 |
GO - Molecular functioni
- 3'-5' DNA helicase activity Source: GO_Central
- ATP binding Source: UniProtKB-KW
- DNA binding Source: UniProtKB-KW
- DNA helicase activity Source: SGD
- DNA translocase activity Source: SGD
- transcription factor binding Source: GO_Central
GO - Biological processi
- DNA duplex unwinding Source: SGD
- nucleotide-excision repair, DNA incision Source: SGD
- phosphorylation of RNA polymerase II C-terminal domain Source: SGD
- poly(A)+ mRNA export from nucleus Source: SGD
- promoter clearance from RNA polymerase II promoter Source: SGD
- regulation of mitotic recombination Source: SGD
- regulation of transposition, RNA-mediated Source: SGD
- response to UV Source: GO_Central
- transcription by RNA polymerase II Source: SGD
- transcription initiation from RNA polymerase II promoter Source: SGD
- transcription open complex formation at RNA polymerase II promoter Source: SGD
Keywordsi
Molecular function | DNA-binding, Helicase, Hydrolase |
Biological process | DNA damage, DNA repair, Transcription, Transcription regulation |
Ligand | ATP-binding, Nucleotide-binding |
Enzyme and pathway databases
Reactomei | R-SCE-113418, Formation of the Early Elongation Complex 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-73772, RNA Polymerase I Promoter Escape 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-75955, RNA Polymerase II Transcription Elongation 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 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000001405, SSL2 |
VEuPathDBi | FungiDB:YIL143C |
Subcellular locationi
Nucleus
Cytosol
- cytosol Source: SGD
Nucleus
- nucleotide-excision repair factor 3 complex Source: SGD
- nucleus Source: SGD
- transcription factor TFIIH core complex Source: SGD
- transcription factor TFIIH holo complex Source: SGD
Other locations
- transcription preinitiation complex Source: SGD
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000101994 | 1 – 843 | General transcription and DNA repair factor IIH helicase subunit XPBAdd BLAST | 843 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 752 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
MaxQBi | Q00578 |
PaxDbi | Q00578 |
PRIDEi | Q00578 |
TopDownProteomicsi | Q00578 |
PTM databases
iPTMneti | Q00578 |
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 PublicationsGO - Molecular functioni
- transcription factor binding Source: GO_Central
Protein-protein interaction databases
BioGRIDi | 34849, 128 interactors |
ComplexPortali | CPX-1659, General transcription factor complex TFIIH |
DIPi | DIP-731N |
IntActi | Q00578, 23 interactors |
MINTi | Q00578 |
STRINGi | 4932.YIL143C |
Miscellaneous databases
RNActi | Q00578, protein |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 373 – 535 | Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST | 163 | |
Domaini | 589 – 743 | Helicase C-terminalPROSITE-ProRule annotationAdd BLAST | 155 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 64 – 75 | Nuclear localization signalSequence analysisAdd BLAST | 12 | |
Motifi | 487 – 491 | DEVH box | 5 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 302 – 309 | Asp/Glu-rich (acidic) | 8 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG1123, Eukaryota |
GeneTreei | ENSGT00390000002204 |
HOGENOMi | CLU_008213_0_0_1 |
InParanoidi | Q00578 |
OMAi | SQEWGLM |
Family and domain databases
InterProi | View 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 |
Pfami | View protein in Pfam PF16203, ERCC3_RAD25_C, 1 hit PF13625, Helicase_C_3, 1 hit PF04851, ResIII, 1 hit |
SMARTi | View protein in SMART SM00487, DEXDc, 1 hit SM00490, HELICc, 1 hit |
SUPFAMi | SSF52540, SSF52540, 2 hits |
TIGRFAMsi | TIGR00603, rad25, 1 hit |
PROSITEi | View protein in PROSITE PS51192, HELICASE_ATP_BIND_1, 1 hit PS51194, HELICASE_CTER, 1 hit |
i Sequence
Sequence statusi: Complete.
Q00578-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 9 | P → S in AAA34942 (PubMed:1333609).Curated | 1 | |
Sequence conflicti | 48 | S → L in AAA34942 (PubMed:1333609).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural varianti | 427 | W → L in suppressor mutant. 1 Publication | 1 |
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 |
PIRi | S31272 |
RefSeqi | NP_012123.1, NM_001179491.1 |
Genome annotation databases
EnsemblFungii | YIL143C_mRNA; YIL143C; YIL143C |
GeneIDi | 854663 |
KEGGi | sce: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 |
PIRi | S31272 |
RefSeqi | NP_012123.1, NM_001179491.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
5FMF | electron microscopy | 6.00 | 1 | 294-785 | [»] | |
5OQJ | electron microscopy | 4.70 | 7 | 1-843 | [»] | |
5OQM | electron microscopy | 5.80 | 7 | 1-843 | [»] | |
5SVA | electron microscopy | 15.30 | Z | 1-843 | [»] | |
6GYM | electron microscopy | 6.70 | 7 | 1-843 | [»] | |
SMRi | Q00578 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 34849, 128 interactors |
ComplexPortali | CPX-1659, General transcription factor complex TFIIH |
DIPi | DIP-731N |
IntActi | Q00578, 23 interactors |
MINTi | Q00578 |
STRINGi | 4932.YIL143C |
PTM databases
iPTMneti | Q00578 |
Proteomic databases
MaxQBi | Q00578 |
PaxDbi | Q00578 |
PRIDEi | Q00578 |
TopDownProteomicsi | Q00578 |
Genome annotation databases
EnsemblFungii | YIL143C_mRNA; YIL143C; YIL143C |
GeneIDi | 854663 |
KEGGi | sce:YIL143C |
Organism-specific databases
SGDi | S000001405, SSL2 |
VEuPathDBi | FungiDB:YIL143C |
Phylogenomic databases
eggNOGi | KOG1123, Eukaryota |
GeneTreei | ENSGT00390000002204 |
HOGENOMi | CLU_008213_0_0_1 |
InParanoidi | Q00578 |
OMAi | SQEWGLM |
Enzyme and pathway databases
Reactomei | R-SCE-113418, Formation of the Early Elongation Complex 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-73772, RNA Polymerase I Promoter Escape 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-75955, RNA Polymerase II Transcription Elongation 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
PROi | PR:Q00578 |
RNActi | Q00578, protein |
Family and domain databases
InterProi | View 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 |
Pfami | View protein in Pfam PF16203, ERCC3_RAD25_C, 1 hit PF13625, Helicase_C_3, 1 hit PF04851, ResIII, 1 hit |
SMARTi | View protein in SMART SM00487, DEXDc, 1 hit SM00490, HELICc, 1 hit |
SUPFAMi | SSF52540, SSF52540, 2 hits |
TIGRFAMsi | TIGR00603, rad25, 1 hit |
PROSITEi | View protein in PROSITE PS51192, HELICASE_ATP_BIND_1, 1 hit PS51194, HELICASE_CTER, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RAD25_YEAST | |
Accessioni | Q00578Primary (citable) accession number: Q00578 Secondary accession number(s): D6VVE4 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 1, 1993 |
Last sequence update: | April 1, 1993 | |
Last modified: | April 7, 2021 | |
This is version 195 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome IX
Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families