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Protein

Vacuolar protein sorting-associated protein 29

Gene

Vps29

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

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

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

  • Golgi to vacuole transport Source: MGI
  • intracellular protein transport Source: GO_Central
  • retrograde transport, endosome to Golgi Source: GO_Central
  • retrograde transport, endosome to plasma membrane Source: UniProtKB

Keywordsi

Biological processProtein transport, Transport
LigandMetal-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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:1928344 Vps29

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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-2DPAGEiQ9QZ88

PTM databases

iPTMnetiQ9QZ88
PhosphoSitePlusiQ9QZ88

Expressioni

Gene expression databases

BgeeiENSMUSG00000029462 Expressed in 289 organ(s), highest expression level in otic placode
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, WASHC5 (By similarity).By similarity5 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi207976, 4 interactors
CORUMiQ9QZ88
DIPiDIP-60495N
IntActiQ9QZ88, 22 interactors
MINTiQ9QZ88
STRINGi10090.ENSMUSP00000121020

Structurei

Secondary structure

1182
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
OMAiKIGLCHG
OrthoDBiEOG091G0M0T
PhylomeDBiQ9QZ88
TreeFamiTF300880

Family and domain databases

CDDicd07394 MPP_Vps29, 1 hit
Gene3Di3.60.21.10, 1 hit
InterProiView protein in InterPro
IPR024654 Calcineurin-like_PHP_lpxH
IPR029052 Metallo-depent_PP-like
IPR000979 Phosphodiesterase_MJ0936/Vps29
IPR028661 Vps29
PANTHERiPTHR11124 PTHR11124, 1 hit
PTHR11124:SF12 PTHR11124:SF12, 1 hit
PfamiView protein in Pfam
PF12850 Metallophos_2, 1 hit
TIGRFAMsiTIGR00040 yfcE, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

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

This entry has 2 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3Z645D3Z645_MOUSE
Vacuolar protein sorting-associated...
Vps29
144Annotation score:
D3YYD5D3YYD5_MOUSE
Vacuolar protein sorting-associated...
Vps29
124Annotation score:
D3YW98D3YW98_MOUSE
Vacuolar protein sorting-associated...
Vps29
91Annotation score:
H7BXA2H7BXA2_MOUSE
Vacuolar protein sorting-associated...
Vps29
53Annotation score:
D6RH43D6RH43_MOUSE
Vacuolar protein sorting-associated...
Vps29
37Annotation score:

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]
CCDS84954.1 [Q9QZ88-2]
RefSeqiNP_001334382.1, NM_001347453.1 [Q9QZ88-2]
NP_062754.1, NM_019780.1 [Q9QZ88-1]
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

Similar proteinsi

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]
CCDS84954.1 [Q9QZ88-2]
RefSeqiNP_001334382.1, NM_001347453.1 [Q9QZ88-2]
NP_062754.1, NM_019780.1 [Q9QZ88-1]
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
CORUMiQ9QZ88
DIPiDIP-60495N
IntActiQ9QZ88, 22 interactors
MINTiQ9QZ88
STRINGi10090.ENSMUSP00000121020

PTM databases

iPTMnetiQ9QZ88
PhosphoSitePlusiQ9QZ88

2D gel databases

REPRODUCTION-2DPAGEiQ9QZ88

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
OMAiKIGLCHG
OrthoDBiEOG091G0M0T
PhylomeDBiQ9QZ88
TreeFamiTF300880

Enzyme and pathway databases

ReactomeiR-MMU-3238698 WNT ligand biogenesis and trafficking

Miscellaneous databases

ChiTaRSiVps29 mouse
EvolutionaryTraceiQ9QZ88
PROiPR:Q9QZ88
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000029462 Expressed in 289 organ(s), highest expression level in otic placode
CleanExiMM_VPS29
ExpressionAtlasiQ9QZ88 baseline and differential
GenevisibleiQ9QZ88 MM

Family and domain databases

CDDicd07394 MPP_Vps29, 1 hit
Gene3Di3.60.21.10, 1 hit
InterProiView protein in InterPro
IPR024654 Calcineurin-like_PHP_lpxH
IPR029052 Metallo-depent_PP-like
IPR000979 Phosphodiesterase_MJ0936/Vps29
IPR028661 Vps29
PANTHERiPTHR11124 PTHR11124, 1 hit
PTHR11124:SF12 PTHR11124:SF12, 1 hit
PfamiView protein in Pfam
PF12850 Metallophos_2, 1 hit
TIGRFAMsiTIGR00040 yfcE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiVPS29_MOUSE
AccessioniPrimary (citable) accession number: Q9QZ88
Secondary accession number(s): Q3UCZ0, Q9D107
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 1, 2000
Last modified: November 7, 2018
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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