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P40087

- DDI1_YEAST

UniProt

P40087 - DDI1_YEAST

Protein

DNA damage-inducible protein 1

Gene

DDI1

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 133 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Acts as a linker between the 19S proteasome and polyubiquitinated proteins like the HO endonuclease and UFO1 via UBA domain interactions with ubiquitin for their subsequent degradation. Required for S-phase checkpoint control. Appears to act as negative regulator of constitutive exocytosis. May act at the level of secretory vesicle docking and fusion as a competitive inhibitor of SNARE assembly.7 Publications

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: SGD
    2. protein binding Source: IntAct
    3. SNARE binding Source: SGD
    4. ubiquitin binding Source: SGD

    GO - Biological processi

    1. protein secretion Source: SGD
    2. ubiquitin-dependent protein catabolic process Source: SGD
    3. vesicle-mediated transport Source: SGD

    Keywords - Biological processi

    Protein transport, Transport

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30304-MONOMER.

    Protein family/group databases

    MEROPSiA28.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA damage-inducible protein 1
    Alternative name(s):
    v-SNARE-master 1
    Gene namesi
    Name:DDI1
    Synonyms:VSM1
    Ordered Locus Names:YER143W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER143w.
    SGDiS000000945. DDI1.

    Subcellular locationi

    Cytoplasm 1 Publication. Cell membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. plasma membrane Source: SGD

    Keywords - Cellular componenti

    Cell membrane, Cytoplasm, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 428428DNA damage-inducible protein 1PRO_0000210997Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki171 – 171Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki257 – 257Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    MaxQBiP40087.
    PaxDbiP40087.
    PeptideAtlasiP40087.

    Expressioni

    Inductioni

    By DNA damage via PDR3.4 Publications

    Gene expression databases

    GenevestigatoriP40087.

    Interactioni

    Subunit structurei

    Forms homodimers. Interacts with RAD23. These interactions are mediated by the UBA domain. Is also able to bind ubiquitin and polyubiquitinated proteins. Interacts with the SNAREs SNC1, SNC2, SSO1, TLG1 and TLG2. Binding to SSO1 is promoted by the phosphorylation of 'Ser-49' of SSO1 by TKP1.7 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    UBCP0CG482EBI-5717,EBI-3390054From a different organism.
    UBI4P0CG633EBI-5717,EBI-7000452

    Protein-protein interaction databases

    BioGridi36892. 40 interactions.
    DIPiDIP-1216N.
    IntActiP40087. 6 interactions.
    MINTiMINT-397186.
    STRINGi4932.YER143W.

    Structurei

    Secondary structure

    1
    428
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi205 – 2106
    Beta strandi213 – 2197
    Beta strandi227 – 2293
    Helixi230 – 2356
    Helixi238 – 2414
    Beta strandi260 – 26910
    Beta strandi272 – 28110
    Beta strandi286 – 2894
    Helixi291 – 2966
    Beta strandi300 – 3023
    Turni303 – 3064
    Beta strandi307 – 3104
    Beta strandi313 – 3164
    Turni320 – 3223

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I1AX-ray2.30A/B/C/D180-325[»]
    ProteinModelPortaliP40087.
    SMRiP40087. Positions 201-323.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40087.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 8080Ubiquitin-likeAdd
    BLAST
    Domaini389 – 42840UBAPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the DDI1 family.Curated
    Contains 1 UBA domain.PROSITE-ProRule annotation
    Contains 1 ubiquitin-like domain.Curated

    Phylogenomic databases

    eggNOGiNOG276681.
    GeneTreeiENSGT00510000047125.
    HOGENOMiHOG000234736.
    KOiK11885.
    OMAiAWEISPE.
    OrthoDBiEOG7327ZT.

    Family and domain databases

    Gene3Di2.40.70.10. 1 hit.
    InterProiIPR001995. Peptidase_A2_cat.
    IPR019103. Peptidase_aspartic_DDI1-type.
    IPR021109. Peptidase_aspartic_dom.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR029071. Ubiquitin-rel_dom.
    [Graphical view]
    PfamiPF09668. Asp_protease. 1 hit.
    PF00627. UBA. 1 hit.
    [Graphical view]
    SMARTiSM00165. UBA. 1 hit.
    [Graphical view]
    SUPFAMiSSF46934. SSF46934. 1 hit.
    SSF50630. SSF50630. 1 hit.
    SSF54236. SSF54236. 1 hit.
    PROSITEiPS50030. UBA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40087-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDLTISNELT GEIYGPIEVS EDMALTDLIA LLQADCGFDK TKHDLYYNMD    50
    ILDSNRTQSL KELGLKTDDL LLIRGKISNS IQTDAATLSD EAFIEQFRQE 100
    LLNNQMLRSQ LILQIPGLND LVNDPLLFRE RLGPLILQRR YGGYNTAMNP 150
    FGIPQDEYTR LMANPDDPDN KKRIAELLDQ QAIDEQLRNA IEYTPEMFTQ 200
    VPMLYINIEI NNYPVKAFVD TGAQTTIMST RLAKKTGLSR MIDKRFIGEA 250
    RGVGTGKIIG RIHQAQVKIE TQYIPCSFTV LDTDIDVLIG LDMLKRHLAC 300
    VDLKENVLRI AEVETSFLSE AEIPKSFQEG LPAPTSVTTS SDKPLTPTKT 350
    SSTLPPQPGA VPALAPRTGM GPTPTGRSTA GATTATGRTF PEQTIKQLMD 400
    LGFPRDAVVK ALKQTNGNAE FAASLLFQ 428
    Length:428
    Mass (Da):47,354
    Last modified:February 1, 1995 - v1
    Checksum:iB43425B029B7658B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U14002 Genomic DNA. Translation: AAB82066.1.
    AF034895 Genomic DNA. Translation: AAC18522.1.
    U18917 Genomic DNA. Translation: AAB64670.1.
    AY692945 Genomic DNA. Translation: AAT92964.1.
    BK006939 Genomic DNA. Translation: DAA07804.1.
    PIRiS50646.
    RefSeqiNP_011070.3. NM_001179033.3.

    Genome annotation databases

    EnsemblFungiiYER143W; YER143W; YER143W.
    GeneIDi856886.
    KEGGisce:YER143W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U14002 Genomic DNA. Translation: AAB82066.1 .
    AF034895 Genomic DNA. Translation: AAC18522.1 .
    U18917 Genomic DNA. Translation: AAB64670.1 .
    AY692945 Genomic DNA. Translation: AAT92964.1 .
    BK006939 Genomic DNA. Translation: DAA07804.1 .
    PIRi S50646.
    RefSeqi NP_011070.3. NM_001179033.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2I1A X-ray 2.30 A/B/C/D 180-325 [» ]
    ProteinModelPortali P40087.
    SMRi P40087. Positions 201-323.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36892. 40 interactions.
    DIPi DIP-1216N.
    IntActi P40087. 6 interactions.
    MINTi MINT-397186.
    STRINGi 4932.YER143W.

    Protein family/group databases

    MEROPSi A28.001.

    Proteomic databases

    MaxQBi P40087.
    PaxDbi P40087.
    PeptideAtlasi P40087.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER143W ; YER143W ; YER143W .
    GeneIDi 856886.
    KEGGi sce:YER143W.

    Organism-specific databases

    CYGDi YER143w.
    SGDi S000000945. DDI1.

    Phylogenomic databases

    eggNOGi NOG276681.
    GeneTreei ENSGT00510000047125.
    HOGENOMi HOG000234736.
    KOi K11885.
    OMAi AWEISPE.
    OrthoDBi EOG7327ZT.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30304-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P40087.
    NextBioi 983281.
    PROi P40087.

    Gene expression databases

    Genevestigatori P40087.

