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Q9UBQ0

- VPS29_HUMAN

UniProt

Q9UBQ0 - VPS29_HUMAN

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Protein

Vacuolar protein sorting-associated protein 29

Gene

VPS29

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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).1 Publication

Catalytic activityi

O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.1 Publication

Cofactori

Zn2+1 PublicationNote: Binds 2 Zn(2+) ions per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Zinc 1By similarity
Metal bindingi10 – 101Zinc 1By similarity
Metal bindingi39 – 391Zinc 1By similarity
Metal bindingi39 – 391Zinc 2By similarity
Metal bindingi62 – 621Zinc 2By similarity
Metal bindingi86 – 861Zinc 2By similarity
Metal bindingi115 – 1151Zinc 2By similarity
Metal bindingi117 – 1171Zinc 1By similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. phosphoserine phosphatase activity Source: UniProtKB-EC

GO - Biological processi

  1. protein transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_163710. WNT ligand biogenesis and trafficking.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 29 (EC:3.1.3.3)
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
ProteomesiUP000005640: Chromosome 12

Organism-specific databases

HGNCiHGNC:14340. VPS29.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: HPA
  2. cytosol Source: Reactome
  3. endosome Source: LIFEdb
  4. extracellular vesicular exosome Source: UniProt
  5. intracellular membrane-bounded organelle Source: HPA
  6. membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi8 – 81D → A: Loss of protein phosphatase activity. 1 Publication
Mutagenesisi39 – 391N → A: Loss of protein phosphatase activity. 1 Publication
Mutagenesisi39 – 391N → D: No effect on protein phosphatase activity. 1 Publication
Mutagenesisi62 – 621D → A or N: Loss of protein phosphatase activity. 1 Publication
Mutagenesisi86 – 861H → A: Loss of protein phosphatase activity. 1 Publication
Mutagenesisi117 – 1171H → A: Loss of protein phosphatase activity. 1 Publication

Organism-specific databases

PharmGKBiPA37875.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182Vacuolar protein sorting-associated protein 29PRO_0000065894Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei50 – 501N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9UBQ0.
PaxDbiQ9UBQ0.
PRIDEiQ9UBQ0.

PTM databases

PhosphoSiteiQ9UBQ0.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiQ9UBQ0.
CleanExiHS_VPS29.
ExpressionAtlasiQ9UBQ0. baseline and differential.
GenevestigatoriQ9UBQ0.

Organism-specific databases

HPAiHPA039748.

Interactioni

Subunit structurei

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.3 Publications

Protein-protein interaction databases

BioGridi119683. 46 interactions.
DIPiDIP-29077N.
IntActiQ9UBQ0. 3 interactions.
MINTiMINT-1422473.
STRINGi9606.ENSP00000380795.

Structurei

Secondary structure

1
182
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Turni11 – 144Combined sources
Beta strandi16 – 183Combined sources
Helixi20 – 256Combined sources
Beta strandi32 – 365Combined sources
Helixi43 – 5210Combined sources
Beta strandi54 – 585Combined sources
Beta strandi71 – 777Combined sources
Beta strandi80 – 856Combined sources
Beta strandi90 – 923Combined sources
Helixi96 – 10611Combined sources
Beta strandi109 – 1135Combined sources
Beta strandi115 – 1184Combined 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
1W24X-ray2.10A1-182[»]
2R17X-ray2.80A/B1-182[»]
ProteinModelPortaliQ9UBQ0.
SMRiQ9UBQ0. Positions 1-181.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UBQ0.

