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Protein

DOA4-independent degradation protein 4

Gene

DID4

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

Required for the sorting and concentration of proteins resulting in the entry of these proteins into the invaginating vesicles of the multivesicular body (MVB). Acts a component of the ESCRT-III complex, which appears to be critical for late steps in MVB sorting, such as membrane invagination and final cargo sorting and recruitment of late-acting components of the sorting machinery. The MVB pathway requires the sequential function of ESCRT-O, -I,-II and -III complex assemblies. Can directly stimulate VPS4 ATPase activity. The DID4/VPS2-VPS24 subcomplex is required for the VPS4-dependent dissociation of ESCRT-III.3 Publications

GO - Biological processi

  • ATP export Source: SGD
  • intralumenal vesicle formation Source: SGD
  • late endosome to vacuole transport Source: SGD
  • protein retention in Golgi apparatus Source: SGD
  • protein transport Source: UniProtKB-KW
  • ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Source: SGD
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-31813-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.
R-SCE-432720. Lysosome Vesicle Biogenesis.

Names & Taxonomyi

Protein namesi
Recommended name:
DOA4-independent degradation protein 4
Alternative name(s):
ESCRT-III complex subunit VPS2
Vacuolar protein-sorting-associated protein 2
Vacuolar protein-targeting protein 14
Gene namesi
Name:DID4
Synonyms:CHM2, GRD7, REN1, VPL2, VPS2, VPT14
Ordered Locus Names:YKL002W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL002W.
SGDiS000001485. DID4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • ESCRT III complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi221L → D: Abolishes interaction with VPS4. 1 Publication1
Mutagenesisi224R → D: Abolishes interaction with VPS4. Impairs sorting. 1 Publication1
Mutagenesisi225L → D: Abolishes interaction with VPS4. 1 Publication1
Mutagenesisi228 – 229LK → DD: Greatly impairs sorting. 2
Mutagenesisi228L → D: Abolishes interaction with VPS4. 1 Publication1
Mutagenesisi229K → D: Abolishes interaction with VPS4. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002114771 – 232DOA4-independent degradation protein 4Add BLAST232

Proteomic databases

MaxQBiP36108.
PRIDEiP36108.

PTM databases

iPTMnetiP36108.

Interactioni

Subunit structurei

Core component of the ESCRT-III complex (endosomal sorting required for transport complex III). ESCRT-III appears to be sequentially assembled as a flat lattice on the endosome membrane and forms a transient 450 kDa complex that contains DID4, oligomerized SNF7, VPS20 and VPS24. SNF7 oligomerization into a membrane-associated filament is nucleated by association of SNF7 with VPS20; the process is terminated through association of VPS24, possibly by capping the SNF7 filament. VPS24 subsequently associates with DID4/VPS2.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SNF7P399294EBI-26574,EBI-17554

Protein-protein interaction databases

BioGridi34131. 114 interactors.
DIPiDIP-1916N.
IntActiP36108. 16 interactors.
MINTiMINT-404147.

Structurei

Secondary structure

1232
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi188 – 191Combined sources4
Helixi197 – 200Combined sources4
Beta strandi201 – 204Combined sources4
Helixi219 – 229Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V6XX-ray1.98B183-232[»]
ProteinModelPortaliP36108.
SMRiP36108.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36108.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni183 – 232Interaction with VPS41 PublicationAdd BLAST50

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili14 – 97Sequence analysisAdd BLAST84

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi219 – 229MIT-interacting motifAdd BLAST11

Sequence similaritiesi

Belongs to the SNF7 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

GeneTreeiENSGT00550000074737.
HOGENOMiHOG000177218.
InParanoidiP36108.
KOiK12191.
OMAiNAKQGQM.
OrthoDBiEOG092C4XGL.

Family and domain databases

InterProiIPR005024. Snf7_fam.
[Graphical view]
PfamiPF03357. Snf7. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36108-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLFEWVFGK NVTPQERLKK NQRALERTQR ELEREKRKLE LQDKKLVSEI
60 70 80 90 100
KKSAKNGQVA AAKVQAKDLV RTRNYIQKFD NMKAQLQAIS LRIQAVRSSD
110 120 130 140 150
QMTRSMSEAT GLLAGMNRTM NLPQLQRISM EFEKQSDLMG QRQEFMDEAI
160 170 180 190 200
DNVMGDEVDE DEEADEIVNK VLDEIGVDLN SQLQSTPQNL VSNAPIAETA
210 220 230
MGIPEPIGAG SEFHGNPDDD LQARLNTLKK QT
Length:232
Mass (Da):26,291
Last modified:October 17, 2006 - v2
Checksum:i200D07DB4C45DCBC
GO

Sequence cautioni

The sequence CAA81834 differs from that shown. Reason: Erroneous gene model prediction.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z28002 Genomic DNA. Translation: CAA81834.1. Sequence problems.
BK006944 Genomic DNA. Translation: DAA09155.1.
PIRiS37812.
RefSeqiNP_012924.2. NM_001179568.1.

Genome annotation databases

EnsemblFungiiYKL002W; YKL002W; YKL002W.
GeneIDi853868.
KEGGisce:YKL002W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z28002 Genomic DNA. Translation: CAA81834.1. Sequence problems.
BK006944 Genomic DNA. Translation: DAA09155.1.
PIRiS37812.
RefSeqiNP_012924.2. NM_001179568.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V6XX-ray1.98B183-232[»]
ProteinModelPortaliP36108.
SMRiP36108.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34131. 114 interactors.
DIPiDIP-1916N.
IntActiP36108. 16 interactors.
MINTiMINT-404147.

PTM databases

iPTMnetiP36108.

Proteomic databases

MaxQBiP36108.
PRIDEiP36108.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL002W; YKL002W; YKL002W.
GeneIDi853868.
KEGGisce:YKL002W.

Organism-specific databases

EuPathDBiFungiDB:YKL002W.
SGDiS000001485. DID4.

Phylogenomic databases

GeneTreeiENSGT00550000074737.
HOGENOMiHOG000177218.
InParanoidiP36108.
KOiK12191.
OMAiNAKQGQM.
OrthoDBiEOG092C4XGL.

Enzyme and pathway databases

BioCyciYEAST:G3O-31813-MONOMER.
ReactomeiR-SCE-1632852. Macroautophagy.
R-SCE-432720. Lysosome Vesicle Biogenesis.

Miscellaneous databases

EvolutionaryTraceiP36108.
PROiP36108.

Family and domain databases

InterProiIPR005024. Snf7_fam.
[Graphical view]
PfamiPF03357. Snf7. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDID4_YEAST
AccessioniPrimary (citable) accession number: P36108
Secondary accession number(s): D6VXT5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: October 17, 2006
Last modified: November 2, 2016
This is version 127 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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 XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: 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.