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Q5SPW0

- VPS54_MOUSE

UniProt

Q5SPW0 - VPS54_MOUSE

Protein

Vacuolar protein sorting-associated protein 54

Gene

Vps54

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    Functioni

    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.By similarity

    GO - Biological processi

    1. growth Source: MGI
    2. homeostasis of number of cells within a tissue Source: MGI
    3. musculoskeletal movement Source: MGI
    4. neurofilament cytoskeleton organization Source: MGI
    5. protein transport Source: UniProtKB-KW
    6. retrograde transport, endosome to Golgi Source: InterPro

    Keywords - Biological processi

    Protein transport, Transport

    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
    ProteomesiUP000000589: Chromosome 11

    Organism-specific databases

    MGIiMGI:2178798. Vps54.

    Subcellular locationi

    GO - Cellular componenti

    1. GARP complex Source: Ensembl

    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.1 Publication

    Keywords - Diseasei

    Disease mutation

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 977977Vacuolar protein sorting-associated protein 54PRO_0000148732Add
    BLAST

    Proteomic databases

    MaxQBiQ5SPW0.
    PaxDbiQ5SPW0.
    PRIDEiQ5SPW0.

    PTM databases

    PhosphoSiteiQ5SPW0.

    Expressioni

    Gene expression databases

    ArrayExpressiQ5SPW0.
    BgeeiQ5SPW0.
    CleanExiMM_VPS54.
    GenevestigatoriQ5SPW0.

    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

    Protein-protein interaction databases

    DIPiDIP-59351N.

    Structurei

    Secondary structure

    1
    977
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi836 – 84712
    Helixi850 – 87324
    Beta strandi880 – 8834
    Helixi885 – 90117
    Turni902 – 9043
    Helixi907 – 93125
    Beta strandi936 – 9394
    Helixi940 – 95718
    Helixi969 – 9735

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3N1BX-ray2.40A/B836-974[»]
    3N1EX-ray1.70A/B836-974[»]
    ProteinModelPortaliQ5SPW0.
    SMRiQ5SPW0. Positions 836-974.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SPW0.

    Family & Domainsi

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili239 – 26123Sequence AnalysisAdd
    BLAST

    Sequence similaritiesi

    Belongs to the VPS54 family.Curated

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiNOG285553.
    GeneTreeiENSGT00390000000583.
    HOGENOMiHOG000045110.
    HOVERGENiHBG068681.
    InParanoidiQ5SPW0.
    KOiK17600.
    OMAiTKMHEAI.
    OrthoDBiEOG71RXHV.
    PhylomeDBiQ5SPW0.
    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 (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    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

    MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTGDSHT    50
    LCVAPSLVTD QHRWTVYHSK VNLPAALNDP TLAKRESDFF TKTWGLDFVD 100
    TEVIPSLYLP QISKENFIAY QQEISQREKI HERCKNICPP KDTFDRTLLH 150
    IHDKSRTDLE QVPKIFMKPD FALDDSLTFN SVLPWSHFNT AGGKGSRDAA 200
    SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE LQDYLKKTTQ 250
    AVKMLRDKIA QIDKVMCEGS LQILRLALTR NNCVKVYNKL KLMATVHQTQ 300
    PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI 350
    DKMMIAEFST YSHSDLNRPL EGECQVLEEE RLVSLVFGLL KQRKLNFLEI 400
    YGEEMIITAK NIIKERVINK VSQIEEIDTD VVVKLADQMR MLNFPQWIDL 450
    LKDIFSKFTV FLQRVKATLN IIHSVVLSVL EKSQRTRELE EIPQQRSAGK 500
    DSSLDTDVAY LTHEGWFISD AFSEGEPASA AVDTTSQRNT SPHSEPCSSD 550
    SVSEPECTTD SSSSKEQTSA CAPPGGIEII VSEDMRLTDL ELGKLASNIQ 600
    ELLCNASDVC HDRAVKFLMS RAKDGFLEKL NSTEFIALSR LMETFIVDTE 650
    QICGRKSTSL LGALQSQANK FVNRFHEERR TKLSLLLDNE RWKQADVPAE 700
    FQDLVDSIAD GKIALPEKKP VVTEERKPAD VLVVEGHQYA VVGTVLLLIR 750
    IILEYCQCVD NIPSVTTDML TRLTDLLKYF NSRSCQLVLG AGALQVVGLK 800
    TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQWSML RHFDHITKDY 850
    HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSPCFRNI CKQMTKMHEA 900
    IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA 950
    FYTGNLQALK GLKDLDLNMA EIWEQKR 977
    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 AAH23474.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti634 – 6341E → K in BAC36741. (PubMed:16141072)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti967 – 9671L → Q in wr; destabilizes and consequently reduces protein levels, as well as those of the GARP complex. 1 Publication

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei46 – 5712Missing in isoform 2. 1 PublicationVSP_013757Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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_006514760.1. XM_006514697.1. [Q5SPW0-1]
    UniGeneiMm.170103.

    Genome annotation databases

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

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS24463.1. [Q5SPW0-1 ]
    CCDS70147.1. [Q5SPW0-2 ]
    RefSeqi NP_001277557.1. NM_001290628.1. [Q5SPW0-2 ]
    NP_620692.3. NM_139061.5. [Q5SPW0-1 ]
    XP_006514760.1. XM_006514697.1. [Q5SPW0-1 ]
    UniGenei Mm.170103.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3N1B X-ray 2.40 A/B 836-974 [» ]
    3N1E X-ray 1.70 A/B 836-974 [» ]
    ProteinModelPortali Q5SPW0.
    SMRi Q5SPW0. Positions 836-974.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-59351N.

    PTM databases

    PhosphoSitei Q5SPW0.

    Proteomic databases

    MaxQBi Q5SPW0.
    PaxDbi Q5SPW0.
    PRIDEi Q5SPW0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000006221 ; ENSMUSP00000006221 ; ENSMUSG00000020128 . [Q5SPW0-1 ]
    ENSMUST00000109578 ; ENSMUSP00000105206 ; ENSMUSG00000020128 . [Q5SPW0-2 ]
    GeneIDi 245944.
    KEGGi mmu:245944.
    UCSCi uc007ido.2. mouse. [Q5SPW0-1 ]
    uc007idp.2. mouse. [Q5SPW0-2 ]

    Organism-specific databases

    CTDi 51542.
    MGIi MGI:2178798. Vps54.

    Phylogenomic databases

    eggNOGi NOG285553.
    GeneTreei ENSGT00390000000583.
    HOGENOMi HOG000045110.
    HOVERGENi HBG068681.
    InParanoidi Q5SPW0.
    KOi K17600.
    OMAi TKMHEAI.
    OrthoDBi EOG71RXHV.
    PhylomeDBi Q5SPW0.
    TreeFami TF313700.

    Miscellaneous databases

    ChiTaRSi VPS54. mouse.
    EvolutionaryTracei Q5SPW0.
    NextBioi 387018.
    PROi Q5SPW0.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q5SPW0.
    Bgeei Q5SPW0.
    CleanExi MM_VPS54.
    Genevestigatori Q5SPW0.

    Family and domain databases

    InterProi IPR019515. Vacuolar_sorting-assoc_54.
    IPR012501. Vps54.
    [Graphical view ]
    Pfami PF10475. DUF2450. 1 hit.
    PF07928. Vps54. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. 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.
      , 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.

    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: October 1, 2014
    This is version 90 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

    External Data

    Dasty 3