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Q5SPW0

- VPS54_MOUSE

UniProt

Q5SPW0 - VPS54_MOUSE

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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

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
Complete GO annotation...

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
Complete GO annotation...

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

BgeeiQ5SPW0.
CleanExiMM_VPS54.
ExpressionAtlasiQ5SPW0. baseline and differential.
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

        10         20         30         40         50
MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTGDSHT
60 70 80 90 100
LCVAPSLVTD QHRWTVYHSK VNLPAALNDP TLAKRESDFF TKTWGLDFVD
110 120 130 140 150
TEVIPSLYLP QISKENFIAY QQEISQREKI HERCKNICPP KDTFDRTLLH
160 170 180 190 200
IHDKSRTDLE QVPKIFMKPD FALDDSLTFN SVLPWSHFNT AGGKGSRDAA
210 220 230 240 250
SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE LQDYLKKTTQ
260 270 280 290 300
AVKMLRDKIA QIDKVMCEGS LQILRLALTR NNCVKVYNKL KLMATVHQTQ
310 320 330 340 350
PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI
360 370 380 390 400
DKMMIAEFST YSHSDLNRPL EGECQVLEEE RLVSLVFGLL KQRKLNFLEI
410 420 430 440 450
YGEEMIITAK NIIKERVINK VSQIEEIDTD VVVKLADQMR MLNFPQWIDL
460 470 480 490 500
LKDIFSKFTV FLQRVKATLN IIHSVVLSVL EKSQRTRELE EIPQQRSAGK
510 520 530 540 550
DSSLDTDVAY LTHEGWFISD AFSEGEPASA AVDTTSQRNT SPHSEPCSSD
560 570 580 590 600
SVSEPECTTD SSSSKEQTSA CAPPGGIEII VSEDMRLTDL ELGKLASNIQ
610 620 630 640 650
ELLCNASDVC HDRAVKFLMS RAKDGFLEKL NSTEFIALSR LMETFIVDTE
660 670 680 690 700
QICGRKSTSL LGALQSQANK FVNRFHEERR TKLSLLLDNE RWKQADVPAE
710 720 730 740 750
FQDLVDSIAD GKIALPEKKP VVTEERKPAD VLVVEGHQYA VVGTVLLLIR
760 770 780 790 800
IILEYCQCVD NIPSVTTDML TRLTDLLKYF NSRSCQLVLG AGALQVVGLK
810 820 830 840 850
TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQWSML RHFDHITKDY
860 870 880 890 900
HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSPCFRNI CKQMTKMHEA
910 920 930 940 950
IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA
960 970
FYTGNLQALK GLKDLDLNMA EIWEQKR
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

Bgeei Q5SPW0.
CleanExi MM_VPS54.
ExpressionAtlasi Q5SPW0. baseline and differential.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 91 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