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Q00578

- RAD25_YEAST

UniProt

Q00578 - RAD25_YEAST

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
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    • History
      Entry version 142 (01 Oct 2014)
      Sequence version 1 (01 Apr 1993)
      Previous versions | rss
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    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

    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.

    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

    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. 36 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.
    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

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    MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG    50
    RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI 100
    PADFVPDSVS GMFRSHDFSY LRLRPDHASR PLWISPSDGR IILESFSPLA 150
    EQAQDFLVTI AEPISRPSHI HEYKITAYSL YAAVSVGLET DDIISVLDRL 200
    SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD ILQMLLNDSV 250
    IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD 300
    NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP 350
    DLDIDLKPST QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA 400
    CTIKKSVIVL CTSSVSVMQW RQQFLQWCTL QPENCAVFTS DNKEMFQTES 450
    GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR EWGFIILDEV HVVPAAMFRR 500
    VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW MELSQKGHIA 550
    NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER 600
    RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN 650
    TIFLSKVGDT SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG 700
    FNAFFYSLVS KDTQEMYYST KRQAFLVDQG YAFKVITHLH GMENIPNLAY 750
    ASPRERRELL QEVLLKNEEA AGIEVGDDAD NSVGRGSNGH KRFKSKAVRG 800
    EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK 843
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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. 36 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.
    KOi K10843.
    OMAi RRTGTMS.
    OrthoDBi EOG7FV3ZX.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31393-MONOMER.

    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

    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: October 1, 2014
    This is version 142 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