Q9UBQ0 (VPS29_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	182 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Protein transport Transport
Cellular component	Cytoplasm Endosome Membrane
Coding sequence diversity	Alternative splicing
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	endosome Inferred from direct assay. Source: LIFEdb endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoserine phosphatase activity Inferred from electronic annotation. Source: 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 182

182

Vacuolar protein sorting-associated protein 29

PRO_0000065894

Sites

Metal binding

8

1

Zinc 1 By similarity

Metal binding

10

1

Zinc 1 By similarity

Metal binding

39

1

Zinc 1 By similarity

Metal binding

39

1

Zinc 2 By similarity

Metal binding

62

1

Zinc 2 By similarity

Metal binding

86

1

Zinc 2 By similarity

Metal binding

115

1

Zinc 2 By similarity

Metal binding

117

1

Zinc 1 By similarity

Amino acid modifications

Modified residue

50

1

N6-acetyllysine Ref.11

Natural variations

Alternative sequence

1

1

M → MAGHR in isoform 2.

VSP_004073

Experimental info

Mutagenesis

8

1

D → A: Loss of protein phosphatase activity. Ref.10

Mutagenesis

39

1

N → A: Loss of protein phosphatase activity. Ref.10

Mutagenesis

39

1

N → D: No effect on protein phosphatase activity. Ref.10

Mutagenesis

62

1

D → A or N: Loss of protein phosphatase activity. Ref.10

Mutagenesis

86

1

H → A: Loss of protein phosphatase activity. Ref.10

Mutagenesis

117

1

H → A: Loss of protein phosphatase activity. Ref.10

Sequence conflict

1 – 2

2

ML → MKIVLYPV in AAF86872. Ref.4

Sequence conflict

119

1

F → S in CAB66549. Ref.5

Sequence conflict

119

1

F → S in CAG38499. Ref.6

Secondary structure

1

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182

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Turn

11 – 14

4

Beta strand

16 – 18

3

Helix

20 – 25

6

Beta strand

32 – 36

5

Helix

43 – 52

10

Beta strand

54 – 58

5

Beta strand

71 – 77

7

Beta strand

80 – 85

6

Beta strand

90 – 92

3

Helix

96 – 106

11

Beta strand

109 – 113

5

Beta strand

115 – 118

4

Beta strand

120 – 124

5

Beta strand

127 – 131

5

Beta strand

149 – 156

8

Beta strand

159 – 168

10

Beta strand

171 – 180

10

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 6E0CDE6B720C9BF8	FASTA	182	20,506
	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
	Isoform 2 [UniParc]. Checksum: 7875116A30665D6F	FASTA	186	20,927
	10 20 30 40 50 60 MAGHRLVLVL GDLHIPHRCN SLPAKFKKLL VPGKIQHILC TGNLCTKESY DYLKTLAGDV 70 80 90 100 110 120 HIVRGDFDEN LNYPEQKVVT VGQFKIGLIH GHQVIPWGDM ASLALLQRQF DVDILISGHT 130 140 150 160 170 180 HKFEAFEHEN KFYINPGSAT GAYNALETNI IPSFVLMDIQ ASTVVTYVYQ LIGDDVKVER IEYKKP

References

	« Hide 'large scale' referencesShow '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. , 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, MASS SPECTROMETRY.
[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.

IPI

IPI00170796.
IPI00184284.

PIR

JC7515.

RefSeq

NP_057310.1. NM_016226.3.
NP_476528.1. NM_057180.1.

UniGene

Hs.600114.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1W24	X-ray	2.10	A	1-182	[»]
2R17	X-ray	2.80	A/B	1-182	[»]

ProteinModelPortal

Q9UBQ0.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29077N.

IntAct

Q9UBQ0. 3 interactions.

MINT

MINT-1422473.

STRING

9606.ENSP00000380795.

PTM databases

PhosphoSite

Q9UBQ0.

Polymorphism databases

DMDM

25453325.

Proteomic databases

PaxDb

Q9UBQ0.

PRIDE

Q9UBQ0.

Protocols and materials databases

DNASU

51699.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000397678; ENSP00000380795; ENSG00000111237.
ENST00000549578; ENSP00000447058; ENSG00000111237.

GeneID

51699.

KEGG

hsa:51699.

UCSC

uc001tqx.3. human.
uc001tqy.3. human.

Organism-specific databases

CTD

51699.

GeneCards

GC12M110929.

HGNC

HGNC:14340. VPS29.

HPA

HPA039748.

MIM

606932. gene.

neXtProt

NX_Q9UBQ0.

PharmGKB

PA37875.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0622.

HOVERGEN

HBG056165.

KO

K07095.

OrthoDB

EOG49PB0G.

Gene expression databases

ArrayExpress

Q9UBQ0.

Bgee

Q9UBQ0.

CleanEx

HS_VPS29.

Genevestigator

Q9UBQ0.

GermOnline

ENSG00000111237. Homo sapiens.

Family and domain databases

InterPro

IPR024654. Calcineurin-like_PEstase_dom.
IPR000979. Phosphodiesterase_MJ0936.
[Graphical view]

PANTHER

PTHR11124. PTHR11124. 1 hit.

Pfam

PF12850. Metallophos_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00040. yfcE. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9UBQ0.

GenomeRNAi

51699.

NextBio

55714.

SOURCE

Search...

Entry information

Entry name

VPS29_HUMAN

Accession

Primary (citable) accession number: Q9UBQ0
Secondary accession number(s): Q502Y5 , Q6FIF8, Q6IAH3, Q9H0W0, Q9NRP1, Q9NRU7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 25, 2002
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 117 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.