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Protein

Vacuolar protein sorting-associated protein 54

Gene

VPS54

Organism
Homo sapiens (Human)
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 (PubMed:18367545). Within the GARP complex, required to tether the complex to the TGN. Not involved in endocytic recycling (PubMed:25799061).2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 54
Alternative name(s):
Hepatocellular carcinoma protein 8
Tumor antigen HOM-HCC-8
Tumor antigen SLP-8p
Gene namesi
Name:VPS54
Synonyms:HCC8
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:18652. VPS54.

Subcellular locationi

GO - Cellular componenti

  • GARP complex Source: MGI
  • Golgi apparatus Source: UniProtKB
  • nucleoplasm Source: HPA
  • perinuclear region of cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Golgi apparatus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134920394.

Polymorphism and mutation databases

BioMutaiVPS54.
DMDMi82583721.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 977977Vacuolar protein sorting-associated protein 54PRO_0000148731Add
BLAST

Proteomic databases

MaxQBiQ9P1Q0.
PaxDbiQ9P1Q0.
PRIDEiQ9P1Q0.

PTM databases

PhosphoSiteiQ9P1Q0.

Expressioni

Gene expression databases

BgeeiQ9P1Q0.
CleanExiHS_VPS54.
ExpressionAtlasiQ9P1Q0. baseline and differential.
GenevisibleiQ9P1Q0. HS.

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 VPS54.2 Publications

Protein-protein interaction databases

BioGridi119600. 7 interactions.
IntActiQ9P1Q0. 2 interactions.
STRINGi9606.ENSP00000272322.

Structurei

3D structure databases

ProteinModelPortaliQ9P1Q0.
SMRiQ9P1Q0. Positions 843-974.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili240 – 26021Sequence AnalysisAdd
BLAST
Coiled coili480 – 50728Sequence AnalysisAdd
BLAST
Coiled coili582 – 60322Sequence AnalysisAdd
BLAST

Sequence similaritiesi

Belongs to the VPS54 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG285553.
GeneTreeiENSGT00390000000583.
HOVERGENiHBG068681.
InParanoidiQ9P1Q0.
KOiK17600.
OMAiTKMHEAI.
OrthoDBiEOG71RXHV.
PhylomeDBiQ9P1Q0.
TreeFamiTF313700.

Family and domain databases

InterProiIPR019515. Vacuolar_sorting-assoc_54.
IPR012501. Vps54.
[Graphical view]
PfamiPF10475. DUF2450. 1 hit.
PF07928. Vps54. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9P1Q0-1) [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 KIEVDPSKHI RPVPSLPDVC PKEPTGDSHS
60 70 80 90 100
LYVAPSLVTD QHRWTVYHSK VNLPAALNDP RLAKRESDFF TKTWGLDFVD
110 120 130 140 150
TEVIPSFYLP QISKEHFTVY QQEISQREKI HERCKNICPP KDTFERTLLH
160 170 180 190 200
THDKSRTDLE QVPKIFMKPD FALDDSLTFN SVLPWSHFNT AGGKGNRDAA
210 220 230 240 250
SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE LQDYLRKTSQ
260 270 280 290 300
AVKMLRDKIA QIDKVMCEGS LHILRLALTR NNCVKVYNKL KLMATVHQTQ
310 320 330 340 350
PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI
360 370 380 390 400
DKMMIAEFST YSHSDLNRPL EDDCQVLEEE RLISLVFGLL KQRKLNFLEI
410 420 430 440 450
YGEKMVITAK NIIKQCVINK VSQTEEIDTD VVVKLADQMR MLNFPQWFDL
460 470 480 490 500
LKDIFSKFTI FLQRVKATLN IIHSVVLSVL DKNQRTRELE EISQQKNAAK
510 520 530 540 550
DNSLDTEVAY LIHEGMFISD AFGEGELTPI AVDTTSQRNA SPNSEPCSSD
560 570 580 590 600
SVSEPECTTD SSSSKEHTSS SAIPGGVDIM VSEDMKLTDS ELGKLANNIQ
610 620 630 640 650
ELLYSASDIC HDRAVKFLMS RAKDGFLEKL NSMEFITLSR LMETFILDTE
660 670 680 690 700
QICGRKSTSL LGALQSQAIK FVNRFHEERK TKLSLLLDNE RWKQADVPAE
710 720 730 740 750
FQDLVDSLSD GKIALPEKKS GATEERKPAE VLIVEGQQYA VVGTVLLLIR
760 770 780 790 800
IILEYCQCVD NIPSVTTDML TRLSDLLKYF NSRSCQLVLG AGALQVVGLK
810 820 830 840 850
TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQYSML RHFDHITKDY
860 870 880 890 900
HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSACFRNI CKQMTKMHEA
910 920 930 940 950
IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA
960 970
FYTGNLQALK GLKDLDLNMA EIWEQKR
Length:977
Mass (Da):110,589
Last modified:May 10, 2005 - v2
Checksum:i3290160E3460C836
GO
Isoform 2 (identifier: Q9P1Q0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     964-977: DLDLNMAEIWEQKR → IWT

