TFB4_YEAST
ID TFB4_YEAST Reviewed; 338 AA.
AC Q12004; D6W462;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=General transcription and DNA repair factor IIH subunit TFB4;
DE Short=TFIIH subunit TFB4;
DE AltName: Full=RNA polymerase II transcription factor B 34 kDa subunit;
DE AltName: Full=RNA polymerase II transcription factor B p34 subunit;
DE AltName: Full=RNA polymerase II transcription factor B subunit 4;
GN Name=TFB4; OrderedLocusNames=YPR056W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP PROTEIN SEQUENCE OF 73-84; 111-131 AND 147-162, AND IDENTIFICATION IN THE
RP TFIIH CORE COMPLEX.
RX PubMed=14500720; DOI=10.1074/jbc.c300417200;
RA Takagi Y., Komori H., Chang W.-H., Hudmon A., Erdjument-Bromage H.,
RA Tempst P., Kornberg R.D.;
RT "Revised subunit structure of yeast transcription factor IIH (TFIIH) and
RT reconciliation with human TFIIH.";
RL J. Biol. Chem. 278:43897-43900(2003).
RN [4]
RP FUNCTION OF TFIIH IN RNA POLYMERASE II TRANSCRIPTION.
RX PubMed=7961739; DOI=10.1016/s0021-9258(18)46892-5;
RA Svejstrup J.Q., Feaver W.J., LaPointe J., Kornberg R.D.;
RT "RNA polymerase transcription factor IIH holoenzyme from yeast.";
RL J. Biol. Chem. 269:28044-28048(1994).
RN [5]
RP FUNCTION OF THE TFIIH CORE COMPLEX IN DNA REPAIR.
RX PubMed=8631896; DOI=10.1074/jbc.271.18.10821;
RA Sung P., Guzder S.N., Prakash L., Prakash S.;
RT "Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3
RT and Rad25, in the incision step of nucleotide excision repair.";
RL J. Biol. Chem. 271:10821-10826(1996).
RN [6]
RP IDENTIFICATION IN THE TFIIH COMPLEX.
RX PubMed=9235928; DOI=10.1074/jbc.272.31.19319;
RA Feaver W.J., Henry N.L., Wang Z., Wu X., Svejstrup J.Q., Bushnell D.A.,
RA Friedberg E.C., Kornberg R.D.;
RT "Genes for Tfb2, Tfb3, and Tfb4 subunits of yeast transcription/repair
RT factor IIH. Homology to human cyclin-dependent kinase activating kinase and
RT IIH subunits.";
RL J. Biol. Chem. 272:19319-19327(1997).
RN [7]
RP FUNCTION.
RX PubMed=10506223; DOI=10.1074/jbc.274.41.29564;
RA Feaver W.J., Huang W., Friedberg E.C.;
RT "The TFB4 subunit of yeast TFIIH is required for both nucleotide excision
RT repair and RNA polymerase II transcription.";
RL J. Biol. Chem. 274:29564-29567(1999).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Component of the general transcription and DNA repair factor
CC IIH (TFIIH) core complex, which is involved in general and
CC transcription-coupled nucleotide excision repair (NER) of damaged DNA
CC and, when complexed to TFIIK, in RNA transcription by RNA polymerase
CC II. In NER, TFIIH acts by opening DNA around the lesion to allow the
CC excision of the damaged oligonucleotide and its replacement by a new
CC DNA fragment. In transcription, TFIIH has an essential role in
CC transcription initiation. When the pre-initiation complex (PIC) has
CC been established, TFIIH is required for promoter opening and promoter
CC escape. Phosphorylation of the C-terminal tail (CTD) of the largest
CC subunit of RNA polymerase II by the kinase module TFIIK controls the
CC initiation of transcription. {ECO:0000269|PubMed:10506223,
CC ECO:0000269|PubMed:7961739, ECO:0000269|PubMed:8631896}.
CC -!- SUBUNIT: Component of the 7-subunit TFIIH core complex composed of
CC XPB/SSL2, XPD/RAD3, SSL1, TFB1, TFB2, TFB4 and TFB5, which is active in
CC NER. The core complex associates with the 3-subunit CTD-kinase module
CC TFIIK composed of CCL1, KIN28 and TFB3 to form the 10-subunit
CC holoenzyme (holo-TFIIH) active in transcription.
CC {ECO:0000269|PubMed:14500720, ECO:0000269|PubMed:7961739,
CC ECO:0000269|PubMed:9235928}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the TFB4 family. {ECO:0000305}.
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DR EMBL; Z71255; CAA95001.1; -; Genomic_DNA.
DR EMBL; Z49219; CAA89174.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11478.1; -; Genomic_DNA.
DR PIR; S54078; S54078.
DR RefSeq; NP_015381.1; NM_001184153.1.
DR PDB; 5OQJ; EM; 4.70 A; 4=1-338.
DR PDB; 5OQM; EM; 5.80 A; 4=1-338.
DR PDB; 6GYM; EM; 6.70 A; 4=1-338.
DR PDB; 7K01; EM; 3.90 A; 4=1-338.
DR PDB; 7K04; EM; 9.25 A; 4=1-338.
DR PDB; 7M2U; EM; 8.20 A; 4=1-338.
