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Q5VIR6 (VPS53_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 90. 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 53 homolog
Gene names
Name:VPS53
ORF Names:PP13624
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length699 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

May be involved in retrograde transport of early and late endosomes to the late Golgi. The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD. Ref.1 Ref.3

Subunit structure

Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. Ref.1

Subcellular location

Golgi apparatustrans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein Ref.1 Ref.3.

Sequence similarities

Belongs to the VPS53 family.

Sequence caution

The sequence AAL55842.1 differs from that shown. Reason: Frameshift at position 562.

Ontologies

Keywords
   Biological processProtein transport
Transport
   Cellular componentEndosome
Golgi apparatus
Membrane
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainCoiled coil
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processprotein transport

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentGARP complex

Inferred from direct assay PubMed 19620288. Source: MGI

endosome membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionprotein binding

Inferred from physical interaction Ref.11. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q5VIR6-1)

Also known as: long;

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: Q5VIR6-2)

Also known as: short;

The sequence of this isoform differs from the canonical sequence as follows:
     96-124: Missing.
Isoform 3 (identifier: Q5VIR6-3)

The sequence of this isoform differs from the canonical sequence as follows:
     656-673: LASTRKYFTQFCVKFANS → PVASTRKYFTQLCVKFAK
     674-699: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q5VIR6-4)

The sequence of this isoform differs from the canonical sequence as follows:
     696-699: VRWT → LLLDTHSLKM...KLEKLIKKRL

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 699699Vacuolar protein sorting-associated protein 53 homolog
PRO_0000215189

Regions

Coiled coil55 – 14288 Potential

Amino acid modifications

Modified residue1101N6-acetyllysine Ref.10
Modified residue3601N6-acetyllysine Ref.10
Modified residue3771Phosphoserine Ref.9
Modified residue3911Phosphothreonine Ref.9
Modified residue5801Phosphoserine Ref.12

Natural variations

Alternative sequence96 – 12429Missing in isoform 2.
VSP_016236
Alternative sequence656 – 67318LASTR…KFANS → PVASTRKYFTQLCVKFAK in isoform 3.
VSP_016237
Alternative sequence674 – 69926Missing in isoform 3.
VSP_016238
Alternative sequence696 – 6994VRWT → LLLDTHSLKMVLLDLPSISS QVVRKAPASYTKIVVKGMTR AEMILKVVMAPHEPLVVFVD NYIKLLTDCNTETFQKILDM KGLKRSEQSSMLELLRQRLP APPSGAESSGSLSLTAPTPE QESSRIRKLEKLIKKRL in isoform 4.
VSP_042106
Natural variant3281L → I.
Corresponds to variant rs16954056 [ dbSNP | Ensembl ].
VAR_059959
Natural variant3751L → R.
Corresponds to variant rs61644407 [ dbSNP | Ensembl ].
VAR_066561

Experimental info

Sequence conflict271I → V in ABW03005. Ref.3
Sequence conflict1151K → N in ABW03005. Ref.3
Sequence conflict4661A → T in AAK27973. Ref.2
Sequence conflict5201T → P in AAK27973. Ref.2
Sequence conflict5251G → E in AAK27973. Ref.2
Sequence conflict658 – 6658STRKYFTQ → NMAKSHLY in AAL55842. Ref.8

Sequences

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

Last modified December 7, 2004. Version 1.
Checksum: 6C07EC07682BF4C6

FASTA69979,653
        10         20         30         40         50         60 
MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT LFPTEQSLAN 

        70         80         90        100        110        120 
IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA QKAIQQLFGK IKDIKDKAEK 

       130        140        150        160        170        180 
SEQMVKEITR DIKQLDHAKR HLTTSITTLN HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG 

       190        200        210        220        230        240 
VMNVLEHFHK YMGIPQIRQL SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD 

       250        260        270        280        290        300 
ACLVANILDP RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE 

       310        320        330        340        350        360 
KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR TTNFEGFLAK 

       370        380        390        400        410        420 
RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE KGDLDQPKKP KAPDNPFHGI 

       430        440        450        460        470        480 
VSKCFEPHLY VYIESQDKNL GELIDRFVAD FKAQGPPKPN TDEGGAVLPS CADLFVYYKK 

       490        500        510        520        530        540 
CMVQCSQLST GEPMIALTTI FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE 

       550        560        570        580        590        600 
VAKFTLEELC LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS 

       610        620        630        640        650        660 
SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP IIRDNLASTR 

       670        680        690 
KYFTQFCVKF ANSFIPKFIT HLFKCKPISM VGAEQVRWT 

« Hide

Isoform 2 (short) [UniParc].

Checksum: 8057AAC082136EC7
Show »

FASTA67076,352
Isoform 3 [UniParc].

