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Protein

Vacuolar protein sorting-associated protein 53 homolog

Gene

VPS53

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

Functioni

Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). 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 (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).3 Publications

GO - Biological processi

  • endocytic recycling Source: UniProtKB
  • lysosomal transport Source: MGI
  • protein transport Source: UniProtKB-KW
  • retrograde transport, endosome to Golgi Source: UniProtKB

Keywordsi

Biological processProtein transport, Transport

Enzyme and pathway databases

ReactomeiR-HSA-6811440 Retrograde transport at the Trans-Golgi-Network

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 53 homolog
Gene namesi
Name:VPS53
ORF Names:PP13624
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000141252.19
HGNCiHGNC:25608 VPS53
MIMi615850 gene
neXtProtiNX_Q5VIR6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 2E (PCH2E)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA neurodegenerative disorder characterized by progressive cerebello-cerebral atrophy, profound mental retardation, progressive microcephaly, spasticity, and early-onset epilepsy.
See also OMIM:615851
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_071803695Q → R in PCH2E. 1 PublicationCorresponds to variant dbSNP:rs587777465EnsemblClinVar.1
Isoform 4 (identifier: Q5VIR6-4)
Natural varianti695Q → R in PCH2E. 1 Publication1

Keywords - Diseasei

Disease mutation, Epilepsy, Mental retardation, Neurodegeneration

Organism-specific databases

DisGeNETi55275
MalaCardsiVPS53
MIMi615851 phenotype
OpenTargetsiENSG00000141252
Orphaneti247198 Progressive cerebello-cerebral atrophy
PharmGKBiPA142670618

Polymorphism and mutation databases

BioMutaiVPS53
DMDMi74746777

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002151891 – 699Vacuolar protein sorting-associated protein 53 homologAdd BLAST699

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei110N6-acetyllysineCombined sources1
Modified residuei360N6-acetyllysineCombined sources1
Modified residuei377PhosphoserineCombined sources1
Modified residuei391PhosphothreonineCombined sources1
Modified residuei580PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ5VIR6
PaxDbiQ5VIR6
PeptideAtlasiQ5VIR6
PRIDEiQ5VIR6
ProteomicsDBi65251
65252 [Q5VIR6-2]
65253 [Q5VIR6-3]
65254 [Q5VIR6-4]

PTM databases

iPTMnetiQ5VIR6
PhosphoSitePlusiQ5VIR6

Expressioni

Gene expression databases

BgeeiENSG00000141252 Expressed in 187 organ(s), highest expression level in frontal cortex
CleanExiHS_VPS53
ExpressionAtlasiQ5VIR6 baseline and differential
GenevisibleiQ5VIR6 HS

Organism-specific databases

HPAiHPA022988
HPA024446

Interactioni

Subunit structurei

Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54 (PubMed:27440922, PubMed:15878329). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061, PubMed:27440922). EIPR1 interacts with both EARP and GARP complexes and mediates the recruitment of the GARP complex to the trans-Golgi network (PubMed:27440922).3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
VPS50Q96JG67EBI-2850511,EBI-11044388

Protein-protein interaction databases

BioGridi120563, 62 interactors
CORUMiQ5VIR6
DIPiDIP-59352N
IntActiQ5VIR6, 7 interactors
STRINGi9606.ENSP00000401435

Structurei

3D structure databases

ProteinModelPortaliQ5VIR6
SMRiQ5VIR6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili55 – 142Sequence analysisAdd BLAST88

Sequence similaritiesi

Belongs to the VPS53 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2180 Eukaryota
ENOG410XNMT LUCA
GeneTreeiENSGT00390000015165
HOGENOMiHOG000265899
HOVERGENiHBG092351
InParanoidiQ5VIR6
KOiK20299
OMAiGEPMIAL
OrthoDBiEOG091G024J
PhylomeDBiQ5VIR6
TreeFamiTF106150

Family and domain databases

InterProiView protein in InterPro
IPR007234 Vps53_N
PfamiView protein in Pfam
PF04100 Vps53_N, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 6 potential isoforms that are computationally mapped.iShow all

Isoform 1 (identifier: Q5VIR6-1) [UniParc]FASTAAdd to basket
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.