Note: No experimental confirmation available.
Show »
Length:966
Mass (Da):109,246
Checksum:i7FA7C844A6026471
GO
Isoform 3 (identifier: Q9P1Q0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-117: Missing.
     118-126: TVYQQEISQ → MLPTKNRIK
     380-415: Missing.

Note: No experimental confirmation available.
Show »
Length:824
Mass (Da):93,274
Checksum:i9EF51F039A9AD46A
GO
Isoform 4 (identifier: Q9P1Q0-4) [UniParc]FASTAAdd to basket

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

Show »
Length:965
Mass (Da):109,362
Checksum:iD91F94CD6CDC72D3
GO
Isoform 5 (identifier: Q9P1Q0-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-838: Missing.

Note: No experimental confirmation available.
Show »
Length:139
Mass (Da):15,982
Checksum:iF6AFBCDA077C7BB4
GO

Sequence cautioni

The sequence BAA92134.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti130 – 1301I → V in AAF37319 (Ref. 1) Curated
Sequence conflicti526 – 5261E → K in AAF37319 (Ref. 1) Curated
Sequence conflicti601 – 6011E → G in AAF37319 (Ref. 1) Curated
Sequence conflicti643 – 6431E → G in AAF37319 (Ref. 1) Curated
Sequence conflicti650 – 6501E → A in AAF37319 (Ref. 1) Curated
Sequence conflicti677 – 6793EER → VGG in AAF37319 (Ref. 1) Curated
Sequence conflicti727 – 7271K → E in BAA92134 (PubMed:14702039).Curated
Sequence conflicti844 – 8441D → G in AAH41868 (PubMed:15489334).Curated
Sequence conflicti904 – 9041L → H in AAH41868 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti561 – 5611S → C.
Corresponds to variant rs34015596 [ dbSNP | Ensembl ].
VAR_052944
Natural varianti912 – 9121M → I.
Corresponds to variant rs11558741 [ dbSNP | Ensembl ].
VAR_061983

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 838838Missing in isoform 5. 1 PublicationVSP_013751Add
BLAST
Alternative sequencei1 – 117117Missing in isoform 3. 1 PublicationVSP_013752Add
BLAST
Alternative sequencei46 – 5712Missing in isoform 4. 1 PublicationVSP_013753Add
BLAST
Alternative sequencei118 – 1269TVYQQEISQ → MLPTKNRIK in isoform 3. 1 PublicationVSP_013754
Alternative sequencei380 – 41536Missing in isoform 3. 1 PublicationVSP_013755Add
BLAST
Alternative sequencei964 – 97714DLDLN…WEQKR → IWT in isoform 2. 1 PublicationVSP_013756Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF102177 mRNA. Translation: AAF37319.1.
AY444798 mRNA. Translation: AAS20945.1.
AL137604 mRNA. Translation: CAB70837.1.
AL359939 mRNA. Translation: CAB95772.1.
CR749701 mRNA. Translation: CAH18479.1.
BC030275 mRNA. Translation: AAH30275.1.
BC041868 mRNA. Translation: AAH41868.1.
AK002205 mRNA. Translation: BAA92134.1. Different initiation.
CCDSiCCDS33208.1. [Q9P1Q0-1]
CCDS46302.1. [Q9P1Q0-4]
PIRiT46308.
RefSeqiNP_001005739.1. NM_001005739.1. [Q9P1Q0-4]
NP_057600.2. NM_016516.2. [Q9P1Q0-1]
UniGeneiHs.48499.

