P36108 (DID4_YEAST) Reviewed, UniProtKB/Swiss-Prot

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 (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	232 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.4 Ref.5 Ref.7
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.5.
Sequence similarities	Belongs to the SNF7 family.
Sequence caution	The sequence CAA81834.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Cytoplasm Endosome Membrane
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	intralumenal vesicle formation Inferred from mutant phenotype. Source: SGD late endosome to vacuole transport Inferred from physical interaction Ref.5. 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 Inferred from direct assay Ref.5. Source: SGD
Complete GO annotation...

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

50

Interaction with VPS4

Coiled coil

14 – 97

84

Potential

Motif

219 – 229

11

MIT-interacting motif

Amino acid modifications

Modified residue

107

1

Phosphoserine Ref.9

Modified residue

211

1

Phosphoserine Ref.9

Experimental info

Mutagenesis

221

1

L → D: Abolishes interaction with VPS4. Ref.10

Mutagenesis

224

1

R → D: Abolishes interaction with VPS4. Impairs sorting. Ref.10

Mutagenesis

225

1

L → D: Abolishes interaction with VPS4. Ref.10

Mutagenesis

228 – 229

2

LK → DD: Greatly impairs sorting. Ref.10

Mutagenesis

228

1

L → D: Abolishes interaction with VPS4. Ref.10

Mutagenesis

229

1

K → D: Abolishes interaction with VPS4. Ref.10

Secondary structure

1

.

.

.

.

.

.

.

.

232

Helix Strand Turn

Details...

Helix

188 – 191

4

Helix

197 – 200

4

Beta strand

201 – 204

4

Helix

219 – 229

11

Sequences

	Sequence		Length	Mass (Da)
	P36108 [UniParc]. Last modified October 17, 2006. Version 2. Checksum: 200D07DB4C45DCBC	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

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. , 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: 8196765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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: 10734188] [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: 11559748] [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: 12194857] [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: 17949747] [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: 18194652] [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: 18854142] [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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-107 AND SER-211, MASS SPECTROMETRY.
[10]	"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z28002 Genomic DNA. Translation: CAA81834.1. Sequence problems.
BK006944 Genomic DNA. Translation: DAA09155.1.

PIR

S37812.

RefSeq

NP_012924.2. NM_001179568.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

P36108.

SMR

P36108. Positions 183-231.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1916N.

IntAct

P36108. 13 interactions.

MINT

MINT-404147.

STRING

P36108.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL002W; YKL002W; YKL002W.

GeneID

853868.

KEGG

sce:YKL002W.

NMPDR

fig|4932.3.peg.3910.

Organism-specific databases

CYGD

YKL002w.

SGD

S000001485. DID4.

Phylogenomic databases

eggNOG

fuNOG08950.

GeneTree

EFGT00050000003857.

HOGENOM

HBG464741.

OMA

VKKFIMM.

OrthoDB

EOG4WT0M1.

Gene expression databases

ArrayExpress

P36108.

Genevestigator

P36108.

GermOnline

YKL002W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005024. Snf7.
[Graphical view]

KO

K12191.

Pfam

PF03357. Snf7. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

975133.

Entry information

Entry name

DID4_YEAST

Accession

Primary (citable) accession number: P36108
Secondary accession number(s): D6VXT5

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	October 17, 2006
Last modified:	December 14, 2011
This is version 86 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program