« Hide
        10         20         30         40         50
MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT
60 70 80 90 100
LFPTEQSLAN IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA
110 120 130 140 150
QKAIQQLFGK IKDIKDKAEK SEQMVKEITR DIKQLDHAKR HLTTSITTLN
160 170 180 190 200
HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG VMNVLEHFHK YMGIPQIRQL
210 220 230 240 250
SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD ACLVANILDP
260 270 280 290 300
RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE
310 320 330 340 350
KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR
360 370 380 390 400
TTNFEGFLAK RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE
410 420 430 440 450
KGDLDQPKKP KAPDNPFHGI VSKCFEPHLY VYIESQDKNL GELIDRFVAD
460 470 480 490 500
FKAQGPPKPN TDEGGAVLPS CADLFVYYKK CMVQCSQLST GEPMIALTTI
510 520 530 540 550
FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE VAKFTLEELC
560 570 580 590 600
LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS
610 620 630 640 650
SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP
660 670 680 690
IIRDNLASTR KYFTQFCVKF ANSFIPKFIT HLFKCKPISM VGAEQVRWT
Length:699
Mass (Da):79,653
Last modified:December 7, 2004 - v1
Checksum:i6C07EC07682BF4C6
GO
Isoform 2 (identifier: Q5VIR6-2) [UniParc]FASTAAdd to basket
Also known as: short

The sequence of this isoform differs from the canonical sequence as follows:
     96-124: Missing.

Show »
Length:670
Mass (Da):76,352
Checksum:i8057AAC082136EC7
GO
Isoform 3 (identifier: Q5VIR6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     656-673: LASTRKYFTQFCVKFANS → PVASTRKYFTQLCVKFAK
     674-699: Missing.

Note: No experimental confirmation available.
Show »
Length:673
Mass (Da):76,569
Checksum:i82C41A7433B5EF79
GO
Isoform 4 (identifier: Q5VIR6-4) [UniParc]FASTAAdd to basket

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

Show »
Length:832
Mass (Da):94,405
Checksum:iEA71D35158E9419E
GO

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
I3L184I3L184_HUMAN
Vacuolar protein sorting-associated...
VPS53
237Annotation score:
I3L0S6I3L0S6_HUMAN
Vacuolar protein sorting-associated...
VPS53
216Annotation score:
F6VX93F6VX93_HUMAN
Vacuolar protein sorting-associated...
VPS53
547Annotation score:
I3L1W6I3L1W6_HUMAN
Vacuolar protein sorting-associated...
VPS53
145Annotation score:
E7EVT8E7EVT8_HUMAN
Vacuolar protein sorting-associated...
VPS53
422Annotation score:
I3L4P9I3L4P9_HUMAN
Vacuolar protein sorting-associated...
VPS53
68Annotation score:

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti27I → V in ABW03005 (PubMed:18367545).Curated1
Sequence conflicti115K → N in ABW03005 (PubMed:18367545).Curated1
Sequence conflicti466A → T in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti520T → P in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti525G → E in AAK27973 (PubMed:12565177).Curated1
Sequence conflicti658 – 665STRKYFTQ → NMAKSHLY in AAL55842 (PubMed:15498874).Curated8

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059959328L → I. Corresponds to variant dbSNP:rs16954056EnsemblClinVar.1
Natural variantiVAR_066561375L → R. Corresponds to variant dbSNP:rs61644407EnsemblClinVar.1
Natural variantiVAR_071803695Q → R in PCH2E. 1 PublicationCorresponds to variant dbSNP:rs587777465EnsemblClinVar.1
Isoform 4 (identifier: Q5VIR6-4)
Natural varianti695Q → R in PCH2E. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01623696 – 124Missing in isoform 2. 2 PublicationsAdd BLAST29
Alternative sequenceiVSP_016237656 – 673LASTR…KFANS → PVASTRKYFTQLCVKFAK in isoform 3. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_016238674 – 699Missing in isoform 3. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_042106696 – 699VRWT → LLLDTHSLKMVLLDLPSISS QVVRKAPASYTKIVVKGMTR AEMILKVVMAPHEPLVVFVD NYIKLLTDCNTETFQKILDM KGLKRSEQSSMLELLRQRLP APPSGAESSGSLSLTAPTPE QESSRIRKLEKLIKKRL in isoform 4. 1 Publication4

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS10995.1 [Q5VIR6-2]
CCDS45558.1 [Q5VIR6-4]
RefSeqiNP_001121631.1, NM_001128159.2 [Q5VIR6-4]
NP_060759.2, NM_018289.3 [Q5VIR6-2]
UniGeneiHs.461819

