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Protein

Vacuolar protein sorting-associated protein 29

Gene

VPS29

Organism
Homo sapiens (Human)
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) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514).3 PublicationsBy similarity2 Publications

Caution

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Zinc 1By similarity1
Metal bindingi10Zinc 1By similarity1
Metal bindingi39Zinc 1By similarity1
Metal bindingi39Zinc 2By similarity1
Metal bindingi62Zinc 2By similarity1
Metal bindingi86Zinc 2By similarity1
Metal bindingi115Zinc 2By similarity1
Metal bindingi117Zinc 1By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Biological processProtein transport, Transport
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3238698 WNT ligand biogenesis and trafficking

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 29
Short name:
hVPS29
Alternative name(s):
PEP11 homolog
Vesicle protein sorting 29
Gene namesi
Name:VPS29
ORF Names:DC15, DC7, MDS007
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000111237.18
HGNCiHGNC:14340 VPS29
MIMi606932 gene
neXtProtiNX_Q9UBQ0

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
Mutagenesisi8D → A: Loss of in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi39N → A: Loss of in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi39N → D: No effect on in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi62D → A or N: Loss of in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi86H → A: Loss of in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi90V → D: Decreases interaction with VPS35. 1
Mutagenesisi91I → D: Disrupts interaction with VPS35. 1
Mutagenesisi117H → A: Loss of in vitro protein phosphatase activity. 1 Publication1
Mutagenesisi152L → E: Disrupts interaction with TBC1D5. 1 Publication1

Organism-specific databases

DisGeNETi51699
OpenTargetsiENSG00000111237
PharmGKBiPA37875

Polymorphism and mutation databases

DMDMi25453325

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000658941 – 182Vacuolar protein sorting-associated protein 29Add BLAST182

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei50N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9UBQ0
PaxDbiQ9UBQ0
PeptideAtlasiQ9UBQ0
PRIDEiQ9UBQ0
TopDownProteomicsiQ9UBQ0-1 [Q9UBQ0-1]
Q9UBQ0-2 [Q9UBQ0-2]

PTM databases

DEPODiQ9UBQ0
iPTMnetiQ9UBQ0
PhosphoSitePlusiQ9UBQ0

Expressioni

Tissue specificityi

Ubiquitous. Highly expressed in heart, lung, placenta, spleen, peripheral blood leukocytes, thymus, colon skeletal muscle, kidney and brain.

Gene expression databases

BgeeiENSG00000111237
CleanExiHS_VPS29
ExpressionAtlasiQ9UBQ0 baseline and differential
GenevisibleiQ9UBQ0 HS

Organism-specific databases

HPAiHPA039748

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:11102511, PubMed:16737443, PubMed:17891154). 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 (Probable). Interacts with VPS26A, VPS35, SNX1, SNX2, SNX27, WASHC5, TBC1D5 (PubMed:11102511, PubMed:20923837, PubMed:23331060, PubMed:23563491). Interacts with VPS26B and ANKRD27 (By similarity).2 PublicationsBy similarity6 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi119683, 78 interactors
CORUMiQ9UBQ0
DIPiDIP-29077N
IntActiQ9UBQ0, 21 interactors
MINTiQ9UBQ0
STRINGi9606.ENSP00000380795

Structurei

Secondary structure

1182
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Turni11 – 14Combined sources4
Beta strandi16 – 18Combined sources3
Helixi20 – 25Combined sources6
Beta strandi28 – 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
Beta strandi90 – 92Combined sources3
Helixi96 – 106Combined sources11
Beta strandi109 – 113Combined sources5
Beta strandi115 – 118Combined sources4
Beta strandi119 – 124Combined sources6
Beta strandi127 – 132Combined sources6
Beta strandi143 – 145Combined sources3
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
1W24X-ray2.10A1-182[»]
2R17X-ray2.80A/B1-182[»]
5GTUX-ray1.50A2-182[»]
5OSHX-ray4.30A/D/G/J1-182[»]
5OSIX-ray2.52A/D/G/J1-182[»]
5WYHX-ray2.46A/C2-182[»]
ProteinModelPortaliQ9UBQ0
SMRiQ9UBQ0
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UBQ0

Family & Domainsi

Sequence similaritiesi

Belongs to the VPS29 family.Curated

Phylogenomic databases

eggNOGiKOG3325 Eukaryota
COG0622 LUCA
GeneTreeiENSGT00390000012669
HOVERGENiHBG056165
InParanoidiQ9UBQ0
KOiK18467
PhylomeDBiQ9UBQ0
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

Isoform 1 (identifier: Q9UBQ0-1) [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 KP
Length:182
Mass (Da):20,506
Last modified:May 1, 2000 - v1
Checksum:i6E0CDE6B720C9BF8
GO
Isoform 2 (identifier: Q9UBQ0-2) [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):20,927
Checksum:i7875116A30665D6F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1 – 2ML → MKIVLYPV in AAF86872 (Ref. 4) Curated2
Sequence conflicti119F → S in CAB66549 (PubMed:11230166).Curated1
Sequence conflicti119F → S in CAG38499 (Ref. 6) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0040731M → MAGHR in isoform 2. 4 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF193795 mRNA Translation: AAF04596.1
AF175264 mRNA Translation: AAF89952.1
AF168716 mRNA Translation: AAF87318.1
AF201936 mRNA Translation: AAF86872.1
AF201946 mRNA Translation: AAF17238.1
AL136614 mRNA Translation: CAB66549.1
CR457182 mRNA Translation: CAG33463.1
CR533468 mRNA Translation: CAG38499.1
BC000880 mRNA Translation: AAH00880.1
BC095446 mRNA Translation: AAH95446.1
CCDSiCCDS41832.1 [Q9UBQ0-1]
CCDS53832.1 [Q9UBQ0-2]
PIRiJC7515
RefSeqiNP_057310.1, NM_016226.4 [Q9UBQ0-1]
NP_476528.1, NM_057180.2 [Q9UBQ0-2]
UniGeneiHs.600114

Genome annotation databases

EnsembliENST00000360579; ENSP00000353786; ENSG00000111237 [Q9UBQ0-2]
ENST00000549578; ENSP00000447058; ENSG00000111237 [Q9UBQ0-1]
GeneIDi51699
KEGGihsa:51699
UCSCiuc001tqx.5 human [Q9UBQ0-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiVPS29_HUMAN
AccessioniPrimary (citable) accession number: Q9UBQ0
Secondary accession number(s): Q502Y5
, Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 1, 2000
Last modified: May 23, 2018
This is version 163 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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