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P35732

- DEF1_YEAST

UniProt

P35732 - DEF1_YEAST

Protein

RNA polymerase II degradation factor 1

Gene

DEF1

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 111 (01 Oct 2014)
      Sequence version 1 (01 Jun 1994)
      Previous versions | rss
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    Functioni

    RNA polymerase II degradation factor recruits the ubiquitination machinery to the RNA polymerase II for polyubiquitination, removal and degradation, when RAD26 fails to efficiently displace stalled RNA polymerase II. Also involved in telomere length regulation.4 Publications

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: SGD
    2. protein ubiquitination Source: SGD
    3. telomere maintenance Source: SGD
    4. transcription-coupled nucleotide-excision repair Source: SGD
    5. ubiquitin-dependent protein catabolic process Source: SGD

    Keywords - Biological processi

    DNA damage, DNA repair, Ubl conjugation pathway

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31854-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA polymerase II degradation factor 1
    Alternative name(s):
    RRM3-interacting protein 1
    Gene namesi
    Name:DEF1
    Synonyms:RIP1, VID31
    Ordered Locus Names:YKL054C
    ORF Names:YKL308
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XI

    Organism-specific databases

    CYGDiYKL054c.
    SGDiS000001537. DEF1.

    Subcellular locationi

    Nucleus 1 Publication. Chromosometelomere 1 Publication

    GO - Cellular componenti

    1. chromosome, telomeric region Source: UniProtKB-SubCell
    2. nucleus Source: SGD

    Keywords - Cellular componenti

    Chromosome, Nucleus, Telomere

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 738738RNA polymerase II degradation factor 1PRO_0000203177Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei260 – 2601Phosphoserine4 Publications
    Modified residuei273 – 2731Phosphoserine1 Publication
    Modified residuei307 – 3071Phosphoserine1 Publication
    Modified residuei338 – 3381Phosphothreonine1 Publication
    Modified residuei646 – 6461Phosphoserine3 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP35732.
    PaxDbiP35732.
    PeptideAtlasiP35732.

    Expressioni

    Gene expression databases

    GenevestigatoriP35732.

    Interactioni

    Subunit structurei

    Interacts with the RNA polymerase II in a DNA-damaged dependent manner. Interacts with RAD26. Binds DNA.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself1EBI-26695,EBI-26695
    ADE17P380091EBI-26695,EBI-14223
    CAF40P538291EBI-26695,EBI-28306
    CDC39P256551EBI-26695,EBI-12139
    CPR6P536911EBI-26695,EBI-5429
    CYS4P325821EBI-26695,EBI-4167
    DCP2P535501EBI-26695,EBI-270
    DHH1P395171EBI-26695,EBI-158
    EAP1P360411EBI-26695,EBI-26995
    HCH1P538341EBI-26695,EBI-28288
    IPP1P008171EBI-26695,EBI-9338
    LSM3P577431EBI-26695,EBI-10227
    LSM4P400701EBI-26695,EBI-188
    MOT2P349091EBI-26695,EBI-12174
    MPT5P390161EBI-26695,EBI-2052996
    PAN2P530101EBI-26695,EBI-12887
    PAT1P256441EBI-26695,EBI-204
    PBP1P532971EBI-26695,EBI-12961
    PEX7P391081EBI-26695,EBI-13183
    POP2P390081EBI-26695,EBI-13629
    PUB1P325881EBI-26695,EBI-14231
    PUF4P253391EBI-26695,EBI-23703
    RIM1P324451EBI-26695,EBI-15206
    RNR2P099381EBI-26695,EBI-15240
    SLF1Q120341EBI-26695,EBI-17335
    SRO9P255671EBI-26695,EBI-18084
    STI1P157051EBI-26695,EBI-18418
    TIP20P338911EBI-26695,EBI-19396
    WHI3P347611EBI-26695,EBI-20537

    Protein-protein interaction databases

    BioGridi34079. 75 interactions.
    DIPiDIP-6354N.
    IntActiP35732. 41 interactions.
    MINTiMINT-693440.
    STRINGi4932.YKL054C.

    Structurei

    3D structure databases

    ProteinModelPortaliP35732.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini21 – 6343CUEPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi382 – 718337Gln-richAdd
    BLAST
    Compositional biasi574 – 5807Poly-Ala
    Compositional biasi708 – 7169Poly-Ala

    Sequence similaritiesi

    Belongs to the DEF1 family.Curated
    Contains 1 CUE domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG16498.
    OMAiWDEVKKP.
    OrthoDBiEOG7Z0K6R.

