ID   VPS54_MOUSE             Reviewed;         977 AA.
AC   Q5SPW0; Q8BPB3; Q8CFZ7; Q8CHL5; Q8R3R4; Q8R3X1;
DT   10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
DT   21-DEC-2004, sequence version 1.
DT   22-JUL-2015, entry version 99.
DE   RecName: Full=Vacuolar protein sorting-associated protein 54;
DE   AltName: Full=Tumor antigen SLP-8p homolog;
GN   Name=Vps54;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi;
OC   Muroidea; Muridae; Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C57BL/6J;
RX   PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA   Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
RA   She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
RA   Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
RA   Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
RA   Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
RA   Lindblad-Toh K., Eichler E.E., Ponting C.P.;
RT   "Lineage-specific biology revealed by a finished genome assembly of
RT   the mouse.";
RL   PLoS Biol. 7:E1000112-E1000112(2009).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=FVB/N; TISSUE=Kidney, and Mammary tumor;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 87-977.
RC   STRAIN=C57BL/6J; TISSUE=Pituitary;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
RA   Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
RA   Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
RA   Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
RA   Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
RA   Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
RA   di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
RA   Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
RA   Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
RA   Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
RA   Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
RA   Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
RA   Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
RA   Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
RA   Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
RA   Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
RA   Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
RA   Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
RA   Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
RA   Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
RA   Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
RA   Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
RA   Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
RA   Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
RA   Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
RA   Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
RA   Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
RA   Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
RA   Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
RA   Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
RA   Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
RA   Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 744-977.
RA   Daigo Y., Takayama I., Fujino M.A.;
RT   "Isolation and characterization of novel human and mouse genes, which
RT   are expressed in the digestive tract.";
RL   Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   DISEASE, AND VARIANT WR GLN-967.
RX   PubMed=16244655; DOI=10.1038/ng1661;
RA   Schmitt-John T., Drepper C., Mussmann A., Hahn P., Kuhlmann M.,
RA   Thiel C., Hafner M., Lengeling A., Heimann P., Jones J.M.,
RA   Meisler M.H., Jockusch H.;
RT   "Mutation of Vps54 causes motor neuron disease and defective
RT   spermiogenesis in the wobbler mouse.";
RL   Nat. Genet. 37:1213-1215(2005).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 836-974, AND CHARACTERIZATION
RP   OF VARIANT WR GLN-967.
RX   PubMed=20615984; DOI=10.1073/pnas.1004756107;
RA   Perez-Victoria F.J., Abascal-Palacios G., Tascon I., Kajava A.,
RA   Magadan J.G., Pioro E.P., Bonifacino J.S., Hierro A.;
RT   "Structural basis for the wobbler mouse neurodegenerative disorder
RT   caused by mutation in the Vps54 subunit of the GARP complex.";
RL   Proc. Natl. Acad. Sci. U.S.A. 107:12860-12865(2010).
CC   -!- FUNCTION: Acts as component of the GARP complex that is involved
CC       in retrograde transport from early and late endosomes to the
CC       trans-Golgi network (TGN). The GARP complex is required for the
CC       maintenance of the cycling of mannose 6-phosphate receptors
CC       between the TGN and endosomes, this cycling is necessary for
CC       proper lysosomal sorting of acid hydrolases such as CTSD. Within
CC       the GARP complex, required to tether the complex to the TGN. Not
CC       involved in endocytic recycling. {ECO:0000250|UniProtKB:Q9P1Q0}.
CC   -!- SUBUNIT: Component of the Golgi-associated retrograde protein
CC       (GARP) complex, also called VFT (VPS fifty-three) complex,
CC       composed of VPS51, VPS52, VPS53 and VPS54.
CC       {ECO:0000250|UniProtKB:Q9P1Q0}.
CC   -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network
CC       {ECO:0000250|UniProtKB:Q9P1Q0}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q5SPW0-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q5SPW0-2; Sequence=VSP_013757;
CC   -!- DISEASE: Note=Defects in Vps54 are the cause of wobbler phenotype
CC       (wr). Wr is autosomal recessive and is a spontaneous mutation
CC       discovered almost 50 years ago. It causes spinal muscular atrophy
CC       and defective spermiogenesis. {ECO:0000269|PubMed:16244655,
CC       ECO:0000269|PubMed:20615984}.
CC   -!- SIMILARITY: Belongs to the VPS54 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAH23474.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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DR   EMBL; AL833772; CAI24173.1; -; Genomic_DNA.
DR   EMBL; AL669979; CAI24173.1; JOINED; Genomic_DNA.
DR   EMBL; AL833772; CAI24174.1; -; Genomic_DNA.
DR   EMBL; AL669979; CAI24174.1; JOINED; Genomic_DNA.
DR   EMBL; AL669979; CAI26092.1; -; Genomic_DNA.
DR   EMBL; AL833772; CAI26092.1; JOINED; Genomic_DNA.
DR   EMBL; AL669979; CAI26093.1; -; Genomic_DNA.
DR   EMBL; AL833772; CAI26093.1; JOINED; Genomic_DNA.
DR   EMBL; BC023474; AAH23474.1; ALT_INIT; mRNA.
DR   EMBL; BC024789; AAH24789.1; -; mRNA.
DR   EMBL; BC025012; AAH25012.1; -; mRNA.
DR   EMBL; AK077306; BAC36741.1; -; mRNA.
DR   EMBL; AB052761; BAC53794.1; -; mRNA.
DR   CCDS; CCDS24463.1; -. [Q5SPW0-1]
DR   CCDS; CCDS70147.1; -. [Q5SPW0-2]
DR   RefSeq; NP_001277557.1; NM_001290628.1. [Q5SPW0-2]
DR   RefSeq; NP_620692.3; NM_139061.5. [Q5SPW0-1]
DR   RefSeq; XP_011242022.1; XM_011243720.1. [Q5SPW0-1]
DR   UniGene; Mm.170103; -.
DR   PDB; 3N1B; X-ray; 2.40 A; A/B=836-974.
DR   PDB; 3N1E; X-ray; 1.70 A; A/B=836-974.
DR   PDBsum; 3N1B; -.
DR   PDBsum; 3N1E; -.
DR   ProteinModelPortal; Q5SPW0; -.
DR   SMR; Q5SPW0; 836-974.
DR   DIP; DIP-59351N; -.
DR   STRING; 10090.ENSMUSP00000006221; -.
DR   PhosphoSite; Q5SPW0; -.
DR   MaxQB; Q5SPW0; -.
DR   PaxDb; Q5SPW0; -.
DR   PRIDE; Q5SPW0; -.
DR   Ensembl; ENSMUST00000006221; ENSMUSP00000006221; ENSMUSG00000020128. [Q5SPW0-1]
DR   Ensembl; ENSMUST00000109578; ENSMUSP00000105206; ENSMUSG00000020128. [Q5SPW0-2]
DR   GeneID; 245944; -.
DR   KEGG; mmu:245944; -.
DR   UCSC; uc007ido.3; mouse. [Q5SPW0-1]
DR   UCSC; uc007idp.3; mouse. [Q5SPW0-2]
DR   CTD; 51542; -.
DR   MGI; MGI:2178798; Vps54.
DR   eggNOG; NOG285553; -.
DR   GeneTree; ENSGT00390000000583; -.
DR   HOGENOM; HOG000045110; -.
DR   HOVERGEN; HBG068681; -.
DR   InParanoid; Q5SPW0; -.
DR   KO; K17600; -.
DR   OMA; TKMHEAI; -.
DR   OrthoDB; EOG71RXHV; -.
DR   PhylomeDB; Q5SPW0; -.
DR   TreeFam; TF313700; -.
DR   ChiTaRS; Vps54; mouse.
DR   EvolutionaryTrace; Q5SPW0; -.
DR   NextBio; 387018; -.
DR   PRO; PR:Q5SPW0; -.
DR   Proteomes; UP000000589; Chromosome 11.
DR   Bgee; Q5SPW0; -.
DR   CleanEx; MM_VPS54; -.
DR   ExpressionAtlas; Q5SPW0; baseline and differential.
DR   Genevisible; Q5SPW0; MM.
DR   GO; GO:0000938; C:GARP complex; ISS:UniProtKB.
DR   GO; GO:0005794; C:Golgi apparatus; ISO:MGI.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:MGI.
DR   GO; GO:0005802; C:trans-Golgi network; ISS:UniProtKB.
DR   GO; GO:0019905; F:syntaxin binding; IBA:GO_Central.
DR   GO; GO:0006896; P:Golgi to vacuole transport; IBA:GO_Central.
DR   GO; GO:0040007; P:growth; IMP:MGI.
DR   GO; GO:0048873; P:homeostasis of number of cells within a tissue; IMP:MGI.
DR   GO; GO:0050881; P:musculoskeletal movement; IMP:MGI.
DR   GO; GO:0060052; P:neurofilament cytoskeleton organization; IMP:MGI.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR   GO; GO:0042147; P:retrograde transport, endosome to Golgi; IBA:GO_Central.
DR   InterPro; IPR019515; Vacuolar_sorting-assoc_54.
DR   InterPro; IPR012501; Vps54.
DR   Pfam; PF10475; DUF2450; 1.
DR   Pfam; PF07928; Vps54; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative splicing; Coiled coil; Complete proteome;
KW   Disease mutation; Golgi apparatus; Protein transport;
KW   Reference proteome; Transport.
FT   CHAIN         1    977       Vacuolar protein sorting-associated
FT                                protein 54.
FT                                /FTId=PRO_0000148732.
FT   COILED      239    261       {ECO:0000255}.
FT   VAR_SEQ      46     57       Missing (in isoform 2).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_013757.
FT   VARIANT     967    967       L -> Q (in wr; destabilizes and
FT                                consequently reduces protein levels, as
FT                                well as those of the GARP complex).
FT                                {ECO:0000269|PubMed:16244655,
FT                                ECO:0000269|PubMed:20615984}.
FT   CONFLICT    634    634       E -> K (in Ref. 3; BAC36741).
FT                                {ECO:0000305}.
FT   HELIX       836    847       {ECO:0000244|PDB:3N1E}.
FT   HELIX       850    873       {ECO:0000244|PDB:3N1E}.
FT   STRAND      880    883       {ECO:0000244|PDB:3N1E}.
FT   HELIX       885    901       {ECO:0000244|PDB:3N1E}.
FT   TURN        902    904       {ECO:0000244|PDB:3N1E}.
FT   HELIX       907    931       {ECO:0000244|PDB:3N1E}.
FT   STRAND      936    939       {ECO:0000244|PDB:3N1E}.
FT   HELIX       940    957       {ECO:0000244|PDB:3N1E}.
FT   HELIX       969    973       {ECO:0000244|PDB:3N1E}.
SQ   SEQUENCE   977 AA;  110397 MW;  BA93F931E92E9E0D CRC64;
     MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTGDSHT LCVAPSLVTD
     QHRWTVYHSK VNLPAALNDP TLAKRESDFF TKTWGLDFVD TEVIPSLYLP QISKENFIAY
     QQEISQREKI HERCKNICPP KDTFDRTLLH IHDKSRTDLE QVPKIFMKPD FALDDSLTFN
     SVLPWSHFNT AGGKGSRDAA SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE
     LQDYLKKTTQ AVKMLRDKIA QIDKVMCEGS LQILRLALTR NNCVKVYNKL KLMATVHQTQ
     PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI DKMMIAEFST
     YSHSDLNRPL EGECQVLEEE RLVSLVFGLL KQRKLNFLEI YGEEMIITAK NIIKERVINK
     VSQIEEIDTD VVVKLADQMR MLNFPQWIDL LKDIFSKFTV FLQRVKATLN IIHSVVLSVL
     EKSQRTRELE EIPQQRSAGK DSSLDTDVAY LTHEGWFISD AFSEGEPASA AVDTTSQRNT
     SPHSEPCSSD SVSEPECTTD SSSSKEQTSA CAPPGGIEII VSEDMRLTDL ELGKLASNIQ
     ELLCNASDVC HDRAVKFLMS RAKDGFLEKL NSTEFIALSR LMETFIVDTE QICGRKSTSL
     LGALQSQANK FVNRFHEERR TKLSLLLDNE RWKQADVPAE FQDLVDSIAD GKIALPEKKP
     VVTEERKPAD VLVVEGHQYA VVGTVLLLIR IILEYCQCVD NIPSVTTDML TRLTDLLKYF
     NSRSCQLVLG AGALQVVGLK TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQWSML
     RHFDHITKDY HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSPCFRNI CKQMTKMHEA
     IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA FYTGNLQALK
     GLKDLDLNMA EIWEQKR
//