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P52490

- UBC13_YEAST

UniProt

P52490 - UBC13_YEAST

Protein

Ubiquitin-conjugating enzyme E2 13

Gene

UBC13

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 131 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    Has a role in the DNA error-free postreplication repair (PRR) pathway. The UBC13/MMS2 heterodimer catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'.

    Catalytic activityi

    ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.PROSITE-ProRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei87 – 871Glycyl thioester intermediate

    GO - Molecular functioni

    1. acid-amino acid ligase activity Source: InterPro
    2. ATP binding Source: UniProtKB-KW
    3. protein binding Source: IntAct

    GO - Biological processi

    1. free ubiquitin chain polymerization Source: SGD
    2. postreplication repair Source: SGD
    3. protein monoubiquitination Source: SGD
    4. protein polyubiquitination Source: SGD

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29697-MONOMER.
    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin-conjugating enzyme E2 13 (EC:6.3.2.19)
    Alternative name(s):
    Ubiquitin carrier protein 13
    Ubiquitin-protein ligase 13
    Gene namesi
    Name:UBC13
    Ordered Locus Names:YDR092W
    ORF Names:YD6652.04
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR092w.
    SGDiS000002499. UBC13.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. nucleus Source: SGD
    3. ubiquitin conjugating enzyme complex Source: SGD

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi55 – 551E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair. 1 Publication
    Mutagenesisi81 – 811D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site.
    Mutagenesisi110 – 1101A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 153153Ubiquitin-conjugating enzyme E2 13PRO_0000082565Add
    BLAST

    Proteomic databases

    PaxDbiP52490.
    PeptideAtlasiP52490.

    Expressioni

    Gene expression databases

    GenevestigatoriP52490.

    Interactioni

    Subunit structurei

    Heterodimer with MMS2.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    MMS2P531524EBI-19777,EBI-11035

    Protein-protein interaction databases

    BioGridi32149. 137 interactions.
    DIPiDIP-5486N.
    IntActiP52490. 6 interactions.
    MINTiMINT-533850.
    STRINGi4932.YDR092W.

    Structurei

    Secondary structure

    1
    153
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712
    Beta strandi23 – 286
    Beta strandi31 – 4010
    Turni46 – 494
    Beta strandi50 – 578
    Turni60 – 645
    Beta strandi68 – 714
    Helixi89 – 913
    Turni92 – 943
    Helixi101 – 11313
    Helixi126 – 1316
    Helixi133 – 14715
    Beta strandi148 – 1503

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JATX-ray1.60A2-153[»]
    1JBBX-ray2.00A/B1-153[»]
    2GMIX-ray2.50A1-152[»]
    4FH1X-ray2.61A1-152[»]
    ProteinModelPortaliP52490.
    SMRiP52490. Positions 2-152.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP52490.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ubiquitin-conjugating enzyme family.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG5078.
    GeneTreeiENSGT00540000070023.
    HOGENOMiHOG000233455.
    KOiK10580.
    OMAiDVAKHYK.
    OrthoDBiEOG7SBP18.

    Family and domain databases

    Gene3Di3.10.110.10. 1 hit.
    InterProiIPR000608. UBQ-conjugat_E2.
    IPR023313. UBQ-conjugating_AS.
    IPR016135. UBQ-conjugating_enzyme/RWD.
    [Graphical view]
    PfamiPF00179. UQ_con. 1 hit.
    [Graphical view]
    SUPFAMiSSF54495. SSF54495. 1 hit.
    PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
    PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P52490-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG    50
    IFELELYLPD DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ 100
    IRTVLLSIQA LLASPNPNDP LANDVAEDWI KNEQGAKAKA REWTKLYAKK 150
    KPE 153
    Length:153
    Mass (Da):17,468
    Last modified:October 1, 1996 - v1
    Checksum:i445558F8F193275B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X99443 Genomic DNA. Translation: CAA67806.1.
    Z50111 Genomic DNA. Translation: CAA90451.1.
    BK006938 Genomic DNA. Translation: DAA11939.1.
    PIRiS58092.
    RefSeqiNP_010377.3. NM_001180400.3.

    Genome annotation databases

    EnsemblFungiiYDR092W; YDR092W; YDR092W.
    GeneIDi851666.
    KEGGisce:YDR092W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X99443 Genomic DNA. Translation: CAA67806.1 .
    Z50111 Genomic DNA. Translation: CAA90451.1 .
    BK006938 Genomic DNA. Translation: DAA11939.1 .
    PIRi S58092.
    RefSeqi NP_010377.3. NM_001180400.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1JAT X-ray 1.60 A 2-153 [» ]
    1JBB X-ray 2.00 A/B 1-153 [» ]
    2GMI X-ray 2.50 A 1-152 [» ]
    4FH1 X-ray 2.61 A 1-152 [» ]
    ProteinModelPortali P52490.
    SMRi P52490. Positions 2-152.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32149. 137 interactions.
    DIPi DIP-5486N.
    IntActi P52490. 6 interactions.
    MINTi MINT-533850.
    STRINGi 4932.YDR092W.

    Proteomic databases

    PaxDbi P52490.
    PeptideAtlasi P52490.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR092W ; YDR092W ; YDR092W .
    GeneIDi 851666.
    KEGGi sce:YDR092W.

    Organism-specific databases

    CYGDi YDR092w.
    SGDi S000002499. UBC13.

    Phylogenomic databases

    eggNOGi COG5078.
    GeneTreei ENSGT00540000070023.
    HOGENOMi HOG000233455.
    KOi K10580.
    OMAi DVAKHYK.
    OrthoDBi EOG7SBP18.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .
    BioCyci YEAST:G3O-29697-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P52490.
    NextBioi 969283.
    PROi P52490.

    Gene expression databases

    Genevestigatori P52490.

    Family and domain databases

    Gene3Di 3.10.110.10. 1 hit.
    InterProi IPR000608. UBQ-conjugat_E2.
    IPR023313. UBQ-conjugating_AS.
    IPR016135. UBQ-conjugating_enzyme/RWD.
    [Graphical view ]
    Pfami PF00179. UQ_con. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54495. SSF54495. 1 hit.
    PROSITEi PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
    PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification of a novel family of ubiquitin-conjugating enzymes with distinct amino-terminal extensions."
      Matuschewski K., Hauser H.P., Treier M., Jentsch S.
      J. Biol. Chem. 271:2789-2794(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 200912 / DF5.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [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. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    5. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    6. "Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer."
      VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., Wolberger C.
      Cell 105:711-720(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH MMS2, MUTAGENESIS OF GLU-55.

    Entry informationi

    Entry nameiUBC13_YEAST
    AccessioniPrimary (citable) accession number: P52490
    Secondary accession number(s): D6VS79
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 131 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 8970 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3