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Protein

Vacuolar protein sorting-associated protein 54

Gene

Vps54

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. Within the GARP complex, required to tether the complex to the TGN. Not involved in endocytic recycling.By similarity

GO - Molecular functioni

GO - Biological processi

  • Golgi to vacuole transport Source: GO_Central
  • growth Source: MGI
  • homeostasis of number of cells within a tissue Source: MGI
  • lysosomal transport Source: MGI
  • musculoskeletal movement Source: MGI
  • neurofilament cytoskeleton organization Source: MGI
  • protein transport Source: UniProtKB-KW
  • retrograde transport, endosome to Golgi Source: MGI
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

ReactomeiR-MMU-6811440. Retrograde transport at the Trans-Golgi-Network.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 54
Alternative name(s):
Tumor antigen SLP-8p homolog
Gene namesi
Name:Vps54
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:2178798. Vps54.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Golgi apparatus

Pathology & Biotechi

Involvement in diseasei

Defects in Vps54 are the cause of wobbler phenotype (wr). Wr is autosomal recessive and is a spontaneous mutation discovered almost 50 years ago. It causes spinal muscular atrophy and defective spermiogenesis.

Keywords - Diseasei

Disease mutation

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001487321 – 977Vacuolar protein sorting-associated protein 54Add BLAST977

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei8PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ5SPW0.
PRIDEiQ5SPW0.

PTM databases

iPTMnetiQ5SPW0.
PhosphoSitePlusiQ5SPW0.

Expressioni

Gene expression databases

BgeeiENSMUSG00000020128.
CleanExiMM_VPS54.
ExpressionAtlasiQ5SPW0. baseline and differential.
GenevisibleiQ5SPW0. MM.

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.By similarity

GO - Molecular functioni

Protein-protein interaction databases

DIPiDIP-59351N.
STRINGi10090.ENSMUSP00000006221.

Structurei

Secondary structure

1977
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi836 – 847Combined sources12
Helixi850 – 873Combined sources24
Beta strandi880 – 883Combined sources4
Helixi885 – 901Combined sources17
Turni902 – 904Combined sources3
Helixi907 – 931Combined sources25
Beta strandi936 – 939Combined sources4
Helixi940 – 957Combined sources18
Helixi969 – 973Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N1BX-ray2.40A/B836-974[»]
3N1EX-ray1.70A/B836-974[»]
ProteinModelPortaliQ5SPW0.
SMRiQ5SPW0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SPW0.

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili239 – 261Sequence analysisAdd BLAST23

Sequence similaritiesi

Belongs to the VPS54 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2115. Eukaryota.
ENOG410XQ3K. LUCA.
GeneTreeiENSGT00390000000583.
HOGENOMiHOG000045110.
HOVERGENiHBG068681.
InParanoidiQ5SPW0.
KOiK17600.
OMAiTKMHEAI.
OrthoDBiEOG091G026I.
PhylomeDBiQ5SPW0.
TreeFamiTF313700.

Family and domain databases

InterProiIPR012501. Vps54_C.
IPR019515. VPS54_N.
[Graphical view]
PfamiPF07928. Vps54. 1 hit.
PF10475. Vps54_N. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5SPW0-1) [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
MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTGDSHT
60 70 80 90 100
LCVAPSLVTD QHRWTVYHSK VNLPAALNDP TLAKRESDFF TKTWGLDFVD
110 120 130 140 150
TEVIPSLYLP QISKENFIAY QQEISQREKI HERCKNICPP KDTFDRTLLH
160 170 180 190 200
IHDKSRTDLE QVPKIFMKPD FALDDSLTFN SVLPWSHFNT AGGKGSRDAA
210 220 230 240 250
SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE LQDYLKKTTQ
260 270 280 290 300
AVKMLRDKIA QIDKVMCEGS LQILRLALTR NNCVKVYNKL KLMATVHQTQ
310 320 330 340 350
PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI
360 370 380 390 400
DKMMIAEFST YSHSDLNRPL EGECQVLEEE RLVSLVFGLL KQRKLNFLEI
410 420 430 440 450
YGEEMIITAK NIIKERVINK VSQIEEIDTD VVVKLADQMR MLNFPQWIDL
460 470 480 490 500
LKDIFSKFTV FLQRVKATLN IIHSVVLSVL EKSQRTRELE EIPQQRSAGK
510 520 530 540 550
DSSLDTDVAY LTHEGWFISD AFSEGEPASA AVDTTSQRNT SPHSEPCSSD
560 570 580 590 600
SVSEPECTTD SSSSKEQTSA CAPPGGIEII VSEDMRLTDL ELGKLASNIQ
610 620 630 640 650
ELLCNASDVC HDRAVKFLMS RAKDGFLEKL NSTEFIALSR LMETFIVDTE
660 670 680 690 700
QICGRKSTSL LGALQSQANK FVNRFHEERR TKLSLLLDNE RWKQADVPAE
710 720 730 740 750
FQDLVDSIAD GKIALPEKKP VVTEERKPAD VLVVEGHQYA VVGTVLLLIR
760 770 780 790 800
IILEYCQCVD NIPSVTTDML TRLTDLLKYF NSRSCQLVLG AGALQVVGLK
810 820 830 840 850
TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQWSML RHFDHITKDY
860 870 880 890 900
HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSPCFRNI CKQMTKMHEA
910 920 930 940 950
IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA
960 970
FYTGNLQALK GLKDLDLNMA EIWEQKR
Length:977
Mass (Da):110,397
Last modified:December 21, 2004 - v1
Checksum:iBA93F931E92E9E0D
GO
Isoform 2 (identifier: Q5SPW0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     46-57: Missing.

