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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

  • 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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi221 – 2211L → D: Abolishes interaction with VPS4. 1 Publication
Mutagenesisi224 – 2241R → D: Abolishes interaction with VPS4. Impairs sorting. 1 Publication
Mutagenesisi225 – 2251L → D: Abolishes interaction with VPS4. 1 Publication
Mutagenesisi228 – 2292LK → DD: Greatly impairs sorting.
Mutagenesisi228 – 2281L → D: Abolishes interaction with VPS4. 1 Publication
Mutagenesisi229 – 2291K → D: Abolishes interaction with VPS4. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 232232DOA4-independent degradation protein 4PRO_0000211477Add
BLAST

Proteomic databases

MaxQBiP36108.

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 interactions.
DIPiDIP-1916N.
IntActiP36108. 16 interactions.
MINTiMINT-404147.

Structurei

Secondary structure

1
232
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi188 – 1914Combined sources
Helixi197 – 2004Combined sources
Beta strandi201 – 2044Combined sources
Helixi219 – 22911Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V6XX-ray1.98B183-232[»]
ProteinModelPortaliP36108.
SMRiP36108. Positions 14-135, 183-231.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36108.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni183 – 23250Interaction with VPS4Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili14 – 9784Sequence analysisAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi219 – 22911MIT-interacting motifAdd
BLAST

Sequence similaritiesi

Belongs to the SNF7 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

GeneTreeiENSGT00550000074737.
HOGENOMiHOG000177218.
InParanoidiP36108.
KOiK12191.
OMAiRTRYHIQ.
OrthoDBiEOG7S7SRV.

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 CAA81834.1 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
EntryMethodResolution (Å)ChainPositionsPDBsum
2V6XX-ray1.98B183-232[»]
ProteinModelPortaliP36108.
SMRiP36108. Positions 14-135, 183-231.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP36108.

Proteomic databases

MaxQBiP36108.

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.
OMAiRTRYHIQ.
OrthoDBiEOG7S7SRV.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP36108.
NextBioi975133.
PROiP36108.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  1. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast."
    Davis C.A., Grate L., Spingola M., Ares M. Jr.
    Nucleic Acids Res. 28:1700-1706(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF INTRON.
  4. "CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins."
    Howard T.L., Stauffer D.R., Degnin C.R., Hollenberg S.M.
    J. Cell Sci. 114:2395-2404(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Escrt-III: an endosome-associated heterooligomeric protein complex required for mvb sorting."
    Babst M., Katzmann D.J., Estepa-Sabal E.J., Meerloo T., Emr S.D.
    Dev. Cell 3:271-282(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE ESCRT-III COMPLEX, INTERACTION WITH VPS24, SUBCELLULAR LOCATION.
  6. "Structural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4."
    Xiao J., Xia H., Yoshino-Koh K., Zhou J., Xu Z.
    J. Mol. Biol. 374:655-670(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VPS4.
  7. "ESCRT-III family members stimulate Vps4 ATPase activity directly or via Vta1."
    Azmi I.F., Davies B.A., Xiao J., Babst M., Xu Z., Katzmann D.J.
    Dev. Cell 14:50-61(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Ordered assembly of the ESCRT-III complex on endosomes is required to sequester cargo during MVB formation."
    Teis D., Saksena S., Emr S.D.
    Dev. Cell 15:578-589(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: ASSEMBLY OF THE ESCRT-III COMPLEX.
  9. "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].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4."
    Obita T., Saksena S., Ghazi-Tabatabai S., Gill D.J., Perisic O., Emr S.D., Williams R.L.
    Nature 449:735-739(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 183-232 IN COMPLEX WITH VPS4, MUTAGENESIS OF LEU-221; ARG-224; LEU-225; LEU-228 AND LYS-229.

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: May 11, 2016
This is version 123 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.