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Protein

Vesicle-associated membrane protein-associated protein A

Gene

Vapa

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds to OSBPL3, which mediates recruitment of VAPA to plasma membrane sites (By similarity). The ORP3-VAPA complex stimulates RRAS signaling which in turn attenuates integrin beta-1 (ITGB1) activation at the cell surface (By similarity). With OSBPL3, may regulate ER morphology (By similarity). May play a role in vesicle trafficking (PubMed:19289470).By similarity1 Publication

GO - Molecular functioni

  • protein heterodimerization activity Source: RGD

GO - Biological processi

  • cell death Source: UniProtKB
  • neuron projection development Source: UniProtKB
  • protein localization to endoplasmic reticulum Source: UniProtKB
Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-RNO-1660661. Sphingolipid de novo biosynthesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Vesicle-associated membrane protein-associated protein A
Short name:
VAMP-A
Short name:
VAMP-associated protein A
Short name:
VAP-A
Alternative name(s):
33 kDa VAMP-associated protein
Short name:
VAP-33
Gene namesi
Name:Vapa
Synonyms:Vap33
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 9

Organism-specific databases

RGDi61803. Vapa.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini2 – 227226CytoplasmicSequence analysisAdd
BLAST
Transmembranei228 – 24821Helical; Anchor for type IV membrane proteinSequence analysisAdd
BLAST

GO - Cellular componenti

  • bicellular tight junction Source: UniProtKB-SubCell
  • endoplasmic reticulum Source: UniProtKB
  • endoplasmic reticulum membrane Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: BHF-UCL
  • nuclear membrane Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Endoplasmic reticulum, Membrane, Nucleus, Tight junction

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi94 – 941K → D: Loss of interaction with OSBPL1A; when associated with D-96. 1 Publication
Mutagenesisi96 – 961M → D: Loss of interaction with OSBPL1A; when associated with D-94. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 249248Vesicle-associated membrane protein-associated protein APRO_0000213472Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei125 – 1251N6-acetyllysineBy similarity
Modified residuei166 – 1661PhosphoserineBy similarity
Modified residuei170 – 1701PhosphothreonineBy similarity
Modified residuei214 – 2141PhosphoserineCombined sources
Modified residuei216 – 2161PhosphoserineBy similarity
Modified residuei219 – 2191PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ9Z270.
PRIDEiQ9Z270.

PTM databases

iPTMnetiQ9Z270.
SwissPalmiQ9Z270.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

ExpressionAtlasiQ9Z270. baseline.
GenevisibleiQ9Z270. RN.

Interactioni

Subunit structurei

Homodimer, and heterodimer with VAPB. Interacts with VAMP1, VAMP2, STX1A, BET1, SEC22C and with the C-terminal domain of OCLN (By similarity). Interacts with OSBP (By similarity). Interacts (via C-terminus) with RSAD2/viperin (via C-terminus) (By similarity). Interacts with OSBPL1A (PubMed:16004875). Interacts (via MSP domain) with ZFYVE27; may retain ZFYVE27 in the endoplasmic reticulum and regulate its function in cell projections formation (PubMed:19289470). Interacts with OSBPL3 (phosphorylated form) (By similarity).By similarity2 Publications

GO - Molecular functioni

  • protein heterodimerization activity Source: RGD

Protein-protein interaction databases

DIPiDIP-48448N.
IntActiQ9Z270. 2 interactions.
MINTiMINT-4581027.
STRINGi10116.ENSRNOP00000020681.

Structurei

Secondary structure

1
249
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 2713Combined sources
Beta strandi33 – 408Combined sources
Beta strandi43 – 453Combined sources
Beta strandi47 – 548Combined sources
Helixi56 – 583Combined sources
Beta strandi59 – 635Combined sources
Beta strandi65 – 684Combined sources
Beta strandi73 – 808Combined sources
Beta strandi94 – 1018Combined sources
Helixi109 – 1146Combined sources
Helixi118 – 1203Combined sources
Beta strandi122 – 13110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Z9LX-ray1.70A8-132[»]
1Z9OX-ray1.90A/B/C/D/E/F8-132[»]
ProteinModelPortaliQ9Z270.
SMRiQ9Z270. Positions 8-132.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Z270.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 131118MSPPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili168 – 20740Sequence analysisAdd
BLAST

Sequence similaritiesi

Contains 1 MSP domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0439. Eukaryota.
COG5066. LUCA.
GeneTreeiENSGT00390000006947.
HOGENOMiHOG000293182.
HOVERGENiHBG028551.
InParanoidiQ9Z270.
KOiK06096.
OMAiFEMPSEN.
OrthoDBiEOG7CK389.
PhylomeDBiQ9Z270.
TreeFamiTF317024.