Checksum: 82C41A7433B5EF79
Show »

FASTA67376,569
Isoform 4 [UniParc].

Checksum: EA71D35158E9419E
Show »

FASTA83294,405

References

« Hide 'large scale' references
[1]"Characterization of the human GARP (Golgi associated retrograde protein) complex."
Liewen H., Meinhold-Heerlein I., Oliveira V., Schwarzenbacher R., Luo G., Wadle A., Jung M., Pfreundschuh M., Stenner-Liewen F.
Exp. Cell Res. 306:24-34(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.
[2]"The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis."
Zhao X., He M., Wan D., Ye Y., He Y., Han L., Guo M., Huang Y., Qin W., Wang M.W., Chong W., Chen J., Zhang L., Yang N., Xu B., Wu M., Zuo L., Gu J.
Cancer Lett. 190:221-232(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
[3]"Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes."
Perez-Victoria F.J., Mardones G.A., Bonifacino J.S.
Mol. Biol. Cell 19:2350-2362(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4), SUBCELLULAR LOCATION, FUNCTION.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 332-699.
Tissue: Placenta and Tongue.
[5]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] (ISOFORM 2).
Tissue: Placenta.
[8]"Large-scale cDNA transfection screening for genes related to cancer development and progression."
Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. expand/collapse author list , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-665 (ISOFORM 1).
[9]"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-377 AND THR-391, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"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-110 AND LYS-360, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex."
Perez-Victoria F.J., Schindler C., Magadan J.G., Mardones G.A., Delevoye C., Romao M., Raposo G., Bonifacino J.S.
Mol. Biol. Cell 21:3386-3395(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH VPS51.
[12]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-580, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[13]"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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY444797 mRNA. Translation: AAS20944.1.
AF246287 mRNA. Translation: AAK27973.1.
EU021218 mRNA. Translation: ABW03005.1.
AK001841 mRNA. Translation: BAA91935.1.
AK290343 mRNA. Translation: BAF83032.1.
AC015853 Genomic DNA. No translation available.
AC027455 Genomic DNA. No translation available.
CH471108 Genomic DNA. Translation: EAW90661.1.
BC006116 mRNA. Translation: AAH06116.1.
AF318335 mRNA. Translation: AAL55842.1. Frameshift.
CCDSCCDS10995.1. [Q5VIR6-2]
CCDS45558.1. [Q5VIR6-4]
RefSeqNP_001121631.1. NM_001128159.2. [Q5VIR6-4]
NP_060759.2. NM_018289.3. [Q5VIR6-2]
UniGeneHs.461819.

3D structure databases

ProteinModelPortalQ5VIR6.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120563. 13 interactions.
DIPDIP-59352N.
IntActQ5VIR6. 2 interactions.
STRING9606.ENSP00000401435.

PTM databases

PhosphoSiteQ5VIR6.

Polymorphism databases

DMDM74746777.

Proteomic databases

MaxQBQ5VIR6.
PaxDbQ5VIR6.
PRIDEQ5VIR6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000291074; ENSP00000291074; ENSG00000141252. [Q5VIR6-2]
ENST00000437048; ENSP00000401435; ENSG00000141252. [Q5VIR6-4]
ENST00000571805; ENSP00000459312; ENSG00000141252. [Q5VIR6-1]
GeneID55275.
KEGGhsa:55275.
UCSCuc002frm.2. human. [Q5VIR6-2]
uc002frn.2. human. [Q5VIR6-1]
uc010cjo.2. human. [Q5VIR6-4]

Organism-specific databases

CTD55275.
GeneCardsGC17M000381.
H-InvDBHIX0013386.
HGNCHGNC:25608. VPS53.
HPAHPA022988.
HPA024446.
neXtProtNX_Q5VIR6.
PharmGKBPA142670618.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG327715.
HOGENOMHOG000265899.
HOVERGENHBG092351.
InParanoidQ5VIR6.
OMAAMSKMPW.
OrthoDBEOG70PBWZ.
PhylomeDBQ5VIR6.
TreeFamTF106150.

Gene expression databases

ArrayExpressQ5VIR6.
BgeeQ5VIR6.
CleanExHS_VPS53.
GenevestigatorQ5VIR6.

Family and domain databases

InterProIPR007234. Vps53_N.
[Graphical view]
PfamPF04100. Vps53_N. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSVPS53. human.
GenomeRNAi55275.
NextBio59405.
PROQ5VIR6.

Entry information

Entry nameVPS53_HUMAN
AccessionPrimary (citable) accession number: Q5VIR6
Secondary accession number(s): A8K2S8 expand/collapse secondary AC list , B3FH42, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 7, 2004
Last modified: July 9, 2014
This is version 90 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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM