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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.
22-NOV-2017, entry version 173.
RecName: Full=DNA repair helicase RAD25;
EC=3.6.4.12;
AltName: Full=General transcription and DNA repair factor IIH subunit RAD25;
Short=TFIIH subunit RAD25;
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 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).
[7]
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).
[8]
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).
[9]
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).
[10]
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).
-!- FUNCTION: Probably an ATP-dependent DNA helicase, which may have a
DNA unwinding function. Has an essential function in translation
initiation. Acts as component of the general transcription and DNA
repair factor IIH (TFIIH) core, which is essential for both basal
and activated transcription, and is involved in nucleotide
excision repair (NER) of damaged DNA. TFIIH has CTD kinase and
DNA-dependent ATPase activity, and is essential for polymerase II
transcription in vitro. {ECO:0000269|PubMed:7961739,
ECO:0000269|PubMed:8631896}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- SUBUNIT: Component of the TFIIH core complex, which is composed of
RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5.
{ECO:0000269|PubMed:14500720}.
-!- 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:0000320}.
-----------------------------------------------------------------------
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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; 5SVA; EM; 15.30 A; Z=1-843.
PDBsum; 5FMF; -.
PDBsum; 5SVA; -.
ProteinModelPortal; Q00578; -.
SMR; Q00578; -.
BioGrid; 34849; 121.
DIP; DIP-731N; -.
IntAct; Q00578; 23.
MINT; MINT-573804; -.
STRING; 4932.YIL143C; -.
iPTMnet; Q00578; -.
MaxQB; Q00578; -.
PRIDE; Q00578; -.
TopDownProteomics; Q00578; -.
EnsemblFungi; YIL143C; YIL143C; YIL143C.
GeneID; 854663; -.
KEGG; sce:YIL143C; -.
EuPathDB; FungiDB: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; HTP:SGD.
GO; GO:0005675; C:holo TFIIH complex; HTP:SGD.
GO; GO:0000112; C:nucleotide-excision repair factor 3 complex; HTP:SGD.
GO; GO:0005634; C:nucleus; HTP:SGD.
GO; GO:0097550; C:transcriptional preinitiation complex; HTP:SGD.
GO; GO:0005524; F:ATP binding; RCA:UniProtKB-KW.
GO; GO:0004003; F:ATP-dependent DNA helicase activity; HTP:SGD.
GO; GO:0003677; F:DNA binding; RCA:UniProtKB-KW.
GO; GO:0015616; F:DNA translocase activity; HDA:SGD.
GO; GO:0032508; P:DNA duplex unwinding; HTP:SGD.
GO; GO:0033683; P:nucleotide-excision repair, DNA incision; HTP:SGD.
GO; GO:0070816; P:phosphorylation of RNA polymerase II C-terminal domain; HTP:SGD.
GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; HDA:SGD.
GO; GO:0001111; P:promoter clearance from RNA polymerase II promoter; HDA:SGD.
GO; GO:0000019; P:regulation of mitotic recombination; HDA:SGD.
GO; GO:0010525; P:regulation of transposition, RNA-mediated; HDA:SGD.
GO; GO:0006366; P:transcription from RNA polymerase II promoter; HTP:SGD.
GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; HDA:SGD.
GO; GO:0001113; P:transcriptional open complex formation at RNA polymerase II promoter; HDA: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; 3.
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 DNA repair helicase RAD25.
/FTId=PRO_0000101994.
DOMAIN 373 535 Helicase ATP-binding.
{ECO:0000270|PROSITE-ProRule:PRU00541}.
DOMAIN 589 743 Helicase C-terminal.
{ECO:0000270|PROSITE-ProRule:PRU00542}.
NP_BIND 386 393 ATP. {ECO:0000270|PROSITE-
ProRule:PRU00541}.
MOTIF 64 75 Nuclear localization signal.
{ECO:0000270}.
MOTIF 487 491 DEVH box.
COMPBIAS 302 309 Asp/Glu-rich (acidic).
MOD_RES 752 752 Phosphoserine.
{ECO:0000307|PubMed:17330950}.
VARIANT 427 427 W -> L (in suppressor mutant).
{ECO:0000269|PubMed:1318786}.
CONFLICT 9 9 P -> S (in Ref. 2; AAA34942).
{ECO:0000320}.
CONFLICT 48 48 S -> L (in Ref. 2; AAA34942).
{ECO:0000320}.
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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