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Q00578 (RAD25_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA repair helicase RAD25

EC=3.6.4.12
Alternative name(s):
General transcription and DNA repair factor IIH subunit RAD25
Short name=TFIIH subunit RAD25
Suppressor of stem-loop mutation 2
Gene names
Name:SSL2
Synonyms:LOM3, RAD25, UVS112
Ordered Locus Names:YIL143C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length843 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.6 Ref.7

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

Component of the TFIIH core complex, which is composed of RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5. Ref.8

Subcellular location

Nucleus.

Miscellaneous

A C-terminal deletion renders yeast hypersensitive to UV light.

Present with 825 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the helicase family. RAD25/XPB subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
Transcription
Transcription regulation
   Cellular componentNucleus
   LigandATP-binding
DNA-binding
Nucleotide-binding
   Molecular functionHelicase
Hydrolase
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA duplex unwinding

Inferred from direct assay PubMed 22751016. Source: SGD

nucleotide-excision repair, DNA incision

Inferred from direct assay Ref.7. Source: SGD

phosphorylation of RNA polymerase II C-terminal domain

Inferred from direct assay PubMed 19450536PubMed 19679665. Source: SGD

poly(A)+ mRNA export from nucleus

Inferred from mutant phenotype PubMed 17212653. Source: SGD

promoter clearance from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 10713451. Source: SGD

regulation of mitotic recombination

Inferred from mutant phenotype PubMed 10713167. Source: SGD

regulation of transposition, RNA-mediated

Inferred from mutant phenotype PubMed 10713167. Source: SGD

transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 19818408. Source: SGD

transcriptional open complex formation at RNA polymerase II promoter

Inferred from mutant phenotype PubMed 10409754. Source: SGD

   Cellular_componentcytosol

Inferred from direct assay PubMed 22932476. Source: SGD

holo TFIIH complex

Inferred from direct assay PubMed 19818408. Source: SGD

nucleotide-excision repair factor 3 complex

Inferred from direct assay PubMed 8855246. Source: SGD

nucleus

Inferred from direct assay PubMed 22932476. Source: SGD

transcriptional preinitiation complex

Inferred from direct assay PubMed 22751016. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent DNA helicase activity

Inferred from direct assay PubMed 8202161. Source: SGD

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 843843DNA repair helicase RAD25
PRO_0000101994

Regions

Domain373 – 535163Helicase ATP-binding
Domain589 – 743155Helicase C-terminal
Nucleotide binding386 – 3938ATP By similarity
Motif64 – 7512Nuclear localization signal Potential
Motif487 – 4915DEVH box
Compositional bias302 – 3098Asp/Glu-rich (acidic)

Amino acid modifications

Modified residue7521Phosphoserine Ref.10

Natural variations

Natural variant4271W → L in suppressor mutant. Ref.1

Experimental info

Sequence conflict91P → S in AAA34942. Ref.2
Sequence conflict481S → L in AAA34942. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q00578 [UniParc].

Last modified April 1, 1993. Version 1.
Checksum: FA4013E8156FE1C5

FASTA84395,341
        10         20         30         40         50         60 
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV 

        70         80         90        100        110        120 
TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI PADFVPDSVS GMFRSHDFSY 

       130        140        150        160        170        180 
LRLRPDHASR PLWISPSDGR IILESFSPLA EQAQDFLVTI AEPISRPSHI HEYKITAYSL 

       190        200        210        220        230        240 
YAAVSVGLET DDIISVLDRL SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD 

       250        260        270        280        290        300 
ILQMLLNDSV IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD 

       310        320        330        340        350        360 
NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP DLDIDLKPST 

       370        380        390        400        410        420 
QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA CTIKKSVIVL CTSSVSVMQW 

       430        440        450        460        470        480 
RQQFLQWCTL QPENCAVFTS DNKEMFQTES GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR 

       490        500        510        520        530        540 
EWGFIILDEV HVVPAAMFRR VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW 

       550        560        570        580        590        600 
MELSQKGHIA NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER 

       610        620        630        640        650        660 
RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN TIFLSKVGDT 

       670        680        690        700        710        720 
SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG FNAFFYSLVS KDTQEMYYST 

       730        740        750        760        770        780 
KRQAFLVDQG YAFKVITHLH GMENIPNLAY ASPRERRELL QEVLLKNEEA AGIEVGDDAD 

       790        800        810        820        830        840 
NSVGRGSNGH KRFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN 


LKK 

« Hide

References

« Hide 'large scale' references
[1]"SSL2, a suppressor of a stem-loop mutation in the HIS4 leader encodes the yeast homolog of human ERCC-3."
Gulyas K.D., Donahue T.F.
Cell 69:1031-1042(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT SUPPRESSOR MUTANT LEU-427.
Strain: ATCC 204508 / S288c.
[2]"RAD25 (SSL2), the yeast homolog of the human Xeroderma pigmentosum group B DNA repair gene, is essential for viability."
Park E.K., Guzder S.N., Weeda G., Hoeijmakers J.H., Prakash S., Prakash L.
Proc. Natl. Acad. Sci. U.S.A. 89:11416-11420(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."
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. expand/collapse author list , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
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.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
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. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"RNA polymerase transcription factor IIH holoenzyme from yeast."
Svejstrup J.Q., Feaver W.J., LaPointe J., Kornberg R.D.
J. Biol. Chem. 269:28044-28048(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF TFIIH IN RNA POLYMERASE II TRANSCRIPTION.
[7]"Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair."
Sung P., Guzder S.N., Prakash L., Prakash S.
J. Biol. Chem. 271:10821-10826(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE TFIIH CORE COMPLEX IN DNA REPAIR.
[8]"Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH."
Takagi Y., Komori H., Chang W.-H., Hudmon A., Erdjument-Bromage H., Tempst P., Kornberg R.D.
J. Biol. Chem. 278:43897-43900(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE TFIIH CORE COMPLEX.
[9]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-752, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS31272.
RefSeqNP_012123.1. NM_001179491.1.

3D structure databases

ProteinModelPortalQ00578.
SMRQ00578. Positions 362-775.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34849. 36 interactions.
DIPDIP-731N.
IntActQ00578. 17 interactions.
MINTMINT-573804.
STRING4932.YIL143C.

Proteomic databases

MaxQBQ00578.
PaxDbQ00578.
PeptideAtlasQ00578.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYIL143C; YIL143C; YIL143C.
GeneID854663.
KEGGsce:YIL143C.

Organism-specific databases

CYGDYIL143c.
SGDS000001405. SSL2.

Phylogenomic databases

eggNOGCOG1061.
GeneTreeENSGT00390000002204.
HOGENOMHOG000160172.
KOK10843.
OMARRTGTMS.
OrthoDBEOG7FV3ZX.

Enzyme and pathway databases

BioCycYEAST:G3O-31393-MONOMER.

Gene expression databases

GenevestigatorQ00578.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR001161. Helicase_Ercc3.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
PRINTSPR00851. XRODRMPGMNTB.
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 3 hits.
TIGRFAMsTIGR00603. rad25. 1 hit.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio977238.
PROQ00578.

Entry information

Entry nameRAD25_YEAST
AccessionPrimary (citable) accession number: Q00578
Secondary accession number(s): D6VVE4
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: June 11, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IX

Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families