Genome annotation databases

EnsembliENST00000272322; ENSP00000272322; ENSG00000143952. [Q9P1Q0-1]
ENST00000354504; ENSP00000346499; ENSG00000143952. [Q9P1Q0-3]
ENST00000409558; ENSP00000386980; ENSG00000143952. [Q9P1Q0-4]
GeneIDi51542.
KEGGihsa:51542.
UCSCiuc002scn.3. human. [Q9P1Q0-5]
uc002sco.3. human. [Q9P1Q0-3]
uc002scp.3. human. [Q9P1Q0-4]
uc002scq.3. human. [Q9P1Q0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF102177 mRNA. Translation: AAF37319.1.
AY444798 mRNA. Translation: AAS20945.1.
AL137604 mRNA. Translation: CAB70837.1.
AL359939 mRNA. Translation: CAB95772.1.
CR749701 mRNA. Translation: CAH18479.1.
BC030275 mRNA. Translation: AAH30275.1.
BC041868 mRNA. Translation: AAH41868.1.
AK002205 mRNA. Translation: BAA92134.1. Different initiation.
CCDSiCCDS33208.1. [Q9P1Q0-1]
CCDS46302.1. [Q9P1Q0-4]
PIRiT46308.
RefSeqiNP_001005739.1. NM_001005739.1. [Q9P1Q0-4]
NP_057600.2. NM_016516.2. [Q9P1Q0-1]
UniGeneiHs.48499.

3D structure databases

ProteinModelPortaliQ9P1Q0.
SMRiQ9P1Q0. Positions 843-974.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119600. 7 interactions.
IntActiQ9P1Q0. 2 interactions.
STRINGi9606.ENSP00000272322.

PTM databases

PhosphoSiteiQ9P1Q0.

Polymorphism and mutation databases

BioMutaiVPS54.
DMDMi82583721.

Proteomic databases

MaxQBiQ9P1Q0.
PaxDbiQ9P1Q0.
PRIDEiQ9P1Q0.

Protocols and materials databases

DNASUi51542.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000272322; ENSP00000272322; ENSG00000143952. [Q9P1Q0-1]
ENST00000354504; ENSP00000346499; ENSG00000143952. [Q9P1Q0-3]
ENST00000409558; ENSP00000386980; ENSG00000143952. [Q9P1Q0-4]
GeneIDi51542.
KEGGihsa:51542.
UCSCiuc002scn.3. human. [Q9P1Q0-5]
uc002sco.3. human. [Q9P1Q0-3]
uc002scp.3. human. [Q9P1Q0-4]
uc002scq.3. human. [Q9P1Q0-1]

Organism-specific databases

CTDi51542.
GeneCardsiGC02M064119.
HGNCiHGNC:18652. VPS54.
MIMi614633. gene.
neXtProtiNX_Q9P1Q0.
PharmGKBiPA134920394.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG285553.
GeneTreeiENSGT00390000000583.
HOVERGENiHBG068681.
InParanoidiQ9P1Q0.
KOiK17600.
OMAiTKMHEAI.
OrthoDBiEOG71RXHV.
PhylomeDBiQ9P1Q0.
TreeFamiTF313700.

Miscellaneous databases

ChiTaRSiVPS54. human.
GenomeRNAii51542.
NextBioi55313.
PROiQ9P1Q0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9P1Q0.
CleanExiHS_VPS54.
ExpressionAtlasiQ9P1Q0. baseline and differential.
GenevisibleiQ9P1Q0. HS.

Family and domain databases

InterProiIPR019515. Vacuolar_sorting-assoc_54.
IPR012501. Vps54.
[Graphical view]
PfamiPF10475. DUF2450. 1 hit.
PF07928. Vps54. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "HOM-HCC-8, a novel tumor antigen associated with hepatocellular carcinoma."
    Stenner-Liewen F., Luo G., Tuereci O., Sahin U., Liewen H., Koslowski M., Pfreundschuh M.
    Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    Tissue: Hepatoma.
  2. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBUNIT.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5).
    Tissue: Testis.
  4. "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 3 AND 4).
    Tissue: Skin and Testis.
  5. "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.
    , 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] OF 579-977.
    Tissue: Placenta.
  6. "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: FUNCTION, SUBCELLULAR LOCATION.
  7. "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.
  8. "EARP is a multisubunit tethering complex involved in endocytic recycling."
    Schindler C., Chen Y., Pu J., Guo X., Bonifacino J.S.
    Nat. Cell Biol. 0:0-0(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, IDENTIFICATION IN THE GARP COMPLEX.

Entry informationi

Entry nameiVPS54_HUMAN
AccessioniPrimary (citable) accession number: Q9P1Q0
Secondary accession number(s): Q5VIR5
, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: May 10, 2005
Last modified: June 24, 2015
This is version 102 of the entry and version 2 of the sequence. [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

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.