Genome annotation databases

EnsembliENST00000291074; ENSP00000291074; ENSG00000141252 [Q5VIR6-2]
ENST00000437048; ENSP00000401435; ENSG00000141252 [Q5VIR6-4]
ENST00000571805; ENSP00000459312; ENSG00000141252 [Q5VIR6-1]
ENST00000638350; ENSP00000492070; ENSG00000283883 [Q5VIR6-2]
ENST00000639801; ENSP00000492761; ENSG00000283883 [Q5VIR6-4]
ENST00000639896; ENSP00000492119; ENSG00000283883 [Q5VIR6-1]
GeneIDi55275
KEGGihsa:55275
UCSCiuc002frm.3 human [Q5VIR6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS10995.1 [Q5VIR6-2]
CCDS45558.1 [Q5VIR6-4]
RefSeqiNP_001121631.1, NM_001128159.2 [Q5VIR6-4]
NP_060759.2, NM_018289.3 [Q5VIR6-2]
UniGeneiHs.461819

3D structure databases

ProteinModelPortaliQ5VIR6
SMRiQ5VIR6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120563, 62 interactors
CORUMiQ5VIR6
DIPiDIP-59352N
IntActiQ5VIR6, 7 interactors
STRINGi9606.ENSP00000401435

PTM databases

iPTMnetiQ5VIR6
PhosphoSitePlusiQ5VIR6

Polymorphism and mutation databases

BioMutaiVPS53
DMDMi74746777

Proteomic databases

MaxQBiQ5VIR6
PaxDbiQ5VIR6
PeptideAtlasiQ5VIR6
PRIDEiQ5VIR6
ProteomicsDBi65251
65252 [Q5VIR6-2]
65253 [Q5VIR6-3]
65254 [Q5VIR6-4]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000291074; ENSP00000291074; ENSG00000141252 [Q5VIR6-2]
ENST00000437048; ENSP00000401435; ENSG00000141252 [Q5VIR6-4]
ENST00000571805; ENSP00000459312; ENSG00000141252 [Q5VIR6-1]
ENST00000638350; ENSP00000492070; ENSG00000283883 [Q5VIR6-2]
ENST00000639801; ENSP00000492761; ENSG00000283883 [Q5VIR6-4]
ENST00000639896; ENSP00000492119; ENSG00000283883 [Q5VIR6-1]
GeneIDi55275
KEGGihsa:55275
UCSCiuc002frm.3 human [Q5VIR6-1]

Organism-specific databases

CTDi55275
DisGeNETi55275
EuPathDBiHostDB:ENSG00000141252.19
GeneCardsiVPS53
H-InvDBiHIX0013386
HGNCiHGNC:25608 VPS53
HPAiHPA022988
HPA024446
MalaCardsiVPS53
MIMi615850 gene
615851 phenotype
neXtProtiNX_Q5VIR6
OpenTargetsiENSG00000141252
Orphaneti247198 Progressive cerebello-cerebral atrophy
PharmGKBiPA142670618
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2180 Eukaryota
ENOG410XNMT LUCA
GeneTreeiENSGT00390000015165
HOGENOMiHOG000265899
HOVERGENiHBG092351
InParanoidiQ5VIR6
KOiK20299
OMAiGEPMIAL
OrthoDBiEOG091G024J
PhylomeDBiQ5VIR6
TreeFamiTF106150

Enzyme and pathway databases

ReactomeiR-HSA-6811440 Retrograde transport at the Trans-Golgi-Network

Miscellaneous databases

ChiTaRSiVPS53 human
GenomeRNAii55275
PROiPR:Q5VIR6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000141252 Expressed in 187 organ(s), highest expression level in frontal cortex
CleanExiHS_VPS53
ExpressionAtlasiQ5VIR6 baseline and differential
GenevisibleiQ5VIR6 HS

Family and domain databases

InterProiView protein in InterPro
IPR007234 Vps53_N
PfamiView protein in Pfam
PF04100 Vps53_N, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiVPS53_HUMAN
AccessioniPrimary (citable) accession number: Q5VIR6
Secondary accession number(s): A8K2S8
, B3FH42, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 7, 2004
Last modified: September 12, 2018
This is version 121 of the entry and version 1 of the sequence. See 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

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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