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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Zinc 1
Metal bindingi10 – 101Zinc 1
Metal bindingi39 – 391Zinc 1
Metal bindingi39 – 391Zinc 2
Metal bindingi62 – 621Zinc 2
Metal bindingi86 – 861Zinc 2
Metal bindingi115 – 1151Zinc 2
Metal bindingi117 – 1171Zinc 1

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi39 – 391N → D: Decreases interaction with VPS35. 1 Publication
Mutagenesisi90 – 901V → D: Decreases interaction with VPS35. 1 Publication
Mutagenesisi91 – 911I → S: Disrupts interaction with VPS35. 1 Publication
Mutagenesisi152 – 1521L → E: Disrupts interaction with ANKRD27. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182Vacuolar protein sorting-associated protein 29PRO_0000065895Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei50 – 501N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9QZ88.
MaxQBiQ9QZ88.
PaxDbiQ9QZ88.
PeptideAtlasiQ9QZ88.
PRIDEiQ9QZ88.
TopDownProteomicsiQ9QZ88-1. [Q9QZ88-1]

2D gel databases

REPRODUCTION-2DPAGEQ9QZ88.

PTM databases

iPTMnetiQ9QZ88.
PhosphoSiteiQ9QZ88.

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 interactions.
DIPiDIP-60495N.
IntActiQ9QZ88. 5 interactions.
MINTiMINT-4140090.
STRINGi10090.ENSMUSP00000121020.

Structurei

Secondary structure

1
182
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Turni12 – 143Combined sources
Beta strandi16 – 183Combined sources
Helixi20 – 234Combined sources
Turni28 – 303Combined sources
Beta strandi32 – 365Combined sources
Helixi43 – 5210Combined sources
Beta strandi54 – 585Combined sources
Beta strandi67 – 693Combined sources
Beta strandi71 – 777Combined sources
Beta strandi80 – 856Combined sources
Helixi96 – 10611Combined sources
Beta strandi107 – 1126Combined sources
Beta strandi120 – 1245Combined sources
Beta strandi127 – 1315Combined sources
Beta strandi149 – 1568Combined sources
Beta strandi159 – 16810Combined sources
Beta strandi171 – 18010Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-182.
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)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MAGHR in isoform 2. 1 PublicationVSP_004074

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_006530427.2. [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_006530427.2. [Q9QZ88-2]
UniGeneiMm.216528.
Mm.445844.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-182.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ9QZ88.
PhosphoSiteiQ9QZ88.

2D gel databases

REPRODUCTION-2DPAGEQ9QZ88.

Proteomic databases

EPDiQ9QZ88.
MaxQBiQ9QZ88.
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: September 7, 2016
This is version 132 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.