    Family and domain databases

    InterProiIPR003892. CUE.
    [Graphical view]
    PfamiPF02845. CUE. 1 hit.
    [Graphical view]
    PROSITEiPS51140. CUE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P35732-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD    50
    LETIIDKITS GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI 100
    TYKSSNNSNS FTSTKHNSSN NYTQARNKKK VQTPRAHTTG KHVNLDKGKH 150
    VPSKPVSNTT SWAAAVSVDT KHDVPQDSND NNNEELEAQG QQAQEKNQEK 200
    EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK KMSWAAIATP 250
    KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE 300
    EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA 350
    APEEEVTVVE EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ 400
    QPQQPQQQQQ PQQPQQPQQQ LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ 450
    QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ HPQPQSQQPQ SQQSPQSQKQ 500
    GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA QNNAQTSGNA 550
    NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM 600
    PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG 650
    VAQHSEDSQQ KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ 700
    FQQQQQQAAA AAAAAAQQGV PYGYNGYDYN SKNSRGFY 738
    Length:738
    Mass (Da):83,973
    Last modified:June 1, 1994 - v1
    Checksum:i05734E2D0B7389AC
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X75781 Genomic DNA. Translation: CAA53418.1.
    Z28054 Genomic DNA. Translation: CAA81890.1.
    BK006944 Genomic DNA. Translation: DAA09103.1.
    PIRiS37876.
    RefSeqiNP_012869.1. NM_001179620.1.

    Genome annotation databases

    EnsemblFungiiYKL054C; YKL054C; YKL054C.
    GeneIDi853811.
    KEGGisce:YKL054C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X75781 Genomic DNA. Translation: CAA53418.1 .
    Z28054 Genomic DNA. Translation: CAA81890.1 .
    BK006944 Genomic DNA. Translation: DAA09103.1 .
    PIRi S37876.
    RefSeqi NP_012869.1. NM_001179620.1.

    3D structure databases

    ProteinModelPortali P35732.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34079. 75 interactions.
    DIPi DIP-6354N.
    IntActi P35732. 41 interactions.
    MINTi MINT-693440.
    STRINGi 4932.YKL054C.

    Proteomic databases

    MaxQBi P35732.
    PaxDbi P35732.
    PeptideAtlasi P35732.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YKL054C ; YKL054C ; YKL054C .
    GeneIDi 853811.
    KEGGi sce:YKL054C.

    Organism-specific databases

    CYGDi YKL054c.
    SGDi S000001537. DEF1.

    Phylogenomic databases

    eggNOGi NOG16498.
    OMAi WDEVKKP.
    OrthoDBi EOG7Z0K6R.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31854-MONOMER.

    Miscellaneous databases

    NextBioi 974978.

    Gene expression databases

    Genevestigatori P35732.

    Family and domain databases

    InterProi IPR003892. CUE.
    [Graphical view ]
    Pfami PF02845. CUE. 1 hit.
    [Graphical view ]
    PROSITEi PS51140. CUE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins."
      Rasmussen S.W.
      Yeast 10:S63-S68(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "Complete DNA sequence of yeast chromosome XI."
      Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
      , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
      Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage."
      Woudstra E.C., Gilbert C., Fellows J., Jansen L., Brouwer J., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
      Nature 415:929-933(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RAD26, FUNCTION.
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro."
      Reid J., Svejstrup J.Q.
      J. Biol. Chem. 279:29875-29878(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RNA POLYMERASE II, FUNCTION.
    7. "Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest."
      Somesh B.P., Reid J., Liu W.F., Sogaard T.M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
      Cell 121:913-923(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "Def1p is involved in telomere maintenance in budding yeast."
      Chen Y.B., Yang C.P., Li R.X., Zeng R., Zhou J.Q.
      J. Biol. Chem. 280:24784-24791(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RRM3, SUBCELLULAR LOCATION, DNA-BINDING, FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY.
    9. "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-260 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    10. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-273, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; THR-338 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; SER-307 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiDEF1_YEAST
    AccessioniPrimary (citable) accession number: P35732
    Secondary accession number(s): D6VXN3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: June 1, 1994
    Last modified: October 1, 2014
    This is version 111 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 3380 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 XI
      Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

    External Data

    Dasty 3