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Q9UBQ0 (VPS29_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vacuolar protein sorting-associated protein 29

Short name=hVPS29
EC=3.1.3.3
Alternative name(s):
PEP11 homolog
Vesicle protein sorting 29
Gene names
Name:VPS29
ORF Names:DC15, DC7, MDS007
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length182 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Essential component of the retromer complex, a complex required to retrieve lysosomal enzyme receptors (IGF2R and M6PR) from endosomes to the trans-Golgi network. Also required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA). Has low protein phosphatase activity towards a serine-phosphorylated peptide derived from IGF2R (in vitro). Ref.9

Catalytic activity

O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate. Ref.10

Cofactor

Binds 2 zinc ions per subunit Probable. Ref.10

Subunit structure

Component of the retromer complex composed of VPS26 (VPS26A or VPS26B), VPS29, VPS35, SNX1 and SNX2. Found in a complex with XPO7, EIF4A1, ARHGAP1, VPS26A, VPS29, VPS35 and SFN. Ref.8 Ref.10

Subcellular location

Cytoplasm. Membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein By similarity.

Tissue specificity

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

Sequence similarities

Belongs to the VPS29 family.

Ontologies

Keywords
   Biological processProtein transport
Transport
   Cellular componentCytoplasm
Endosome
Membrane
   Coding sequence diversityAlternative splicing
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processprotein transport

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

cytosol

Traceable author statement. Source: Reactome

endosome

Inferred from direct assay. Source: LIFEdb

endosome membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

intracellular membrane-bounded organelle

Inferred from direct assay. Source: HPA

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

phosphoserine phosphatase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UBQ0-1)

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.
Isoform 2 (identifier: Q9UBQ0-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 182182Vacuolar protein sorting-associated protein 29
PRO_0000065894

Sites

Metal binding81Zinc 1 By similarity
Metal binding101Zinc 1 By similarity
Metal binding391Zinc 1 By similarity
Metal binding391Zinc 2 By similarity
Metal binding621Zinc 2 By similarity
Metal binding861Zinc 2 By similarity
Metal binding1151Zinc 2 By similarity
Metal binding1171Zinc 1 By similarity

Amino acid modifications

Modified residue501N6-acetyllysine Ref.11

Natural variations

Alternative sequence11M → MAGHR in isoform 2.
VSP_004073

Experimental info

Mutagenesis81D → A: Loss of protein phosphatase activity. Ref.10
Mutagenesis391N → A: Loss of protein phosphatase activity. Ref.10
Mutagenesis391N → D: No effect on protein phosphatase activity. Ref.10
Mutagenesis621D → A or N: Loss of protein phosphatase activity. Ref.10
Mutagenesis861H → A: Loss of protein phosphatase activity. Ref.10
Mutagenesis1171H → A: Loss of protein phosphatase activity. Ref.10
Sequence conflict1 – 22ML → MKIVLYPV in AAF86872. Ref.4
Sequence conflict1191F → S in CAB66549. Ref.5
Sequence conflict1191F → S in CAG38499. Ref.6

Secondary structure

..................................... 182
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 6E0CDE6B720C9BF8

FASTA18220,506
        10         20         30         40         50         60 
MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR 

        70         80         90        100        110        120 
GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA LLQRQFDVDI LISGHTHKFE 

       130        140        150        160        170        180 
AFEHENKFYI NPGSATGAYN ALETNIIPSF VLMDIQASTV VTYVYQLIGD DVKVERIEYK 


KP 

« Hide

Isoform 2 [UniParc].

Checksum: 7875116A30665D6F
Show »

