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Protein

General transcription and DNA repair factor IIH subunit TFB4

Gene

TFB4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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. 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. 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.3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri289 – 308C4-typeAdd BLAST20

GO - Molecular functioni

GO - Biological processi

  • nucleotide-excision repair Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • transcription by RNA polymerase II Source: SGD

Keywordsi

Biological processDNA damage, DNA repair, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-34208-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 subunit TFB4
Short name:
TFIIH subunit TFB4
Alternative name(s):
RNA polymerase II transcription factor B 34 kDa subunit
RNA polymerase II transcription factor B p34 subunit
RNA polymerase II transcription factor B subunit 4
Gene namesi
Name:TFB4
Ordered Locus Names:YPR056W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

SGDiS000006260 TFB4

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_00001192751 – 338General transcription and DNA repair factor IIH subunit TFB4Add BLAST338

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ12004
PaxDbiQ12004
PRIDEiQ12004
TopDownProteomicsiQ12004

PTM databases

iPTMnetiQ12004

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

Protein-protein interaction databases

BioGridi36230, 150 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-5634N
IntActiQ12004, 38 interactors
MINTiQ12004
STRINGi4932.YPR056W

Structurei

3D structure databases

ProteinModelPortaliQ12004
SMRiQ12004
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the TFB4 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri289 – 308C4-typeAdd BLAST20

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000013143
HOGENOMiHOG000175900
InParanoidiQ12004
KOiK03143
OMAiFGNAHLM
OrthoDBiEOG092C38GP

Family and domain databases

Gene3Di3.40.50.410, 1 hit
InterProiView protein in InterPro
IPR004600 TFIIH_Tfb4/GTF2H3
IPR036465 vWFA_dom_sf
PANTHERiPTHR12831 PTHR12831, 1 hit
PfamiView protein in Pfam
PF03850 Tfb4, 1 hit
TIGRFAMsiTIGR00627 tfb4, 1 hit

Sequencei

Sequence statusi: Complete.

Q12004-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI
60 70 80 90 100
IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPES TSALKASESE
110 120 130 140 150
NKTRSDLKII NSDMYRRFRN VDETLVEEIY KLFELEKKQI EQNSQRSTLA
160 170 180 190 200
GAMSAGLTYV NRISKESVTT SLKSRLLVLT CGSGSSKDEI FQYIPIMNCI
210 220 230 240 250
FSATKMKCPI DVVKIGGSKE STFLQQTTDA TNGVYLHVES TEGLIQYLAT
260 270 280 290 300
AMFIDPSLRP IIVKPNHGSV DFRTSCYLTG RVVAVGFICS VCLCVLSIIP
310 320 330
PGNKCPACDS QFDEHVIAKL KRKPVVPRLK AKKKVTKP
Length:338
Mass (Da):37,457
Last modified:November 1, 1996 - v1
Checksum:iB5C0CA95858453E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71255 Genomic DNA Translation: CAA95001.1
Z49219 Genomic DNA Translation: CAA89174.1
BK006949 Genomic DNA Translation: DAA11478.1
PIRiS54078
RefSeqiNP_015381.1, NM_001184153.1

Genome annotation databases

EnsemblFungiiYPR056W; YPR056W; YPR056W
GeneIDi856169
KEGGisce:YPR056W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71255 Genomic DNA Translation: CAA95001.1
Z49219 Genomic DNA Translation: CAA89174.1
BK006949 Genomic DNA Translation: DAA11478.1
PIRiS54078
RefSeqiNP_015381.1, NM_001184153.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5OQJelectron microscopy4.7041-338[»]
5OQMelectron microscopy5.8041-338[»]
ProteinModelPortaliQ12004
SMRiQ12004
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36230, 150 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-5634N
IntActiQ12004, 38 interactors
MINTiQ12004
STRINGi4932.YPR056W

PTM databases

iPTMnetiQ12004

Proteomic databases

MaxQBiQ12004
PaxDbiQ12004
PRIDEiQ12004
TopDownProteomicsiQ12004

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR056W; YPR056W; YPR056W
GeneIDi856169
KEGGisce:YPR056W

Organism-specific databases

SGDiS000006260 TFB4

Phylogenomic databases

GeneTreeiENSGT00390000013143
HOGENOMiHOG000175900
InParanoidiQ12004
KOiK03143
OMAiFGNAHLM
OrthoDBiEOG092C38GP

Enzyme and pathway databases

BioCyciYEAST:G3O-34208-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:Q12004

Family and domain databases

Gene3Di3.40.50.410, 1 hit
InterProiView protein in InterPro
IPR004600 TFIIH_Tfb4/GTF2H3
IPR036465 vWFA_dom_sf
PANTHERiPTHR12831 PTHR12831, 1 hit
PfamiView protein in Pfam
PF03850 Tfb4, 1 hit
TIGRFAMsiTIGR00627 tfb4, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTFB4_YEAST
AccessioniPrimary (citable) accession number: Q12004
Secondary accession number(s): D6W462
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: November 1, 1996
Last modified: November 7, 2018
This is version 129 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, Direct protein sequencing, Reference proteome

Documents

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