Q9QZ88 (VPS29_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Vacuolar protein sorting-associated protein 29
EC=3.1.3.3

Alternative name(s):
Vesicle protein sorting 29

Gene names

Name:

Vps29

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

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) By similarity. Has no activity towards p-nitrophenylphosphate, p-nitrophenylphosphorylcholine or phosphatidylinositlphosphates (in vitro).
Catalytic activity	O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate. Ref.5
Cofactor	Binds 2 zinc ions per subunit By similarity.
Subunit structure	Found in a complex with XPO7, EIF4A1, ARHGAP1, VPS26A, VPS29, VPS35 and SFN By similarity. Component of the retromer complex composed of VPS26 (VPS26A or VPS26B), VPS29, VPS35, SNX1 and SNX2. Ref.5
Subcellular location	Cytoplasm By similarity. Membrane; Peripheral membrane protein By similarity. Endosome membrane; Peripheral membrane protein Ref.5.
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 Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	protein transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	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: Q9QZ88-1)

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: Q9QZ88-2)

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_0000065895

Sites

Metal binding

8

1

Zinc 1

Metal binding

10

1

Zinc 1

Metal binding

39

1

Zinc 1

Metal binding

39

1

Zinc 2

Metal binding

62

1

Zinc 2

Metal binding

86

1

Zinc 2

Metal binding

115

1

Zinc 2

Metal binding

117

1

Zinc 1

Amino acid modifications

Modified residue

50

1

N6-acetyllysine By similarity

Natural variations

Alternative sequence

1

1

M → MAGHR in isoform 2.

VSP_004074

Secondary structure

1

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182

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Turn

12 – 14

3

Helix

20 – 23

4

Beta strand

32 – 36

5

Helix

43 – 52

10

Beta strand

54 – 58

5

Beta strand

71 – 77

7

Beta strand

80 – 85

6

Helix

96 – 106

11

Beta strand

107 – 112

6

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: 6CDCDE6B720C9BF8	FASTA	182	20,496
	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 KS
	Isoform 2 [UniParc]. Checksum: 7AA5116A30665D6F	FASTA	186	20,917
	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 IEYKKS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning of mouse vacuolar sorting protein VPS29." Edgar A.J. Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Tissue: Lung.
[2]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed: 16141072] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Strain: C57BL/6J. Tissue: Bone marrow and Embryo.
[3]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Mammary tumor.
[4]	Lubec G., Klug S. Submitted (MAR-2007) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-14, MASS SPECTROMETRY. Tissue: Hippocampus.
[5]	"Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly." Collins B.M., Skinner C.F., Watson P.J., Seaman M.N., Owen D.J. Nat. Struct. Mol. Biol. 12:594-602(2005) [PubMed: 15965486] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH MANGANESE IONS, ABSENCE OF CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF193794 mRNA. Translation: AAF04595.1.
AK004103 mRNA. Translation: BAB23170.1.
AK150330 mRNA. Translation: BAE29472.1.
BC005663 mRNA. Translation: AAH05663.1.

IPI

IPI00136936.
IPI00230513.

RefSeq

NP_062754.1. NM_019780.1.

UniGene

Mm.216528.
Mm.445844.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Z2W	X-ray	2.00	A/B	1-182	[»]
1Z2X	X-ray	2.22	A/B	1-182	[»]
3PSN	X-ray	2.20	A/B	1-182	[»]
3PSO	X-ray	3.00	A/B	1-182	[»]

ProteinModelPortal

Q9QZ88.

SMR

Q9QZ88. Positions 1-182.

ModBase

Search...

Protein-protein interaction databases

STRING

Q9QZ88.

PTM databases

PhosphoSite

Q9QZ88.

2D gel databases

REPRODUCTION-2DPAGE

Q9QZ88.

Proteomic databases

PRIDE

Q9QZ88.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000118830; ENSMUSP00000113525; ENSMUSG00000029462.
ENSMUST00000155671; ENSMUSP00000121020; ENSMUSG00000029462.

GeneID

56433.

KEGG

mmu:56433.

UCSC

uc008zlb.1. mouse.
uc008zlc.1. mouse.

Organism-specific databases

CTD

51699.

MGI

MGI:1928344. Vps29.

Phylogenomic databases

eggNOG

roNOG06599.

GeneTree

ENSGT00390000012669.

HOVERGEN

HBG056165.

OrthoDB

EOG49PB0G.

PhylomeDB

Q9QZ88.

Gene expression databases

ArrayExpress

Q9QZ88.

Bgee

Q9QZ88.

CleanEx

MM_VPS29.

Genevestigator

Q9QZ88.

GermOnline

ENSMUSG00000029462. Mus musculus.

Family and domain databases

InterPro

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

KO

K07095.

PANTHER

PTHR11124. PTHR11124. 1 hit.

Pfam

PF12850. Metallophos_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00040. YfcE. 1 hit.

ProtoNet

Search...

Other

NextBio

312610.

SOURCE

Search...

Entry information

Entry name

VPS29_MOUSE

Accession

Primary (citable) accession number: Q9QZ88
Secondary accession number(s): Q3UCZ0, Q9D107

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 25, 2002
Last sequence update:	May 1, 2000
Last modified:	November 16, 2011
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program