FASTA18620,927

References

« Hide 'large scale' references
[1]"Human homologues of yeast vacuolar protein sorting 29 and 35."
Edgar A.J., Polak J.M.
Biochem. Biophys. Res. Commun. 277:622-630(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
Tissue: Lung.
[2]"Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes."
Renfrew Haft C., de la Luz Sierra M., Bafford R., Lesniak M.A., Barr V.A., Taylor S.I.
Mol. Biol. Cell 11:4105-4116(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH VPS26A; VPS35; SNX1 AND SNX2.
Tissue: Parathyroid.
[3]"Novel genes expressed in hematopoietic stem/progenitor cells from myelodysplastic syndrome patients."
Huang C., Zhang C., Tu Y., Gu W., Wang Y., Han Z., Chen Z., Zhou J., Gu J., Huang Q., Yu Y., Xu S., Ren S., Fu G., Li N.
Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Hematopoietic stem cell.
[4]"Novel genes expressed in human dendritic cells."
Peng Y., Li Y., Tu Y., Xu S., Han Z., Fu G., Chen Z.
Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Dendritic cell.
[5]"Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs."
Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S., Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J., Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W., Ottenwaelder B., Obermaier B. expand/collapse author list , Tampe J., Heubner D., Wambutt R., Korn B., Klein M., Poustka A.
Genome Res. 11:422-435(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Fetal brain.
[6]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
[7]"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] (ISOFORMS 1 AND 2).
Tissue: Brain and Cervix.
[8]"Exportin 7 defines a novel general nuclear export pathway."
Mingot J.-M., Bohnsack M.T., Jaekle U., Goerlich D.
EMBO J. 23:3227-3236(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A COMPLEX WITH XPO7; ARHGAP1; EIF4A1; VPS26A; VPS35 AND SFN.
[9]"The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor."
Verges M., Luton F., Gruber C., Tiemann F., Reinders L.G., Huang L., Burlingame A.L., Haft C.R., Mostov K.E.
Nat. Cell Biol. 6:763-769(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[10]"The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide."
Damen E., Krieger E., Nielsen J.E., Eygensteyn J., van Leeuwen J.E.M.
Biochem. J. 398:399-409(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF ASP-8; ASN-39; ASP-62; HIS-86 AND HIS-117, SUBUNIT.
[11]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-50, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites."
Wang D., Guo M., Liang Z., Fan J., Zhu Z., Zang J., Zhu Z., Li X., Teng M., Niu L., Dong Y., Liu P.
J. Biol. Chem. 280:22962-22967(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), METAL-BINDING.
[14]"Functional architecture of the retromer cargo-recognition complex."
Hierro A., Rojas A.L., Rojas R., Murthy N., Effantin G., Kajava A.V., Steven A.C., Bonifacino J.S., Hurley J.H.
Nature 449:1063-1067(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH VPS35, ELECTRON MICROSCOPY OF THE RETROMER COMPLEX CONTAINING VPS29; VPS35 AND VPS26.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS41832.1. [Q9UBQ0-1]
CCDS53832.1. [Q9UBQ0-2]
PIRJC7515.
RefSeqNP_057310.1. NM_016226.4. [Q9UBQ0-1]
NP_476528.1. NM_057180.2. [Q9UBQ0-2]
UniGeneHs.600114.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1W24X-ray2.10A1-182[»]
2R17X-ray2.80A/B1-182[»]
ProteinModelPortalQ9UBQ0.
SMRQ9UBQ0. Positions 1-181.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119683. 46 interactions.
DIPDIP-29077N.
IntActQ9UBQ0. 3 interactions.
MINTMINT-1422473.
STRING9606.ENSP00000380795.

PTM databases

PhosphoSiteQ9UBQ0.

Polymorphism databases

DMDM25453325.

Proteomic databases

MaxQBQ9UBQ0.
PaxDbQ9UBQ0.
PRIDEQ9UBQ0.

Protocols and materials databases

DNASU51699.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000360579; ENSP00000353786; ENSG00000111237. [Q9UBQ0-2]
ENST00000549578; ENSP00000447058; ENSG00000111237. [Q9UBQ0-1]
GeneID51699.
KEGGhsa:51699.
UCSCuc001tqx.3. human. [Q9UBQ0-2]
uc001tqy.3. human. [Q9UBQ0-1]

Organism-specific databases

CTD51699.
GeneCardsGC12M110929.
HGNCHGNC:14340. VPS29.
HPAHPA039748.
MIM606932. gene.
neXtProtNX_Q9UBQ0.
PharmGKBPA37875.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0622.
HOVERGENHBG056165.
KOK07095.
OrthoDBEOG7JHM6S.
PhylomeDBQ9UBQ0.
TreeFamTF300880.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.

Gene expression databases

ArrayExpressQ9UBQ0.
BgeeQ9UBQ0.
CleanExHS_VPS29.
GenevestigatorQ9UBQ0.

Family and domain databases

Gene3D3.60.21.10. 1 hit.
InterProIPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view]
PANTHERPTHR11124. PTHR11124. 1 hit.
PfamPF12850. Metallophos_2. 1 hit.
[Graphical view]
SUPFAMSSF56300. SSF56300. 1 hit.
TIGRFAMsTIGR00040. yfcE. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9UBQ0.
GeneWikiVPS29.
GenomeRNAi51699.
NextBio55714.
PROQ9UBQ0.
SOURCESearch...

Entry information

Entry nameVPS29_HUMAN
AccessionPrimary (citable) accession number: Q9UBQ0
Secondary accession number(s): Q502Y5 expand/collapse secondary AC list , Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7
Entry history
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 1, 2000
Last modified: July 9, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM