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Q5SPW0 (VPS54_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 86. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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 54
Alternative name(s):
Tumor antigen SLP-8p homolog
Gene names
Name:Vps54
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length977 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

May be involved in retrograde transport from 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 By similarity.

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 By similarity.

Subcellular location

Golgi apparatustrans-Golgi network By similarity.

Involvement in disease

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. Ref.5

Sequence similarities

Belongs to the VPS54 family.

Sequence caution

The sequence AAH23474.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q5SPW0-1)

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: Q5SPW0-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 977977Vacuolar protein sorting-associated protein 54
PRO_0000148732

Regions

Coiled coil239 – 26123 Potential

Natural variations

Alternative sequence46 – 5712Missing in isoform 2.
VSP_013757
Natural variant9671L → Q in wr; destabilizes and consequently reduces protein levels, as well as those of the GARP complex. Ref.5 Ref.6

Experimental info

Sequence conflict6341E → K in BAC36741. Ref.3

Secondary structure

................. 977
Helix Strand Turn

Details...

Sequences

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

Last modified December 21, 2004. Version 1.
Checksum: BA93F931E92E9E0D

FASTA977110,397
        10         20         30         40         50         60 
MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTGDSHT LCVAPSLVTD 

        70         80         90        100        110        120 
QHRWTVYHSK VNLPAALNDP TLAKRESDFF TKTWGLDFVD TEVIPSLYLP QISKENFIAY 

       130        140        150        160        170        180 
QQEISQREKI HERCKNICPP KDTFDRTLLH IHDKSRTDLE QVPKIFMKPD FALDDSLTFN 

       190        200        210        220        230        240 
SVLPWSHFNT AGGKGSRDAA SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE 

       250        260        270        280        290        300 
LQDYLKKTTQ AVKMLRDKIA QIDKVMCEGS LQILRLALTR NNCVKVYNKL KLMATVHQTQ 

       310        320        330        340        350        360 
PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI DKMMIAEFST 

       370        380        390        400        410        420 
YSHSDLNRPL EGECQVLEEE RLVSLVFGLL KQRKLNFLEI YGEEMIITAK NIIKERVINK 

       430        440        450        460        470        480 
VSQIEEIDTD VVVKLADQMR MLNFPQWIDL LKDIFSKFTV FLQRVKATLN IIHSVVLSVL 

       490        500        510        520        530        540 
EKSQRTRELE EIPQQRSAGK DSSLDTDVAY LTHEGWFISD AFSEGEPASA AVDTTSQRNT 

       550        560        570        580        590        600 
SPHSEPCSSD SVSEPECTTD SSSSKEQTSA CAPPGGIEII VSEDMRLTDL ELGKLASNIQ 

       610        620        630        640        650        660 
ELLCNASDVC HDRAVKFLMS RAKDGFLEKL NSTEFIALSR LMETFIVDTE QICGRKSTSL 

       670        680        690        700        710        720 
LGALQSQANK FVNRFHEERR TKLSLLLDNE RWKQADVPAE FQDLVDSIAD GKIALPEKKP 

       730        740        750        760        770        780 
VVTEERKPAD VLVVEGHQYA VVGTVLLLIR IILEYCQCVD NIPSVTTDML TRLTDLLKYF 

       790        800        810        820        830        840 
NSRSCQLVLG AGALQVVGLK TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQWSML 

       850        860        870        880        890        900 
RHFDHITKDY HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSPCFRNI CKQMTKMHEA 

       910        920        930        940        950        960 
IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA FYTGNLQALK 

       970 
GLKDLDLNMA EIWEQKR 

« Hide

Isoform 2 [UniParc].

Checksum: 5C704137B4C4F075
Show »

FASTA965109,215

References

« Hide 'large scale' references
[1]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[2]"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).
Strain: FVB/N.
Tissue: Kidney and Mammary tumor.
[3]"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. expand/collapse author list , 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 87-977.
Strain: C57BL/6J.
Tissue: Pituitary.
[4]"Isolation and characterization of novel human and mouse genes, which are expressed in the digestive tract."
Daigo Y., Takayama I., Fujino M.A.
Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 744-977.
[5]"Mutation of Vps54 causes motor neuron disease and defective spermiogenesis in the wobbler mouse."
Schmitt-John T., Drepper C., Mussmann A., Hahn P., Kuhlmann M., Thiel C., Hafner M., Lengeling A., Heimann P., Jones J.M., Meisler M.H., Jockusch H.
Nat. Genet. 37:1213-1215(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: DISEASE, VARIANT WR GLN-967.
[6]"Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex."
Perez-Victoria F.J., Abascal-Palacios G., Tascon I., Kajava A., Magadan J.G., Pioro E.P., Bonifacino J.S., Hierro A.
Proc. Natl. Acad. Sci. U.S.A. 107:12860-12865(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 836-974, CHARACTERIZATION OF VARIANT WR GLN-967.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_620692.3. NM_139061.4.
XP_006514760.1. XM_006514697.1.
XP_006514761.1. XM_006514698.1.
UniGeneMm.170103.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3N1BX-ray2.40A/B836-974[»]
3N1EX-ray1.70A/B836-974[»]
ProteinModelPortalQ5SPW0.
SMRQ5SPW0. Positions 836-974.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-59351N.

PTM databases

PhosphoSiteQ5SPW0.

Proteomic databases

PaxDbQ5SPW0.
PRIDEQ5SPW0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000006221; ENSMUSP00000006221; ENSMUSG00000020128. [Q5SPW0-1]
ENSMUST00000109578; ENSMUSP00000105206; ENSMUSG00000020128. [Q5SPW0-2]
GeneID245944.
KEGGmmu:245944.
UCSCuc007ido.2. mouse. [Q5SPW0-1]
uc007idp.2. mouse. [Q5SPW0-2]

Organism-specific databases

CTD51542.
MGIMGI:2178798. Vps54.

Phylogenomic databases

eggNOGNOG285553.
GeneTreeENSGT00390000000583.
HOGENOMHOG000045110.
HOVERGENHBG068681.
InParanoidQ5SPW0.
KOK17600.
OMATKMHEAI.
OrthoDBEOG71RXHV.
PhylomeDBQ5SPW0.
TreeFamTF313700.

Gene expression databases

ArrayExpressQ5SPW0.
BgeeQ5SPW0.
CleanExMM_VPS54.
GenevestigatorQ5SPW0.

Family and domain databases

InterProIPR019515. Vacuolar_sorting-assoc_54.
IPR012501. Vps54.
[Graphical view]
PfamPF10475. DUF2450. 1 hit.
PF07928. Vps54. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSVPS54. mouse.
EvolutionaryTraceQ5SPW0.
NextBio387018.
PROQ5SPW0.
SOURCESearch...

Entry information

Entry nameVPS54_MOUSE
AccessionPrimary (citable) accession number: Q5SPW0
Secondary accession number(s): Q8BPB3 expand/collapse secondary AC list , Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1
Entry history
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: December 21, 2004
Last modified: April 16, 2014
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot