Q12241 (VAM3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Syntaxin VAM3

Alternative name(s):
Vacuolar morphogenesis protein 3

Gene names

Name:	VAM3
Synonyms:	PTH1
Ordered Locus Names:	YOR106W
ORF Names:	YOR3220W

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	283 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for vacuolar assembly. Provides the t-SNARE function in a late step of the vacuolar assembly. Required for homotypic vacuole membrane fusion, autophagy and fusion of biosynthetic transport vesicles with the vacuole. Required for the delivery of alpha-factor receptor-ligand complexes to the vacuole.
Subunit structure	Associates with VAM7.
Subcellular location	Vacuole membrane; Single-pass type IV membrane protein.
Miscellaneous	Present with 414 molecules/cell in log phase SD medium. Ref.7
Sequence similarities	Belongs to the syntaxin family. Contains 1 t-SNARE coiled-coil homology domain.

Ontologies

Keywords
Biological process	Autophagy
Cellular component	Membrane Vacuole
Domain	Coiled coil Transmembrane Transmembrane helix
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	autophagic vacuole fusion Inferred from mutant phenotype Ref.1. Source: SGD intracellular protein transport Inferred from electronic annotation. Source: InterPro piecemeal microautophagy of nucleus Inferred from mutant phenotype. Source: SGD vacuole fusion, non-autophagic Inferred from direct assay. Source: SGD vesicle docking Inferred from genetic interaction Ref.5. Source: SGD vesicle fusion with vacuole Inferred from genetic interaction Ref.5. Source: SGD
Cellular component	SNARE complex Inferred from direct assay. Source: SGD fungal-type vacuole membrane Inferred from direct assay Ref.1. Source: SGD integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	SNAP receptor activity Inferred from direct assay. Source: SGD protein homodimerization activity Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
VAM7	P32912	4	EBI-20227,EBI-20232

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 283

283

Syntaxin VAM3

PRO_0000210280

Regions

Topological domain

1 – 261

261

Cytoplasmic Potential

Transmembrane

262 – 282

21

Helical; Anchor for type IV membrane protein; Potential

Topological domain

283

1

Vacuolar Potential

Domain

190 – 252

63

t-SNARE coiled-coil homology

Coiled coil

28 – 48

21

Potential

Coiled coil

84 – 111

28

Potential

Coiled coil

169 – 189

21

Potential

Compositional bias

174 – 179

6

Poly-Gln

Compositional bias

268 – 271

4

Poly-Ile

Amino acid modifications

Modified residue

108

1

Phosphoserine Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

283

Helix Strand Turn

Details...

Helix

25 – 50

26

Beta strand

53 – 55

3

Helix

58 – 66

9

Helix

68 – 81

14

Helix

84 – 87

4

Helix

89 – 115

27

Sequences

	Sequence		Length	Mass (Da)
	Q12241 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 6415D9D852C6C64D	FASTA	283	32,498
	10 20 30 40 50 60 MSFFDIEAQS SKGNSQQEPQ FSTNQKTKEL SNLIETFAEQ SRVLEKECTK IGSKRDSKEL 70 80 90 100 110 120 RYKIETELIP NCTSVRDKIE SNILIHQNGK LSADFKNLKT KYQSLQQSYN QRKSLFPLKT 130 140 150 160 170 180 PISPGTSKER KDIHPRTEAV RQDPESSYIS IKVNEQSPLL HNEGQHQLQL QEEQEQQQQG 190 200 210 220 230 240 LSQEELDFQT IIHQERSQQI GRIHTAVQEV NAIFHQLGSL VKEQGEQVTT IDENISHLHD 250 260 270 280 NMQNANKQLT RADQHQRDRN KCGKVTLIII IVVCMVVLLA VLS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Vam3p, a new member of syntaxin related protein, is required for vacuolar assembly in the yeast Saccharomyces cerevisiae." Wada Y., Nakamura N., Ohsumi Y., Hirata A. J. Cell Sci. 110:1299-1306(1997) [PubMed: 9202390] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 26786 / X2180-1A.
[2]	"DNA sequencing and analysis of 130 kb from yeast chromosome XV." Voss H., Benes V., Andrade M.A., Valencia A., Rechmann S., Teodoru C., Schwager C., Paces V., Sander C., Ansorge W. Yeast 13:655-672(1997) [PubMed: 9200815] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole." Darsow T., Rieder S.E., Emr S.D. J. Cell Biol. 138:517-529(1997) [PubMed: 9245783] [Abstract] Cited for: CHARACTERIZATION.
[6]	"A syntaxin homolog encoded by VAM3 mediates down-regulation of a yeast G protein-coupled receptor." Stefan C.J., Blumer K.J. J. Biol. Chem. 274:1835-1841(1999) [PubMed: 9880567] [Abstract] Cited for: CHARACTERIZATION.
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[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-108, MASS SPECTROMETRY.
[9]	"Vam3p structure reveals conserved and divergent properties of syntaxins." Dulubova I., Yamaguchi T., Wang Y., Suedhof T.C., Rizo J. Nat. Struct. Biol. 8:258-264(2001) [PubMed: 11224573] [Abstract] Cited for: STRUCTURE BY NMR OF 23-119.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U57827 Genomic DNA. Translation: AAC49737.1.
X94335 Genomic DNA. Translation: CAA64026.1.
Z75014 Genomic DNA. Translation: CAA99304.1.
BK006948 Genomic DNA. Translation: DAA10881.1.

PIR

S61664.

RefSeq

NP_014749.1. NM_001183525.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HS7	NMR	-	A	23-119	[»]

ProteinModelPortal

Q12241.

SMR

Q12241. Positions 23-119, 195-260.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1726N.

IntAct

Q12241. 6 interactions.

MINT

MINT-384960.

STRING

Q12241.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR106W; YOR106W; YOR106W.

GeneID

854273.

KEGG

sce:YOR106W.

NMPDR

fig|4932.3.peg.5851.

Organism-specific databases

CYGD

YOR106w.

SGD

S000005632. VAM3.

Phylogenomic databases

eggNOG

fuNOG10843.

GeneTree

EFGT00050000002424.

HOGENOM

HBG202844.

OMA

KAHEYQK.

OrthoDB

EOG4ZKNWR.

Gene expression databases

ArrayExpress

Q12241.

Genevestigator

Q12241.

GermOnline

YOR106W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR006012. Syntaxin/epimorphin_CS.
IPR010989. t-SNARE.
IPR000727. T_SNARE_dom.
[Graphical view]

KO

K08488.

Pfam

PF05739. SNARE. 1 hit.
[Graphical view]

SMART

SM00397. t_SNARE. 1 hit.
[Graphical view]

SUPFAM

SSF47661. t-snare. 1 hit.

PROSITE

PS00914. SYNTAXIN. 1 hit.
PS50192. T_SNARE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

976227.

Entry information

Entry name

VAM3_YEAST

Accession

Primary (citable) accession number: Q12241
Secondary accession number(s): D6W2G5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	December 14, 2011
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program