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DNA repair helicase RAD25 (EC 3.6.4.12) (General transcription and DNA repair factor IIH subunit RAD25) (TFIIH subunit RAD25) (Suppressor of stem-loop mutation 2)

 RAD25_YEAST             Reviewed;         843 AA.
Q00578; D6VVE4;
01-APR-1993, integrated into UniProtKB/Swiss-Prot.
01-APR-1993, sequence version 1.
05-DEC-2018, entry version 182.
RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB;
Short=TFIIH subunit XPB;
EC=3.6.4.12;
AltName: Full=DNA repair helicase RAD25;
AltName: Full=RNA polymerase II transcription factor B subunit SSL2;
Short=TFB subunit SSL2;
AltName: Full=Suppressor of stem-loop mutation 2;
Name=SSL2; Synonyms=LOM3, RAD25, UVS112; OrderedLocusNames=YIL143C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT SUPPRESSOR MUTANT
LEU-427.
STRAIN=ATCC 204508 / S288c;
PubMed=1318786; DOI=10.1016/0092-8674(92)90621-I;
Gulyas K.D., Donahue T.F.;
"SSL2, a suppressor of a stem-loop mutation in the HIS4 leader encodes
the yeast homolog of human ERCC-3.";
Cell 69:1031-1042(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=1333609; DOI=10.1073/pnas.89.23.11416;
Park E.K., Guzder S.N., Weeda G., Hoeijmakers J.H., Prakash S.,
Prakash L.;
"RAD25 (SSL2), the yeast homolog of the human Xeroderma pigmentosum
group B DNA repair gene, is essential for viability.";
Proc. Natl. Acad. Sci. U.S.A. 89:11416-11420(1992).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169870;
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N.,
Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G.,
Moule S., Odell C., Pearson D., Rajandream M.A., Rice P., Rowley N.,
Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
Nature 387:84-87(1997).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[6]
FUNCTION.
PubMed=8269516; DOI=10.1016/0092-8674(93)90624-Y;
Feaver W.J., Svejstrup J.Q., Bardwell L., Bardwell A.J.,
Buratowski S., Gulyas K.D., Donahue T.F., Friedberg E.C.,
Kornberg R.D.;
"Dual roles of a multiprotein complex from S. cerevisiae in
transcription and DNA repair.";
Cell 75:1379-1387(1993).
[7]
FUNCTION.
PubMed=7693549;
Qiu H., Park E., Prakash L., Prakash S.;
"The Saccharomyces cerevisiae DNA repair gene RAD25 is required for
transcription by RNA polymerase II.";
Genes Dev. 7:2161-2171(1993).
[8]
FUNCTION OF TFIIH IN RNA POLYMERASE II TRANSCRIPTION.
PubMed=7961739;
Svejstrup J.Q., Feaver W.J., LaPointe J., Kornberg R.D.;
"RNA polymerase transcription factor IIH holoenzyme from yeast.";
J. Biol. Chem. 269:28044-28048(1994).
[9]
FUNCTION.
PubMed=8202161; DOI=10.1038/369578a0;
Guzder S.N., Sung P., Bailly V., Prakash L., Prakash S.;
"RAD25 is a DNA helicase required for DNA repair and RNA polymerase II
transcription.";
Nature 369:578-581(1994).
[10]
FUNCTION, AND SUBUNIT.
PubMed=7813015; DOI=10.1016/0092-8674(95)90447-6;
Svejstrup J.Q., Wang Z., Feaver W.J., Wu X., Bushnell D.A.,
Donahue T.F., Friedberg E.C., Kornberg R.D.;
"Different forms of TFIIH for transcription and DNA repair: holo-TFIIH
and a nucleotide excision repairosome.";
Cell 80:21-28(1995).
[11]
FUNCTION OF THE TFIIH CORE COMPLEX IN DNA REPAIR.
PubMed=8631896; DOI=10.1074/jbc.271.18.10821;
Sung P., Guzder S.N., Prakash L., Prakash S.;
"Reconstitution of TFIIH and requirement of its DNA helicase subunits,
Rad3 and Rad25, in the incision step of nucleotide excision repair.";
J. Biol. Chem. 271:10821-10826(1996).
[12]
IDENTIFICATION IN THE TFIIH CORE COMPLEX.
PubMed=14500720; DOI=10.1074/jbc.C300417200;
Takagi Y., Komori H., Chang W.-H., Hudmon A., Erdjument-Bromage H.,
Tempst P., Kornberg R.D.;
"Revised subunit structure of yeast transcription factor IIH (TFIIH)
and reconciliation with human TFIIH.";
J. Biol. Chem. 278:43897-43900(2003).
[13]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-752, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[15]
FUNCTION.
