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Protein

Vacuolar protein sorting-associated protein 29

Gene

Vps29

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (By similarity). Has no activity towards p-nitrophenylphosphate, p-nitrophenylphosphorylcholine or phosphatidylinositlphosphates or a phosphorylated peptide derived from retromer cargo (in vitro) (PubMed:21629666, PubMed:15965486).By similarity2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Zinc 11
Metal bindingi10Zinc 11
Metal bindingi39Zinc 11
Metal bindingi39Zinc 21
Metal bindingi62Zinc 21
Metal bindingi86Zinc 21
Metal bindingi115Zinc 21
Metal bindingi117Zinc 11

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-3238698. WNT ligand biogenesis and trafficking.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 29
Alternative name(s):
Vesicle protein sorting 29
Gene namesi
Name:Vps29
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:1928344. Vps29.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi39N → D: Decreases interaction with VPS35. 1 Publication1
Mutagenesisi90V → D: Decreases interaction with VPS35. 1 Publication1
Mutagenesisi91I → S: Disrupts interaction with VPS35. 1 Publication1
Mutagenesisi152L → E: Disrupts interaction with ANKRD27. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000658951 – 182Vacuolar protein sorting-associated protein 29Add BLAST182

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei50N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9QZ88.
PaxDbiQ9QZ88.
PeptideAtlasiQ9QZ88.
PRIDEiQ9QZ88.
TopDownProteomicsiQ9QZ88-1. [Q9QZ88-1]

2D gel databases

REPRODUCTION-2DPAGEQ9QZ88.

PTM databases

iPTMnetiQ9QZ88.
PhosphoSitePlusiQ9QZ88.

Expressioni

Gene expression databases

BgeeiENSMUSG00000029462.
CleanExiMM_VPS29.
ExpressionAtlasiQ9QZ88. baseline and differential.
GenevisibleiQ9QZ88. MM.

Interactioni

Subunit structurei

Component of the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting subcomplex (VPS) formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35 (PubMed:21040701, PubMed:20875039, PubMed:21920005). The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform (By similarity). The CSC is believed to associate with variable sorting nexins to form functionally distinct retromer complex variants. The originally described retromer complex (also called SNX-BAR retromer) is a pentamer containing the CSC and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. The CSC associates with SNX3 to form a SNX3-retromer complex. The CSC associates with SNX27, the WASH complex and the SNX-BAR subcomplex to form the SNX27-retromer complex (By similarity). Interacts with VPS26A, VPS26B, VPS35, ANKRD27 (PubMed:20875039, PubMed:21920005, PubMed:24856514). Interacts with SNX1, SNX2, SNX27, KIAA0196 (By similarity).By similarity5 Publications

Protein-protein interaction databases

BioGridi207976. 4 interactors.
DIPiDIP-60495N.
IntActiQ9QZ88. 5 interactors.
MINTiMINT-4140090.
STRINGi10090.ENSMUSP00000121020.

Structurei

Secondary structure

1182
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Turni12 – 14Combined sources3
Beta strandi16 – 18Combined sources3
Helixi20 – 23Combined sources4
Turni28 – 30Combined sources3
Beta strandi32 – 36Combined sources5
Helixi43 – 52Combined sources10
Beta strandi54 – 58Combined sources5
Beta strandi67 – 69Combined sources3
Beta strandi71 – 77Combined sources7
Beta strandi80 – 85Combined sources6
Helixi96 – 106Combined sources11
Beta strandi107 – 112Combined sources6
Beta strandi120 – 124Combined sources5
Beta strandi127 – 131Combined sources5
Beta strandi149 – 156Combined sources8
Beta strandi159 – 168Combined sources10
Beta strandi171 – 180Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Z2WX-ray2.00A/B1-182[»]
1Z2XX-ray2.22A/B1-182[»]
3PSNX-ray2.20A/B1-182[»]
3PSOX-ray3.00A/B1-182[»]
ProteinModelPortaliQ9QZ88.
SMRiQ9QZ88.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9QZ88.

Family & Domainsi

Sequence similaritiesi

Belongs to the VPS29 family.Curated

Phylogenomic databases

eggNOGiKOG3325. Eukaryota.
COG0622. LUCA.
GeneTreeiENSGT00390000012669.
HOGENOMiHOG000293431.
HOVERGENiHBG056165.
InParanoidiQ9QZ88.
KOiK18467.
OMAiAFENENK.
OrthoDBiEOG091G0M0T.
PhylomeDBiQ9QZ88.
TreeFamiTF300880.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view]
PANTHERiPTHR11124. PTHR11124. 1 hit.
PfamiPF12850. Metallophos_2. 1 hit.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR00040. yfcE. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9QZ88-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK
60 70 80 90 100
TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA
110 120 130 140 150
LLQRQFDVDI LISGHTHKFE AFEHENKFYI NPGSATGAYN ALETNIIPSF
160 170 180
VLMDIQASTV VTYVYQLIGD DVKVERIEYK KS
Length:182
Mass (Da):20,496
Last modified:May 1, 2000 - v1
Checksum:i6CDCDE6B720C9BF8
GO
Isoform 2 (identifier: Q9QZ88-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAGHR

Show »
Length:186
Mass (Da):20,917
Checksum:i7AA5116A30665D6F
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0040741M → MAGHR in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF193794 mRNA. Translation: AAF04595.1.
AK004103 mRNA. Translation: BAB23170.1.
AK150330 mRNA. Translation: BAE29472.1.
BC005663 mRNA. Translation: AAH05663.1.
CCDSiCCDS39256.1. [Q9QZ88-1]
RefSeqiNP_062754.1. NM_019780.1. [Q9QZ88-1]
XP_006530490.1. XM_006530427.3. [Q9QZ88-2]
UniGeneiMm.216528.
Mm.445844.

Genome annotation databases

EnsembliENSMUST00000118830; ENSMUSP00000113525; ENSMUSG00000029462. [Q9QZ88-2]
ENSMUST00000155671; ENSMUSP00000121020; ENSMUSG00000029462. [Q9QZ88-1]
GeneIDi56433.
KEGGimmu:56433.
UCSCiuc008zlb.1. mouse. [Q9QZ88-1]
uc008zlc.1. mouse. [Q9QZ88-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF193794 mRNA. Translation: AAF04595.1.
AK004103 mRNA. Translation: BAB23170.1.
AK150330 mRNA. Translation: BAE29472.1.
BC005663 mRNA. Translation: AAH05663.1.
CCDSiCCDS39256.1. [Q9QZ88-1]
RefSeqiNP_062754.1. NM_019780.1. [Q9QZ88-1]
XP_006530490.1. XM_006530427.3. [Q9QZ88-2]
UniGeneiMm.216528.
Mm.445844.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Z2WX-ray2.00A/B1-182[»]
1Z2XX-ray2.22A/B1-182[»]
3PSNX-ray2.20A/B1-182[»]
3PSOX-ray3.00A/B1-182[»]
ProteinModelPortaliQ9QZ88.
SMRiQ9QZ88.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi207976. 4 interactors.
DIPiDIP-60495N.
IntActiQ9QZ88. 5 interactors.
MINTiMINT-4140090.
STRINGi10090.ENSMUSP00000121020.

PTM databases

iPTMnetiQ9QZ88.
PhosphoSitePlusiQ9QZ88.

2D gel databases

REPRODUCTION-2DPAGEQ9QZ88.

Proteomic databases

EPDiQ9QZ88.
PaxDbiQ9QZ88.
PeptideAtlasiQ9QZ88.
PRIDEiQ9QZ88.
TopDownProteomicsiQ9QZ88-1. [Q9QZ88-1]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000118830; ENSMUSP00000113525; ENSMUSG00000029462. [Q9QZ88-2]
ENSMUST00000155671; ENSMUSP00000121020; ENSMUSG00000029462. [Q9QZ88-1]
GeneIDi56433.
KEGGimmu:56433.
UCSCiuc008zlb.1. mouse. [Q9QZ88-1]
uc008zlc.1. mouse. [Q9QZ88-2]

Organism-specific databases

CTDi51699.
MGIiMGI:1928344. Vps29.

Phylogenomic databases

eggNOGiKOG3325. Eukaryota.
COG0622. LUCA.
GeneTreeiENSGT00390000012669.
HOGENOMiHOG000293431.
HOVERGENiHBG056165.
InParanoidiQ9QZ88.
KOiK18467.
OMAiAFENENK.
OrthoDBiEOG091G0M0T.
PhylomeDBiQ9QZ88.
TreeFamiTF300880.

Enzyme and pathway databases

ReactomeiR-MMU-3238698. WNT ligand biogenesis and trafficking.

Miscellaneous databases

ChiTaRSiVPS29. mouse.
EvolutionaryTraceiQ9QZ88.
PROiQ9QZ88.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000029462.
CleanExiMM_VPS29.
ExpressionAtlasiQ9QZ88. baseline and differential.
GenevisibleiQ9QZ88. MM.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view]
PANTHERiPTHR11124. PTHR11124. 1 hit.
PfamiPF12850. Metallophos_2. 1 hit.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR00040. yfcE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiVPS29_MOUSE
AccessioniPrimary (citable) accession number: Q9QZ88
Secondary accession number(s): Q3UCZ0, Q9D107
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

Was originally believed to be a metal-dependent phosphatase but shown to lack catalytic activity; can bind metals (Zn2+ and Mn2+) with very low affinity suggesting that metal binding is not required for its function.2 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.