Show »
Length:965
Mass (Da):109,215
Checksum:i5C704137B4C4F075
GO

Sequence cautioni

The sequence AAH23474 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti634E → K in BAC36741 (PubMed:16141072).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti967L → Q in wr; destabilizes and consequently reduces protein levels, as well as those of the GARP complex. 2 Publications1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01375746 – 57Missing in isoform 2. 1 PublicationAdd BLAST12

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL833772, AL669979 Genomic DNA. Translation: CAI24173.1.
AL833772, AL669979 Genomic DNA. Translation: CAI24174.1.
AL669979, AL833772 Genomic DNA. Translation: CAI26092.1.
AL669979, AL833772 Genomic DNA. Translation: CAI26093.1.
BC023474 mRNA. Translation: AAH23474.1. Different initiation.
BC024789 mRNA. Translation: AAH24789.1.
BC025012 mRNA. Translation: AAH25012.1.
AK077306 mRNA. Translation: BAC36741.1.
AB052761 mRNA. Translation: BAC53794.1.
CCDSiCCDS24463.1. [Q5SPW0-1]
CCDS70147.1. [Q5SPW0-2]
RefSeqiNP_001277557.1. NM_001290628.1. [Q5SPW0-2]
NP_620692.3. NM_139061.5. [Q5SPW0-1]
XP_011242022.1. XM_011243720.1. [Q5SPW0-1]
UniGeneiMm.170103.

Genome annotation databases

EnsembliENSMUST00000006221; ENSMUSP00000006221; ENSMUSG00000020128. [Q5SPW0-1]
ENSMUST00000109578; ENSMUSP00000105206; ENSMUSG00000020128. [Q5SPW0-2]
GeneIDi245944.
KEGGimmu:245944.
UCSCiuc007ido.3. mouse. [Q5SPW0-1]
uc007idp.3. mouse. [Q5SPW0-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL833772, AL669979 Genomic DNA. Translation: CAI24173.1.
AL833772, AL669979 Genomic DNA. Translation: CAI24174.1.
AL669979, AL833772 Genomic DNA. Translation: CAI26092.1.
AL669979, AL833772 Genomic DNA. Translation: CAI26093.1.
BC023474 mRNA. Translation: AAH23474.1. Different initiation.
BC024789 mRNA. Translation: AAH24789.1.
BC025012 mRNA. Translation: AAH25012.1.
AK077306 mRNA. Translation: BAC36741.1.
AB052761 mRNA. Translation: BAC53794.1.
CCDSiCCDS24463.1. [Q5SPW0-1]
CCDS70147.1. [Q5SPW0-2]
RefSeqiNP_001277557.1. NM_001290628.1. [Q5SPW0-2]
NP_620692.3. NM_139061.5. [Q5SPW0-1]
XP_011242022.1. XM_011243720.1. [Q5SPW0-1]
UniGeneiMm.170103.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N1BX-ray2.40A/B836-974[»]
3N1EX-ray1.70A/B836-974[»]
ProteinModelPortaliQ5SPW0.
SMRiQ5SPW0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59351N.
STRINGi10090.ENSMUSP00000006221.

PTM databases

iPTMnetiQ5SPW0.
PhosphoSitePlusiQ5SPW0.

Proteomic databases

PaxDbiQ5SPW0.
PRIDEiQ5SPW0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000006221; ENSMUSP00000006221; ENSMUSG00000020128. [Q5SPW0-1]
ENSMUST00000109578; ENSMUSP00000105206; ENSMUSG00000020128. [Q5SPW0-2]
GeneIDi245944.
KEGGimmu:245944.
UCSCiuc007ido.3. mouse. [Q5SPW0-1]
uc007idp.3. mouse. [Q5SPW0-2]

Organism-specific databases

CTDi51542.
MGIiMGI:2178798. Vps54.

Phylogenomic databases

eggNOGiKOG2115. Eukaryota.
ENOG410XQ3K. LUCA.
GeneTreeiENSGT00390000000583.
HOGENOMiHOG000045110.
HOVERGENiHBG068681.
InParanoidiQ5SPW0.
KOiK17600.
OMAiTKMHEAI.
OrthoDBiEOG091G026I.
PhylomeDBiQ5SPW0.
TreeFamiTF313700.

Enzyme and pathway databases

ReactomeiR-MMU-6811440. Retrograde transport at the Trans-Golgi-Network.

Miscellaneous databases

ChiTaRSiVps54. mouse.
EvolutionaryTraceiQ5SPW0.
PROiQ5SPW0.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000020128.
CleanExiMM_VPS54.
ExpressionAtlasiQ5SPW0. baseline and differential.
GenevisibleiQ5SPW0. MM.

Family and domain databases

InterProiIPR012501. Vps54_C.
IPR019515. VPS54_N.
[Graphical view]
PfamiPF07928. Vps54. 1 hit.
PF10475. Vps54_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVPS54_MOUSE
AccessioniPrimary (citable) accession number: Q5SPW0
Secondary accession number(s): Q8BPB3
, Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: December 21, 2004
Last modified: November 2, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.