Family & Domainsi

Sequence similaritiesi

Belongs to the VPS29 family.Curated

Phylogenomic databases

eggNOGiCOG0622.
GeneTreeiENSGT00390000012669.
HOVERGENiHBG056165.
InParanoidiQ9UBQ0.
KOiK18467.
OrthoDBiEOG7JHM6S.
PhylomeDBiQ9UBQ0.
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. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1 – 22ML → MKIVLYPV in AAF86872. 1 PublicationCurated
Sequence conflicti119 – 1191F → S in CAB66549. (PubMed:11230166)Curated
Sequence conflicti119 – 1191F → S in CAG38499. 1 PublicationCurated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MAGHR in isoform 2. 4 PublicationsVSP_004073

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.3. human. [Q9UBQ0-2]
uc001tqy.3. human. [Q9UBQ0-1]

Polymorphism databases

DMDMi25453325.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

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 .
CCDSi CCDS41832.1. [Q9UBQ0-1 ]
CCDS53832.1. [Q9UBQ0-2 ]
PIRi JC7515.
RefSeqi NP_057310.1. NM_016226.4. [Q9UBQ0-1 ]
NP_476528.1. NM_057180.2. [Q9UBQ0-2 ]
UniGenei Hs.600114.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1W24 X-ray 2.10 A 1-182 [» ]
2R17 X-ray 2.80 A/B 1-182 [» ]
ProteinModelPortali Q9UBQ0.
SMRi Q9UBQ0. Positions 1-181.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 119683. 46 interactions.
DIPi DIP-29077N.
IntActi Q9UBQ0. 3 interactions.
MINTi MINT-1422473.
STRINGi 9606.ENSP00000380795.

PTM databases

PhosphoSitei Q9UBQ0.

Polymorphism databases

DMDMi 25453325.

Proteomic databases

MaxQBi Q9UBQ0.
PaxDbi Q9UBQ0.
PRIDEi Q9UBQ0.

Protocols and materials databases

DNASUi 51699.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000360579 ; ENSP00000353786 ; ENSG00000111237 . [Q9UBQ0-2 ]
ENST00000549578 ; ENSP00000447058 ; ENSG00000111237 . [Q9UBQ0-1 ]
GeneIDi 51699.
KEGGi hsa:51699.
UCSCi uc001tqx.3. human. [Q9UBQ0-2 ]
uc001tqy.3. human. [Q9UBQ0-1 ]

Organism-specific databases

CTDi 51699.
GeneCardsi GC12M110929.
HGNCi HGNC:14340. VPS29.
HPAi HPA039748.
MIMi 606932. gene.
neXtProti NX_Q9UBQ0.
PharmGKBi PA37875.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0622.
GeneTreei ENSGT00390000012669.
HOVERGENi HBG056165.
InParanoidi Q9UBQ0.
KOi K18467.
OrthoDBi EOG7JHM6S.
PhylomeDBi Q9UBQ0.
TreeFami TF300880.

Enzyme and pathway databases

Reactomei REACT_163710. WNT ligand biogenesis and trafficking.

Miscellaneous databases

ChiTaRSi VPS29. human.
EvolutionaryTracei Q9UBQ0.
GeneWikii VPS29.
GenomeRNAii 51699.
NextBioi 55714.
PROi Q9UBQ0.
SOURCEi Search...

Gene expression databases

Bgeei Q9UBQ0.
CleanExi HS_VPS29.
ExpressionAtlasi Q9UBQ0. baseline and differential.
Genevestigatori Q9UBQ0.

Family and domain databases

Gene3Di 3.60.21.10. 1 hit.
InterProi IPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view ]
PANTHERi PTHR11124. PTHR11124. 1 hit.
Pfami PF12850. Metallophos_2. 1 hit.
[Graphical view ]
SUPFAMi SSF56300. SSF56300. 1 hit.
TIGRFAMsi TIGR00040. yfcE. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH VPS35, ELECTRON MICROSCOPY OF THE RETROMER COMPLEX CONTAINING VPS29; VPS35 AND VPS26.

Entry informationi

Entry nameiVPS29_HUMAN
AccessioniPrimary (citable) accession number: Q9UBQ0
Secondary accession number(s): Q502Y5
, Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: May 1, 2000
Last modified: November 26, 2014
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
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

External Data

Dasty 3