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P40087

- DDI1_YEAST

UniProt

P40087 - DDI1_YEAST

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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

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. SNARE binding Source: SGD
  3. 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
Complete GO annotation...

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-KW
  2. plasma membrane Source: SGD
Complete GO annotation...

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. 41 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 – 2106Combined sources
Beta strandi213 – 2197Combined sources
Beta strandi227 – 2293Combined sources
Helixi230 – 2356Combined sources
Helixi238 – 2414Combined sources
Beta strandi260 – 26910Combined sources
Beta strandi272 – 28110Combined sources
Beta strandi286 – 2894Combined sources
Helixi291 – 2966Combined sources
Beta strandi300 – 3023Combined sources
Turni303 – 3064Combined sources
Beta strandi307 – 3104Combined sources
Beta strandi313 – 3164Combined sources
Turni320 – 3223Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP40087.
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

        10         20         30         40         50
MDLTISNELT GEIYGPIEVS EDMALTDLIA LLQADCGFDK TKHDLYYNMD
60 70 80 90 100
ILDSNRTQSL KELGLKTDDL LLIRGKISNS IQTDAATLSD EAFIEQFRQE
110 120 130 140 150
LLNNQMLRSQ LILQIPGLND LVNDPLLFRE RLGPLILQRR YGGYNTAMNP
160 170 180 190 200
FGIPQDEYTR LMANPDDPDN KKRIAELLDQ QAIDEQLRNA IEYTPEMFTQ
210 220 230 240 250
VPMLYINIEI NNYPVKAFVD TGAQTTIMST RLAKKTGLSR MIDKRFIGEA
260 270 280 290 300
RGVGTGKIIG RIHQAQVKIE TQYIPCSFTV LDTDIDVLIG LDMLKRHLAC
310 320 330 340 350
VDLKENVLRI AEVETSFLSE AEIPKSFQEG LPAPTSVTTS SDKPLTPTKT
360 370 380 390 400
SSTLPPQPGA VPALAPRTGM GPTPTGRSTA GATTATGRTF PEQTIKQLMD
410 420
LGFPRDAVVK ALKQTNGNAE FAASLLFQ
Length:428
Mass (Da):47,354
Last modified:February 1, 1995 - v1
Checksum:iB43425B029B7658B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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. 41 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.
InParanoidi P40087.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 135 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