PubMed=25775526; DOI=10.1073/pnas.1417709112;
Fishburn J., Tomko E., Galburt E., Hahn S.;
"Double-stranded DNA translocase activity of transcription factor
TFIIH and the mechanism of RNA polymerase II open complex formation.";
Proc. Natl. Acad. Sci. U.S.A. 112:3961-3966(2015).
[16]
STRUCTURE BY ELECTRON MICROSCOPY (6.00 ANGSTROMS) OF 294-785.
PubMed=26483468; DOI=10.1073/pnas.1518255112;
Murakami K., Tsai K.L., Kalisman N., Bushnell D.A., Asturias F.J.,
Kornberg R.D.;
"Structure of an RNA polymerase II preinitiation complex.";
Proc. Natl. Acad. Sci. U.S.A. 112:13543-13548(2015).
[17]
STRUCTURE BY ELECTRON MICROSCOPY (15.30 ANGSTROMS).
PubMed=27610567; DOI=10.1016/j.cell.2016.08.050;
Robinson P.J., Trnka M.J., Bushnell D.A., Davis R.E., Mattei P.J.,
Burlingame A.L., Kornberg R.D.;
"Structure of a complete mediator-RNA polymerase II pre-initiation
complex.";
Cell 166:1411-1422(2016).
-!- FUNCTION: 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).
{ECO:0000269|PubMed:25775526, ECO:0000269|PubMed:7693549,
ECO:0000269|PubMed:7813015, ECO:0000269|PubMed:7961739,
ECO:0000269|PubMed:8202161, ECO:0000269|PubMed:8269516,
ECO:0000269|PubMed:8631896}.
-!- CATALYTIC ACTIVITY:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
-!- SUBUNIT: 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.
{ECO:0000269|PubMed:14500720, ECO:0000269|PubMed:7813015,
ECO:0000269|PubMed:7961739}.
-!- SUBCELLULAR LOCATION: Nucleus.
-!- MISCELLANEOUS: A C-terminal deletion renders yeast hypersensitive
to UV light.
-!- MISCELLANEOUS: Present with 825 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the helicase family. RAD25/XPB subfamily.
{ECO:0000305}.
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EMBL; Z38059; CAA86135.1; -; Genomic_DNA.
EMBL; M94176; AAA35102.1; -; Genomic_DNA.
EMBL; L01414; AAA34942.1; -; Genomic_DNA.
EMBL; AY692883; AAT92902.1; -; Genomic_DNA.
EMBL; BK006942; DAA08410.1; -; Genomic_DNA.
PIR; S31272; S31272.
RefSeq; NP_012123.1; NM_001179491.1.
PDB; 5FMF; EM; 6.00 A; 1=294-785.
PDB; 5OQJ; EM; 4.70 A; 7=1-843.
PDB; 5OQM; EM; 5.80 A; 7=1-843.
PDB; 5SVA; EM; 15.30 A; Z=1-843.
PDBsum; 5FMF; -.
PDBsum; 5OQJ; -.
PDBsum; 5OQM; -.
PDBsum; 5SVA; -.
ProteinModelPortal; Q00578; -.
SMR; Q00578; -.
BioGrid; 34849; 126.
ComplexPortal; CPX-1659; General transcription factor complex TFIIH.
DIP; DIP-731N; -.
IntAct; Q00578; 23.
MINT; Q00578; -.
STRING; 4932.YIL143C; -.
iPTMnet; Q00578; -.
MaxQB; Q00578; -.
PaxDb; Q00578; -.
PRIDE; Q00578; -.
TopDownProteomics; Q00578; -.
EnsemblFungi; YIL143C_mRNA; YIL143C_mRNA; YIL143C.
GeneID; 854663; -.
KEGG; sce:YIL143C; -.
SGD; S000001405; SSL2.
GeneTree; ENSGT00390000002204; -.
HOGENOM; HOG000160172; -.
InParanoid; Q00578; -.
KO; K10843; -.
OMA; TKHVHPL; -.
OrthoDB; EOG092C0I1P; -.
BioCyc; YEAST:G3O-31393-MONOMER; -.
Reactome; R-SCE-113418; Formation of the Early Elongation Complex.
Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
Reactome; R-SCE-5696400; Dual Incision in GG-NER.
Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-SCE-6782135; Dual incision in TC-NER.
Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.
Reactome; R-SCE-72086; mRNA Capping.
Reactome; R-SCE-73776; RNA Polymerase II Promoter Escape.
