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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: 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

  • aspartic-type endopeptidase activity Source: InterPro
  • SNARE binding Source: SGD
  • ubiquitin binding Source: SGD

GO - Biological processi

  • protein secretion Source: SGD
  • ubiquitin-dependent protein catabolic process Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER143W.
SGDiS000000945. DDI1.

Subcellular locationi

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

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • 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.

PTM databases

iPTMnetiP40087.

Expressioni

Inductioni

By DNA damage via PDR3.4 Publications

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

GO - Molecular functioni

  • SNARE binding Source: SGD
  • ubiquitin binding Source: SGD

Protein-protein interaction databases

BioGridi36892. 44 interactions.
DIPiDIP-1216N.
IntActiP40087. 6 interactions.
MINTiMINT-397186.

Structurei

Secondary structure

1
428
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 64Combined sources
Turni8 – 103Combined sources
Beta strandi13 – 175Combined sources
Helixi25 – 3410Combined sources
Helixi40 – 423Combined sources
Beta strandi44 – 474Combined sources
Helixi60 – 634Combined sources
Beta strandi70 – 745Combined sources
Turni76 – 794Combined sources
Beta strandi205 – 2106Combined sources
Beta strandi213 – 2197Combined sources
Beta strandi227 – 2293Combined sources
Helixi230 – 2356Combined sources
Helixi239 – 2413Combined 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
Helixi320 – 3223Combined sources
Helixi392 – 3998Combined sources
Turni400 – 4023Combined sources
Helixi405 – 41511Combined sources
Helixi419 – 4268Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2I1AX-ray2.30A/B/C/D180-325[»]
2MR9NMR-A389-428[»]
2MRONMR-B389-428[»]
2MRPNMR-A2-80[»]
2MWSNMR-B2-80[»]
4Z2ZX-ray1.80A/B185-325[»]
ProteinModelPortaliP40087.
SMRiP40087. Positions 2-80, 201-323, 389-428.
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

GeneTreeiENSGT00510000047125.
HOGENOMiHOG000234736.
InParanoidiP40087.
KOiK11885.
OMAiYINIEIN.
OrthoDBiEOG092C4Q00.

Family and domain databases

Gene3Di2.40.70.10. 1 hit.
InterProiIPR033322. DDI1.
IPR001995. Peptidase_A2_cat.
IPR019103. Peptidase_aspartic_DDI1-type.
IPR021109. Peptidase_aspartic_dom.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PANTHERiPTHR12917:SF1. PTHR12917:SF1. 1 hit.
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.
PIRiS50646.
RefSeqiNP_011070.3. NM_001179033.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2I1AX-ray2.30A/B/C/D180-325[»]
2MR9NMR-A389-428[»]
2MRONMR-B389-428[»]
2MRPNMR-A2-80[»]
2MWSNMR-B2-80[»]
4Z2ZX-ray1.80A/B185-325[»]
ProteinModelPortaliP40087.
SMRiP40087. Positions 2-80, 201-323, 389-428.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36892. 44 interactions.
DIPiDIP-1216N.
IntActiP40087. 6 interactions.
MINTiMINT-397186.

Protein family/group databases

MEROPSiA28.001.

PTM databases

iPTMnetiP40087.

Proteomic databases

MaxQBiP40087.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YER143W.
SGDiS000000945. DDI1.

Phylogenomic databases

GeneTreeiENSGT00510000047125.
HOGENOMiHOG000234736.
InParanoidiP40087.
KOiK11885.
OMAiYINIEIN.
OrthoDBiEOG092C4Q00.

Enzyme and pathway databases

BioCyciYEAST:G3O-30304-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP40087.
PROiP40087.

Family and domain databases

Gene3Di2.40.70.10. 1 hit.
InterProiIPR033322. DDI1.
IPR001995. Peptidase_A2_cat.
IPR019103. Peptidase_aspartic_DDI1-type.
IPR021109. Peptidase_aspartic_dom.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PANTHERiPTHR12917:SF1. PTHR12917:SF1. 1 hit.
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]
ProtoNetiSearch...

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: September 7, 2016
This is version 151 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.