Family and domain databases

Gene3Di2.60.40.360. 1 hit.
InterProiIPR000535. MSP_dom.
IPR008962. PapD-like.
IPR016763. VAP.
IPR030229. VAPA.
[Graphical view]
PANTHERiPTHR10809. PTHR10809. 1 hit.
PTHR10809:SF40. PTHR10809:SF40. 1 hit.
PfamiPF00635. Motile_Sperm. 1 hit.
[Graphical view]
PIRSFiPIRSF019693. VAMP-associated. 1 hit.
SUPFAMiSSF49354. SSF49354. 1 hit.
PROSITEiPS50202. MSP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9Z270-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASASGAMAK HEQILVLDPP SDLKFKGPFT DVVTTNLKLQ NPSDRKVCFK
60 70 80 90 100
VKTTAPRRYC VRPNSGVIDP GSIVTVSVML QPFDYDPNEK SKHKFMVQTI
110 120 130 140 150
FAPPNISDME AVWKEAKPDE LMDSKLRCVF EMPNENDKLN DMEPSKAVPL
160 170 180 190 200
NASKQDGPLP KPHSVSLNDT ETRKLMEECK RLQGEMMKLS EENRHLRDEG
210 220 230 240
LRLRKVAHSD KPGSTSAVSF RDNVTSPLPS LLVVIAAIFI GFFLGKFIL
Length:249
Mass (Da):27,841
Last modified:January 9, 2007 - v3
Checksum:iA30D08E31F3379C1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti126 – 1261L → P in AAD13579 (PubMed:9920726).Curated
Sequence conflicti249 – 2491L → S in AAD13579 (PubMed:9920726).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC061875 mRNA. Translation: AAH61875.2.
AF086630 mRNA. Translation: AAD13579.1.
RefSeqiNP_113819.3. NM_031631.2.
UniGeneiRn.162275.

Genome annotation databases

EnsembliENSRNOT00000020681; ENSRNOP00000020681; ENSRNOG00000014765.
GeneIDi58857.
KEGGirno:58857.
UCSCiRGD:61803. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC061875 mRNA. Translation: AAH61875.2.
AF086630 mRNA. Translation: AAD13579.1.
RefSeqiNP_113819.3. NM_031631.2.
UniGeneiRn.162275.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Z9LX-ray1.70A8-132[»]
1Z9OX-ray1.90A/B/C/D/E/F8-132[»]
ProteinModelPortaliQ9Z270.
SMRiQ9Z270. Positions 8-132.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48448N.
IntActiQ9Z270. 2 interactions.
MINTiMINT-4581027.
STRINGi10116.ENSRNOP00000020681.

PTM databases

iPTMnetiQ9Z270.
SwissPalmiQ9Z270.

Proteomic databases

PaxDbiQ9Z270.
PRIDEiQ9Z270.

Protocols and materials databases

DNASUi58857.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000020681; ENSRNOP00000020681; ENSRNOG00000014765.
GeneIDi58857.
KEGGirno:58857.
UCSCiRGD:61803. rat.

Organism-specific databases

CTDi9218.
RGDi61803. Vapa.

Phylogenomic databases

eggNOGiKOG0439. Eukaryota.
COG5066. LUCA.
GeneTreeiENSGT00390000006947.
HOGENOMiHOG000293182.
HOVERGENiHBG028551.
InParanoidiQ9Z270.
KOiK06096.
OMAiFEMPSEN.
OrthoDBiEOG7CK389.
PhylomeDBiQ9Z270.
TreeFamiTF317024.

Enzyme and pathway databases

ReactomeiR-RNO-1660661. Sphingolipid de novo biosynthesis.

Miscellaneous databases

EvolutionaryTraceiQ9Z270.
PROiQ9Z270.

Gene expression databases

ExpressionAtlasiQ9Z270. baseline.
GenevisibleiQ9Z270. RN.

Family and domain databases

Gene3Di2.60.40.360. 1 hit.
InterProiIPR000535. MSP_dom.
IPR008962. PapD-like.
IPR016763. VAP.
IPR030229. VAPA.
[Graphical view]
PANTHERiPTHR10809. PTHR10809. 1 hit.
PTHR10809:SF40. PTHR10809:SF40. 1 hit.
PfamiPF00635. Motile_Sperm. 1 hit.
[Graphical view]
PIRSFiPIRSF019693. VAMP-associated. 1 hit.
SUPFAMiSSF49354. SSF49354. 1 hit.
PROSITEiPS50202. MSP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Prostate.
  2. "Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated (VAMP-associated) proteins."
    Nishimura Y., Hayashi M., Inada H., Tanaka T.
    Biochem. Biophys. Res. Commun. 254:21-26(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 8-249.
    Tissue: Heart.
  3. "Promotion of neurite extension by protrudin requires its interaction with vesicle-associated membrane protein-associated protein."
    Saita S., Shirane M., Natume T., Iemura S., Nakayama K.I.
    J. Biol. Chem. 284:13766-13777(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH ZFYVE27.
  4. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-214, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "Arl6IP1 has the ability to shape the mammalian ER membrane in a reticulon-like fashion."
    Yamamoto Y., Yoshida A., Miyazaki N., Iwasaki K., Sakisaka T.
    Biochem. J. 458:69-79(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 8-132 IN COMPLEX WITH OSBPL1A, MUTAGENESIS OF LYS-94 AND MET-96.

Entry informationi

Entry nameiVAPA_RAT
AccessioniPrimary (citable) accession number: Q9Z270
Secondary accession number(s): Q6P723
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: January 9, 2007
Last modified: July 6, 2016
This is version 121 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata 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

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.