Reactome; R-SCE-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
Reactome; R-SCE-75953; RNA Polymerase II Transcription Initiation.
Reactome; R-SCE-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
Reactome; R-SCE-77075; RNA Pol II CTD phosphorylation and interaction with CE.
PRO; PR:Q00578; -.
Proteomes; UP000002311; Chromosome IX.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0000112; C:nucleotide-excision repair factor 3 complex; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0000439; C:transcription factor TFIIH core complex; IDA:SGD.
GO; GO:0005675; C:transcription factor TFIIH holo complex; IDA:SGD.
GO; GO:0097550; C:transcriptional preinitiation complex; IDA:SGD.
GO; GO:0043138; F:3'-5' DNA helicase activity; IBA:GO_Central.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004003; F:ATP-dependent DNA helicase activity; IDA:SGD.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0015616; F:DNA translocase activity; IMP:SGD.
GO; GO:0008134; F:transcription factor binding; IBA:GO_Central.
GO; GO:0032508; P:DNA duplex unwinding; IDA:SGD.
GO; GO:0000717; P:nucleotide-excision repair, DNA duplex unwinding; IBA:GO_Central.
GO; GO:0033683; P:nucleotide-excision repair, DNA incision; IDA:SGD.
GO; GO:0070816; P:phosphorylation of RNA polymerase II C-terminal domain; IDA:SGD.
GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; IMP:SGD.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
GO; GO:0001111; P:promoter clearance from RNA polymerase II promoter; IMP:SGD.
GO; GO:1901990; P:regulation of mitotic cell cycle phase transition; IBA:GO_Central.
GO; GO:0000019; P:regulation of mitotic recombination; IMP:SGD.
GO; GO:1903025; P:regulation of RNA polymerase II regulatory region sequence-specific DNA binding; IBA:GO_Central.
GO; GO:0010525; P:regulation of transposition, RNA-mediated; IMP:SGD.
GO; GO:0009411; P:response to UV; IBA:GO_Central.
GO; GO:0006366; P:transcription by RNA polymerase II; IDA:SGD.
GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IMP:SGD.
GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
GO; GO:0001113; P:transcriptional open complex formation at RNA polymerase II promoter; IMP:SGD.
CDD; cd00079; HELICc; 1.
InterPro; IPR032438; ERCC3_RAD25_C.
InterPro; IPR006935; Helicase/UvrB_N.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR001161; XPB/Ssl2.
InterPro; IPR032830; XPB/Ssl2_N.
Pfam; PF16203; ERCC3_RAD25_C; 1.
Pfam; PF13625; Helicase_C_3; 1.
Pfam; PF04851; ResIII; 1.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF52540; SSF52540; 2.
TIGRFAMs; TIGR00603; rad25; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; DNA damage; DNA repair;
DNA-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
Phosphoprotein; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 843 General transcription and DNA repair
factor IIH helicase subunit XPB.
/FTId=PRO_0000101994.
DOMAIN 373 535 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 589 743 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
NP_BIND 386 393 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 64 75 Nuclear localization signal.
{ECO:0000255}.
MOTIF 487 491 DEVH box.
COMPBIAS 302 309 Asp/Glu-rich (acidic).
MOD_RES 752 752 Phosphoserine.
{ECO:0000244|PubMed:17330950}.
VARIANT 427 427 W -> L (in suppressor mutant).
{ECO:0000269|PubMed:1318786}.
CONFLICT 9 9 P -> S (in Ref. 2; AAA34942).
{ECO:0000305}.
CONFLICT 48 48 S -> L (in Ref. 2; AAA34942).
{ECO:0000305}.
SEQUENCE 843 AA; 95341 MW; FA4013E8156FE1C5 CRC64;
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV
TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI PADFVPDSVS GMFRSHDFSY
LRLRPDHASR PLWISPSDGR IILESFSPLA EQAQDFLVTI AEPISRPSHI HEYKITAYSL
YAAVSVGLET DDIISVLDRL SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD
ILQMLLNDSV IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD
NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP DLDIDLKPST
QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA CTIKKSVIVL CTSSVSVMQW
RQQFLQWCTL QPENCAVFTS DNKEMFQTES GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR
EWGFIILDEV HVVPAAMFRR VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW
MELSQKGHIA NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER
RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN TIFLSKVGDT
SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG FNAFFYSLVS KDTQEMYYST
KRQAFLVDQG YAFKVITHLH GMENIPNLAY ASPRERRELL QEVLLKNEEA AGIEVGDDAD
NSVGRGSNGH KRFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN
LKK


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