DOA4-independent degradation protein 4 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P36108 (DID4_YEAST)

Last modified December 15, 2009. Version 68. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

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 names

Name:	DID4
Synonyms:	CHM2, GRD7, REN1, VPL2, VPS2, VPT14
Ordered Locus Names:	YKL002W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	232 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	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. Ref.3 Ref.4 Ref.6
Subunit structure	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.
Subcellular location	Cytoplasm. Endosome membrane; Peripheral membrane protein Ref.4.
Sequence similarities	Belongs to the SNF7 family.
Sequence caution	The sequence CAA81834.1 differs from that shown. Reason: Erroneous gene model prediction.

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Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Cytoplasm Endosome Membrane
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	intralumenal vesicle formation Inferred from mutant phenotype. Source: SGD late endosome to vacuole transport Ref.4 Inferred from physical interaction. Source: SGD protein retention in Golgi apparatus Inferred from mutant phenotype. Source: SGD protein transport Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Inferred by curator. Source: SGD
Cellular component	ESCRT III complex Ref.4 Inferred from direct assay. Source: SGD extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	identical protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
itself		1	EBI-26574,EBI-26574
ATG17	Q06410	1	EBI-26574,EBI-30856
DID2	P69771	1	EBI-26574,EBI-2053489
JSN1	P47135	1	EBI-26574,EBI-9422
MOB2	P43563	1	EBI-26574,EBI-11125
NOT2	P06100	1	EBI-26574,EBI-12153
SNF7	P39929	1	EBI-26574,EBI-17554
STD1	Q02794	1	EBI-26574,EBI-18344

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 232

232

DOA4-independent degradation protein 4

PRO_0000211477

Regions

Region

183 – 232

Interaction with VPS4

Coiled coil

14 – 97

Potential

Motif

219 – 229

MIT-interacting motif

Amino acid modifications

Modified residue

107

Phosphoserine Ref.8

Modified residue

211

Phosphoserine Ref.8

Experimental info

Mutagenesis

221

L → D: Abolishes interaction with VPS4. Ref.9

Mutagenesis

224

R → D: Abolishes interaction with VPS4. Impairs sorting. Ref.9

Mutagenesis

225

L → D: Abolishes interaction with VPS4. Ref.9

Mutagenesis

228 – 229

LK → DD: Greatly impairs sorting. Ref.9

Mutagenesis

228

L → D: Abolishes interaction with VPS4. Ref.9

Mutagenesis

229

K → D: Abolishes interaction with VPS4. Ref.9

Secondary structure

232

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P36108-1 [UniParc].

Last modified October 17, 2006. Version 2.
Checksum: 200D07DB4C45DCBC
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FASTA

232

26,291

        10         20         30         40         50         60 
MSLFEWVFGK NVTPQERLKK NQRALERTQR ELEREKRKLE LQDKKLVSEI KKSAKNGQVA 

        70         80         90        100        110        120 
AAKVQAKDLV RTRNYIQKFD NMKAQLQAIS LRIQAVRSSD QMTRSMSEAT GLLAGMNRTM 

       130        140        150        160        170        180 
NLPQLQRISM EFEKQSDLMG QRQEFMDEAI DNVMGDEVDE DEEADEIVNK VLDEIGVDLN 

       190        200        210        220        230 
SQLQSTPQNL VSNAPIAETA MGIPEPIGAG SEFHGNPDDD LQARLNTLKK QT

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. Mewes H.-W. Nature 369:371-378(1994) [PubMed: 8196765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	"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: 10734188] [Abstract] Cited for: IDENTIFICATION OF INTRON.
[3]	"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: 11559748] [Abstract] Cited for: FUNCTION.
[4]	"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: 12194857] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE ESCRT-III COMPLEX, INTERACTION WITH VPS24, SUBCELLULAR LOCATION.
[5]	"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: 17949747] [Abstract] Cited for: INTERACTION WITH VPS4.
[6]	"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: 18194652] [Abstract] Cited for: FUNCTION.
[7]	"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: 18854142] [Abstract] Cited for: ASSEMBLY OF THE ESCRT-III COMPLEX.
[8]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-107 AND SER-211, MASS SPECTROMETRY.
[9]	"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: 17928861] [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.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

Z28002 Genomic DNA. Translation: CAA81834.1. Sequence problems.

PIR

S37812.

RefSeq

NP_012924.2.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2V6X	X-ray	1.98	B	183-232	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1916N.

IntAct

P36108. 47 interactions.

STRING

P36108.

Genome annotation databases

Ensembl

YKL002W; YKL002W; YKL002W; Saccharomyces cerevisiae. [Genome view]

GeneID

853868.

KEGG

sce:YKL002W.

NMPDR

fig|4932.3.peg.3910.

Organism-specific databases

CYGD

YKL002w.

SGD

S000001485. DID4.

Phylogenomic databases

HOGENOM

HBG464741.

OMA

FEKQSEI.

OrthoDB

EOG92VB01.

Gene expression databases

ArrayExpress

P36108.

Genevestigator

P36108.

GermOnline

YKL002W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005024. Snf7.
[Graphical view]

Pfam

PF03357. Snf7. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

975133.

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Entry information

Entry name

DID4_YEAST

Accession

Primary (citable) accession number: P36108

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	October 17, 2006
Last modified:	December 15, 2009
This is version 68 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

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

Yeast chromosome XI

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

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents