VPS54_MOUSE
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 03-AUG-2022, entry version 134.
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; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC 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., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT 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 project:
RT 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., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., 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., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., 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 are
RT 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., Thiel C.,
RA Hafner M., Lengeling A., Heimann P., Jones J.M., Meisler M.H., Jockusch H.;
RT "Mutation of Vps54 causes motor neuron disease and defective spermiogenesis
RT 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 OF
RP 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 caused
RT 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 in
CC retrograde transport from early and late endosomes to the trans-Golgi
CC network (TGN). The GARP complex is required for the maintenance of the
CC cycling of mannose 6-phosphate receptors between the TGN and endosomes,
CC this cycling is necessary for proper lysosomal sorting of acid
CC hydrolases such as CTSD. Within the GARP complex, required to tether
CC the complex to the TGN. Not involved in endocytic recycling.
CC {ECO:0000250|UniProtKB:Q9P1Q0}.
CC -!- SUBUNIT: Component of the Golgi-associated retrograde protein (GARP)
CC complex, also called VFT (VPS fifty-three) complex, composed of VPS51,
CC VPS52, VPS53 and VPS54 (By similarity). EIPR1 interacts with GARP
CC complex and mediates its recruitment to the trans-Golgi network (By
CC similarity). Interacts with VPS51 in an EIPR1-independent manner (By
CC similarity). {ECO:0000250|UniProtKB:Q9P1Q0}.
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network
CC {ECO:0000250|UniProtKB:Q9P1Q0}. Membrane
CC {ECO:0000250|UniProtKB:Q9JMK8}. Note=Associates with membranes in an
CC EIPR1-independent manner. {ECO:0000250|UniProtKB:Q9JMK8}.
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 (wr).
CC Wr is autosomal recessive and is a spontaneous mutation discovered
CC almost 50 years ago. It causes spinal muscular atrophy and defective
CC 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=Truncated N-terminus.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL669979; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL833772; -; NOT_ANNOTATED_CDS; 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 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 AlphaFoldDB; Q5SPW0; -.
DR SMR; Q5SPW0; -.
DR BioGRID; 232854; 7.
DR DIP; DIP-59351N; -.
DR IntAct; Q5SPW0; 1.
DR STRING; 10090.ENSMUSP00000006221; -.
DR iPTMnet; Q5SPW0; -.
DR PhosphoSitePlus; Q5SPW0; -.
DR EPD; Q5SPW0; -.
DR MaxQB; Q5SPW0; -.
DR PaxDb; Q5SPW0; -.
DR PRIDE; Q5SPW0; -.
DR ProteomicsDB; 275187; -. [Q5SPW0-1]
DR ProteomicsDB; 275188; -. [Q5SPW0-2]
DR Antibodypedia; 30808; 154 antibodies from 26 providers.
DR DNASU; 245944; -.
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 VEuPathDB; HostDB:ENSMUSG00000020128; -.
DR eggNOG; KOG2115; Eukaryota.
DR GeneTree; ENSGT00390000000583; -.
DR InParanoid; Q5SPW0; -.
DR OMA; SQKQAVM; -.
DR PhylomeDB; Q5SPW0; -.
DR TreeFam; TF313700; -.
DR Reactome; R-MMU-6811440; Retrograde transport at the Trans-Golgi-Network.
DR BioGRID-ORCS; 245944; 13 hits in 74 CRISPR screens.
DR ChiTaRS; Vps54; mouse.
DR EvolutionaryTrace; Q5SPW0; -.
DR PRO; PR:Q5SPW0; -.
DR Proteomes; UP000000589; Chromosome 11.
DR RNAct; Q5SPW0; protein.
DR Bgee; ENSMUSG00000020128; Expressed in parotid gland and 259 other tissues.
DR ExpressionAtlas; Q5SPW0; baseline and differential.
DR Genevisible; Q5SPW0; MM.
DR GO; GO:0005829; C:cytosol; IEA:GOC.
DR GO; GO:0000938; C:GARP complex; ISS:UniProtKB.
DR GO; GO:0005794; C:Golgi apparatus; ISO:MGI.
DR GO; GO:0016020; C:membrane; ISS:UniProtKB.
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:0048873; P:homeostasis of number of cells within a tissue; IMP:MGI.
DR GO; GO:0001701; P:in utero embryonic development; IMP:MGI.
DR GO; GO:0007041; P:lysosomal transport; ISO:MGI.
DR GO; GO:0050881; P:musculoskeletal movement; IMP:MGI.
DR GO; GO:2000672; P:negative regulation of motor neuron apoptotic process; 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:0040008; P:regulation of growth; IMP:MGI.
DR GO; GO:0042147; P:retrograde transport, endosome to Golgi; ISO:MGI.
DR GO; GO:0048515; P:spermatid differentiation; IMP:MGI.
DR InterPro; IPR039745; Vps54.
DR InterPro; IPR012501; Vps54_C.
DR InterPro; IPR019515; VPS54_N.
DR PANTHER; PTHR12965; PTHR12965; 1.
DR Pfam; PF07928; Vps54; 1.
DR Pfam; PF10475; Vps54_N; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Coiled coil; Disease variant;
KW Golgi apparatus; Membrane; Phosphoprotein; Protein transport;
KW Reference proteome; Transport.
FT CHAIN 1..977
FT /note="Vacuolar protein sorting-associated protein 54"
FT /id="PRO_0000148732"
FT REGION 528..573
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 239..261
FT /evidence="ECO:0000255"
FT COMPBIAS 529..570
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 8
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9P1Q0"
FT VAR_SEQ 46..57
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_013757"
FT VARIANT 967
FT /note="L -> Q (in wr; destabilizes and consequently reduces
FT protein levels, as well as those of the GARP complex)"
FT /evidence="ECO:0000269|PubMed:16244655,
FT ECO:0000269|PubMed:20615984"
FT CONFLICT 634
FT /note="E -> K (in Ref. 3; BAC36741)"
FT /evidence="ECO:0000305"
FT HELIX 836..847
FT /evidence="ECO:0007829|PDB:3N1E"
FT HELIX 850..873
FT /evidence="ECO:0007829|PDB:3N1E"
FT STRAND 880..883
FT /evidence="ECO:0007829|PDB:3N1E"
FT HELIX 885..901
FT /evidence="ECO:0007829|PDB:3N1E"
FT TURN 902..904
FT /evidence="ECO:0007829|PDB:3N1E"
FT HELIX 907..931
FT /evidence="ECO:0007829|PDB:3N1E"
FT STRAND 936..939
FT /evidence="ECO:0007829|PDB:3N1E"
FT HELIX 940..957
FT /evidence="ECO:0007829|PDB:3N1E"
FT HELIX 969..973
FT /evidence="ECO:0007829|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