DR PDB; 7O4I; EM; 3.20 A; 4=1-338.
DR PDB; 7O4J; EM; 2.90 A; 4=1-338.
DR PDB; 7O4K; EM; 3.60 A; 4=1-338.
DR PDB; 7O4L; EM; 3.40 A; 4=1-338.
DR PDB; 7O72; EM; 3.40 A; 4=1-338.
DR PDB; 7O73; EM; 3.40 A; 4=1-338.
DR PDB; 7O75; EM; 3.20 A; 4=1-338.
DR PDBsum; 5OQJ; -.
DR PDBsum; 5OQM; -.
DR PDBsum; 6GYM; -.
DR PDBsum; 7K01; -.
DR PDBsum; 7K04; -.
DR PDBsum; 7M2U; -.
DR PDBsum; 7O4I; -.
DR PDBsum; 7O4J; -.
DR PDBsum; 7O4K; -.
DR PDBsum; 7O4L; -.
DR PDBsum; 7O72; -.
DR PDBsum; 7O73; -.
DR PDBsum; 7O75; -.
DR AlphaFoldDB; Q12004; -.
DR SMR; Q12004; -.
DR BioGRID; 36230; 154.
DR ComplexPortal; CPX-1659; General transcription factor complex TFIIH.
DR DIP; DIP-5634N; -.
DR IntAct; Q12004; 38.
DR MINT; Q12004; -.
DR STRING; 4932.YPR056W; -.
DR iPTMnet; Q12004; -.
DR MaxQB; Q12004; -.
DR PaxDb; Q12004; -.
DR PRIDE; Q12004; -.
DR TopDownProteomics; Q12004; -.
DR EnsemblFungi; YPR056W_mRNA; YPR056W; YPR056W.
DR GeneID; 856169; -.
DR KEGG; sce:YPR056W; -.
DR SGD; S000006260; TFB4.
DR VEuPathDB; FungiDB:YPR056W; -.
DR eggNOG; KOG2487; Eukaryota.
DR GeneTree; ENSGT00390000013143; -.
DR HOGENOM; CLU_040211_1_0_1; -.
DR InParanoid; Q12004; -.
DR OMA; CFCHRKV; -.
DR BioCyc; YEAST:G3O-34208-MON; -.
DR Reactome; R-SCE-113418; Formation of the Early Elongation Complex.
DR Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-SCE-6782135; Dual incision in TC-NER.
DR Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-SCE-72086; mRNA Capping.
DR Reactome; R-SCE-73772; RNA Polymerase I Promoter Escape.
DR Reactome; R-SCE-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-SCE-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-SCE-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-SCE-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-SCE-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR PRO; PR:Q12004; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q12004; protein.
DR GO; GO:0000112; C:nucleotide-excision repair factor 3 complex; IPI:SGD.
DR GO; GO:0000439; C:transcription factor TFIIH core complex; IDA:SGD.
DR GO; GO:0005675; C:transcription factor TFIIH holo complex; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006289; P:nucleotide-excision repair; IDA:ComplexPortal.
DR GO; GO:0070816; P:phosphorylation of RNA polymerase II C-terminal domain; IDA:SGD.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IDA:SGD.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IDA:ComplexPortal.
DR Gene3D; 3.40.50.410; -; 1.
DR InterPro; IPR004600; TFIIH_Tfb4/GTF2H3.
DR InterPro; IPR036465; vWFA_dom_sf.
DR PANTHER; PTHR12831; PTHR12831; 1.
DR Pfam; PF03850; Tfb4; 1.
DR TIGRFAMs; TIGR00627; tfb4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; DNA damage;
KW DNA repair; Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..338
FT /note="General transcription and DNA repair factor IIH
FT subunit TFB4"
FT /id="PRO_0000119275"
FT ZN_FING 289..308
FT /note="C4-type"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT STRAND 24..31
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 34..43
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 49..67
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 73..79
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 82..88
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 116..138
FT /evidence="ECO:0007829|PDB:7O4J"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 149..166
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 173..180
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 190..192
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 193..205
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 210..217
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 222..230
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 244..250
FT /evidence="ECO:0007829|PDB:7O4J"
FT TURN 251..253
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:7O4J"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 284..289
FT /evidence="ECO:0007829|PDB:7O4J"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:7O4J"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:7O4J"
FT TURN 306..308
FT /evidence="ECO:0007829|PDB:7O4J"
FT HELIX 314..321
FT /evidence="ECO:0007829|PDB:7O4J"
SQ SEQUENCE 338 AA; 37457 MW; B5C0CA95858453E0 CRC64;
MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF
LNAHLAFNSA NKVAVIAAYS QGIKYLYPES TSALKASESE NKTRSDLKII NSDMYRRFRN
VDETLVEEIY KLFELEKKQI EQNSQRSTLA GAMSAGLTYV NRISKESVTT SLKSRLLVLT
CGSGSSKDEI FQYIPIMNCI FSATKMKCPI DVVKIGGSKE STFLQQTTDA TNGVYLHVES
TEGLIQYLAT AMFIDPSLRP IIVKPNHGSV DFRTSCYLTG RVVAVGFICS VCLCVLSIIP
PGNKCPACDS QFDEHVIAKL KRKPVVPRLK AKKKVTKP
