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Q00578

- RAD25_YEAST

UniProt

Q00578 - RAD25_YEAST

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Protein

DNA repair helicase RAD25

Gene

SSL2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi386 – 3938ATPPROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent DNA helicase activity Source: SGD
  3. DNA binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA duplex unwinding Source: SGD
  2. nucleotide-excision repair, DNA incision Source: SGD
  3. phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  4. poly(A)+ mRNA export from nucleus Source: SGD
  5. promoter clearance from RNA polymerase II promoter Source: SGD
  6. regulation of mitotic recombination Source: SGD
  7. regulation of transposition, RNA-mediated Source: SGD
  8. transcriptional open complex formation at RNA polymerase II promoter Source: SGD
  9. transcription from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31393-MONOMER.
ReactomeiREACT_229646. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_233196. Formation of incision complex in GG-NER.
REACT_235070. Dual incision reaction in TC-NER.
REACT_236803. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_240372. mRNA Capping.
REACT_247354. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_249293. RNA Polymerase II Transcription Initiation.
REACT_249645. Formation of the Early Elongation Complex.
REACT_250453. Dual incision reaction in GG-NER.
REACT_250507. RNA Polymerase II Pre-transcription Events.
REACT_252915. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_257112. RNA Polymerase II Promoter Escape.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:SSL2
Synonyms:LOM3, RAD25, UVS112
Ordered Locus Names:YIL143C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IX

Organism-specific databases

CYGDiYIL143c.
SGDiS000001405. SSL2.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: SGD
  2. holo TFIIH complex Source: SGD
  3. nucleotide-excision repair factor 3 complex Source: SGD
  4. nucleus Source: SGD
  5. transcriptional preinitiation complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 843843DNA repair helicase RAD25PRO_0000101994Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei752 – 7521Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ00578.
PaxDbiQ00578.
PeptideAtlasiQ00578.

Expressioni

Gene expression databases

GenevestigatoriQ00578.

Interactioni

Subunit structurei

Component of the TFIIH core complex, which is composed of RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5.1 Publication

Protein-protein interaction databases

BioGridi34849. 37 interactions.
DIPiDIP-731N.
IntActiQ00578. 17 interactions.
MINTiMINT-573804.
STRINGi4932.YIL143C.

Structurei

3D structure databases

ProteinModelPortaliQ00578.
SMRiQ00578. Positions 362-775.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini373 – 535163Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini589 – 743155Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi64 – 7512Nuclear localization signalSequence AnalysisAdd
BLAST
Motifi487 – 4915DEVH box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi302 – 3098Asp/Glu-rich (acidic)

Sequence similaritiesi

Belongs to the helicase family. RAD25/XPB subfamily.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG1061.
GeneTreeiENSGT00390000002204.
HOGENOMiHOG000160172.
InParanoidiQ00578.
KOiK10843.
OMAiRRTGTMS.
OrthoDBiEOG7FV3ZX.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR001161. Helicase_Ercc3.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
PRINTSiPR00851. XRODRMPGMNTB.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR00603. rad25. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q00578-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG
60 70 80 90 100
RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI
110 120 130 140 150
PADFVPDSVS GMFRSHDFSY LRLRPDHASR PLWISPSDGR IILESFSPLA
160 170 180 190 200
EQAQDFLVTI AEPISRPSHI HEYKITAYSL YAAVSVGLET DDIISVLDRL
210 220 230 240 250
SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD ILQMLLNDSV
260 270 280 290 300
IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD
310 320 330 340 350
NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP
360 370 380 390 400
DLDIDLKPST QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA
410 420 430 440 450
CTIKKSVIVL CTSSVSVMQW RQQFLQWCTL QPENCAVFTS DNKEMFQTES
460 470 480 490 500
GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR EWGFIILDEV HVVPAAMFRR
510 520 530 540 550
VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW MELSQKGHIA
560 570 580 590 600
NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER
610 620 630 640 650
RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN
660 670 680 690 700
TIFLSKVGDT SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG
710 720 730 740 750
FNAFFYSLVS KDTQEMYYST KRQAFLVDQG YAFKVITHLH GMENIPNLAY
760 770 780 790 800
ASPRERRELL QEVLLKNEEA AGIEVGDDAD NSVGRGSNGH KRFKSKAVRG
810 820 830 840
EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK
Length:843
Mass (Da):95,341
Last modified:April 1, 1993 - v1
Checksum:iFA4013E8156FE1C5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti9 – 91P → S in AAA34942. (PubMed:1333609)Curated
Sequence conflicti48 – 481S → L in AAA34942. (PubMed:1333609)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti427 – 4271W → L in suppressor mutant. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS31272.
RefSeqiNP_012123.1. NM_001179491.1.

Genome annotation databases

EnsemblFungiiYIL143C; YIL143C; YIL143C.
GeneIDi854663.
KEGGisce:YIL143C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi S31272.
RefSeqi NP_012123.1. NM_001179491.1.

3D structure databases

ProteinModelPortali Q00578.
SMRi Q00578. Positions 362-775.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34849. 37 interactions.
DIPi DIP-731N.
IntActi Q00578. 17 interactions.
MINTi MINT-573804.
STRINGi 4932.YIL143C.

Proteomic databases

MaxQBi Q00578.
PaxDbi Q00578.
PeptideAtlasi Q00578.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YIL143C ; YIL143C ; YIL143C .
GeneIDi 854663.
KEGGi sce:YIL143C.

Organism-specific databases

CYGDi YIL143c.
SGDi S000001405. SSL2.

Phylogenomic databases

eggNOGi COG1061.
GeneTreei ENSGT00390000002204.
HOGENOMi HOG000160172.
InParanoidi Q00578.
KOi K10843.
OMAi RRTGTMS.
OrthoDBi EOG7FV3ZX.

Enzyme and pathway databases

BioCyci YEAST:G3O-31393-MONOMER.
Reactomei REACT_229646. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_233196. Formation of incision complex in GG-NER.
REACT_235070. Dual incision reaction in TC-NER.
REACT_236803. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_240372. mRNA Capping.
REACT_247354. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_249293. RNA Polymerase II Transcription Initiation.
REACT_249645. Formation of the Early Elongation Complex.
REACT_250453. Dual incision reaction in GG-NER.
REACT_250507. RNA Polymerase II Pre-transcription Events.
REACT_252915. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_257112. RNA Polymerase II Promoter Escape.

Miscellaneous databases

NextBioi 977238.
PROi Q00578.

Gene expression databases

Genevestigatori Q00578.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR001161. Helicase_Ercc3.
IPR027417. P-loop_NTPase.
[Graphical view ]
Pfami PF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view ]
PRINTSi PR00851. XRODRMPGMNTB.
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 3 hits.
TIGRFAMsi TIGR00603. rad25. 1 hit.
PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. 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. 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.

Entry informationi

Entry nameiRAD25_YEAST
AccessioniPrimary (citable) accession number: Q00578
Secondary accession number(s): D6VVE4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: November 26, 2014
This is version 144 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

A C-terminal deletion renders yeast hypersensitive to UV light.
Present with 825 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3