    Family and domain databases

    Gene3Di 2.40.70.10. 1 hit.
    InterProi IPR001995. Peptidase_A2_cat.
    IPR019103. Peptidase_aspartic_DDI1-type.
    IPR021109. Peptidase_aspartic_dom.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR029071. Ubiquitin-rel_dom.
    [Graphical view ]
    Pfami PF09668. Asp_protease. 1 hit.
    PF00627. UBA. 1 hit.
    [Graphical view ]
    SMARTi SM00165. UBA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46934. SSF46934. 1 hit.
    SSF50630. SSF50630. 1 hit.
    SSF54236. SSF54236. 1 hit.
    PROSITEi PS50030. UBA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Bidirectional regulation of two DNA-damage-inducible genes, MAG1 and DDI1, from Saccharomyces cerevisiae."
      Liu Y., Xiao W.
      Mol. Microbiol. 23:777-789(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
      Strain: ATCC 64665 / S288c / DC5.
    2. "Yeast VSM1 encodes a v-SNARE binding protein that may act as a negative regulator of constitutive exocytosis."
      Lustgarten V., Gerst J.E.
      Mol. Cell. Biol. 19:4480-4494(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH SNC1 AND SNC2, SUBCELLULAR LOCATION.
    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. "Differential regulation of two closely clustered yeast genes, MAG1 and DDI1, by cell-cycle checkpoints."
      Zhu Y., Xiao W.
      Nucleic Acids Res. 26:5402-5408(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    7. "UBA domains mediate protein-protein interactions between two DNA damage-inducible proteins."
      Bertolaet B.L., Clarke D.J., Wolff M., Watson M.H., Henze M., Divita G., Reed S.I.
      J. Mol. Biol. 313:955-963(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, INTERACTION WITH RAD23.
    8. "Dosage suppressors of pds1 implicate ubiquitin-associated domains in checkpoint control."
      Clarke D.J., Mondesert G., Segal M., Bertolaet B.L., Jensen S., Wolff M., Henze M., Reed S.I.
      Mol. Cell. Biol. 21:1997-2007(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Two alternative cell cycle checkpoint pathways differentially control DNA damage-dependent induction of MAG1 and DDI1 expression in yeast."
      Zhu Y., Xiao W.
      Mol. Genet. Genomics 266:436-444(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    10. "Ubiquitin-like proteins and Rpn10 play cooperative roles in ubiquitin-dependent proteolysis."
      Saeki Y., Saitoh A., Toh-e A., Yokosawa H.
      Biochem. Biophys. Res. Commun. 293:986-992(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "Phosphorylation of the autoinhibitory domain of the Sso t-SNAREs promotes binding of the Vsm1 SNARE regulator in yeast."
      Marash M., Gerst J.E.
      Mol. Biol. Cell 14:3114-3125(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH SNC1; SNC2; SSO; TLG1 AND TLG2.
    12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    13. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-171.
      Strain: SUB592.
    14. "A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
      Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
      Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-257.
    15. "Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element."
      Zhu Y., Xiao W.
      Nucleic Acids Res. 32:5066-5075(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    16. "The DNA damage-inducible UbL-UbA protein Ddi1 participates in Mec1-mediated degradation of Ho endonuclease."
      Kaplun L., Tzirkin R., Bakhrat A., Shabek N., Ivantsiv Y., Raveh D.
      Mol. Cell. Biol. 25:5355-5362(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH THE HO ENDONUCLEASE.
    17. "Yeast UBL-UBA proteins have partially redundant functions in cell cycle control."
      Diaz-Martinez L.A., Kang Y., Walters K.J., Clarke D.J.
      Cell Div. 1:28-28(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    18. "Unique role for the UbL-UbA protein Ddi1 in turnover of SCFUfo1 complexes."
      Ivantsiv Y., Kaplun L., Tzirkin-Goldin R., Shabek N., Raveh D.
      Mol. Cell. Biol. 26:1579-1588(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH UFO1.
    19. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    20. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    21. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    22. "Ddi1, a eukaryotic protein with the retroviral protease fold."
      Sirkis R., Gerst J.E., Fass D.
      J. Mol. Biol. 364:376-387(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 180-325, SUBUNIT.

    Entry informationi

    Entry nameiDDI1_YEAST
    AccessioniPrimary (citable) accession number: P40087
    Secondary accession number(s): D3DM50
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 133 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 6510 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3