Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P40087 (DDI1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA damage-inducible protein 1
Alternative name(s):
v-SNARE-master 1
Gene names
Name:DDI1
Synonyms:VSM1
Ordered Locus Names:YER143W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length428 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.8 Ref.10 Ref.11 Ref.16 Ref.17 Ref.18

Subunit structure

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. Ref.2 Ref.7 Ref.11 Ref.16 Ref.17 Ref.18 Ref.22

Subcellular location

Cytoplasm. Cell membrane; Peripheral membrane protein; Cytoplasmic side Ref.2.

Induction

By DNA damage via PDR3. Ref.1 Ref.6 Ref.9 Ref.15

Miscellaneous

Present with 6510 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the DDI1 family.

Contains 1 UBA domain.

Contains 1 ubiquitin-like domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

UBCP0CG482EBI-5717,EBI-3390054From a different organism.
UBI4P0CG633EBI-5717,EBI-7000452

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 428428DNA damage-inducible protein 1
PRO_0000210997

Regions

Domain1 – 8080Ubiquitin-like
Domain389 – 42840UBA

Amino acid modifications

Cross-link171Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.13
Cross-link257Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.14

Secondary structure

.......................... 428
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40087 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: B43425B029B7658B

FASTA42847,354
        10         20         30         40         50         60 
MDLTISNELT GEIYGPIEVS EDMALTDLIA LLQADCGFDK TKHDLYYNMD ILDSNRTQSL 

        70         80         90        100        110        120 
KELGLKTDDL LLIRGKISNS IQTDAATLSD EAFIEQFRQE LLNNQMLRSQ LILQIPGLND 

       130        140        150        160        170        180 
LVNDPLLFRE RLGPLILQRR YGGYNTAMNP FGIPQDEYTR LMANPDDPDN KKRIAELLDQ 

       190        200        210        220        230        240 
QAIDEQLRNA IEYTPEMFTQ VPMLYINIEI NNYPVKAFVD TGAQTTIMST RLAKKTGLSR 

       250        260        270        280        290        300 
MIDKRFIGEA RGVGTGKIIG RIHQAQVKIE TQYIPCSFTV LDTDIDVLIG LDMLKRHLAC 

       310        320        330        340        350        360 
VDLKENVLRI AEVETSFLSE AEIPKSFQEG LPAPTSVTTS SDKPLTPTKT SSTLPPQPGA 

       370        380        390        400        410        420 
VPALAPRTGM GPTPTGRSTA GATTATGRTF PEQTIKQLMD LGFPRDAVVK ALKQTNGNAE 


FAASLLFQ 

« Hide

References

« Hide 'large scale' references
[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]"The nucleotide sequence of Saccharomyces cerevisiae chromosome V."
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. expand/collapse author list , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.
Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[13]"A proteomics approach to understanding protein ubiquitination."
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.
Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS50646.
RefSeqNP_011070.3. NM_001179033.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2I1AX-ray2.30A/B/C/D180-325[»]
ProteinModelPortalP40087.
SMRP40087. Positions 1-88, 201-323, 391-428.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36892. 40 interactions.
DIPDIP-1216N.
IntActP40087. 6 interactions.
MINTMINT-397186.
STRING4932.YER143W.

Protein family/group databases

MEROPSA28.001.

Proteomic databases

PaxDbP40087.
PeptideAtlasP40087.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYER143W; YER143W; YER143W.
GeneID856886.
KEGGsce:YER143W.

Organism-specific databases

CYGDYER143w.
SGDS000000945. DDI1.

Phylogenomic databases

eggNOGNOG276681.
GeneTreeENSGT00510000047125.
HOGENOMHOG000234736.
KOK11885.
OMANQARISE.
OrthoDBEOG7327ZT.

Enzyme and pathway databases

BioCycYEAST:G3O-30304-MONOMER.

Gene expression databases

GenevestigatorP40087.

Family and domain databases

Gene3D2.40.70.10. 1 hit.
InterProIPR001995. 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.
[Graphical view]
PfamPF09668. Asp_protease. 1 hit.
PF00627. UBA. 1 hit.
[Graphical view]
SMARTSM00165. UBA. 1 hit.
[Graphical view]
SUPFAMSSF46934. SSF46934. 1 hit.
SSF50630. SSF50630. 1 hit.
PROSITEPS50030. UBA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP40087.
NextBio983281.
PROP40087.

Entry information

Entry nameDDI1_YEAST
AccessionPrimary (citable) accession number: P40087
Secondary accession number(s): D3DM50
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: March 19, 2014
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome V

Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references