Q5SPW0 (VPS54_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Vacuolar protein sorting-associated protein 54

Alternative name(s):
Tumor antigen SLP-8p homolog

Gene names

Name:

Vps54

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	977 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
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.

Ontologies

Keywords
Biological process	Protein transport Transport
Coding sequence diversity	Alternative splicing
Disease	Disease mutation
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	growth Inferred from mutant phenotype PubMed 8815872. Source: MGI homeostasis of number of cells within a tissue Inferred from mutant phenotype PubMed 8815872. Source: MGI musculoskeletal movement Inferred from mutant phenotype PubMed 8815872. Source: MGI neurofilament cytoskeleton organization Inferred from mutant phenotype PubMed 11493023. Source: MGI protein transport Inferred from electronic annotation. Source: UniProtKB-KW retrograde transport, endosome to Golgi Inferred from electronic annotation. Source: InterPro
Cellular_component	GARP complex Inferred from electronic annotation. Source: Compara
Complete GO annotation...

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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 977

977

Vacuolar protein sorting-associated protein 54

PRO_0000148732

Regions

Coiled coil

239 – 261

23

Potential

Amino acid modifications

Modified residue

541

1

Phosphoserine Ref.6

Natural variations

Alternative sequence

46 – 57

12

Missing in isoform 2.

VSP_013757

Natural variant

967

1

L → Q in wr; destabilizes and consequently reduces protein levels, as well as those of the GARP complex. Ref.5 Ref.7

Experimental info

Sequence conflict

634

1

E → K in BAC36741. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

977

Helix Strand Turn

Details...

Helix

836 – 847

12

Helix

850 – 873

24

Beta strand

880 – 883

4

Helix

885 – 901

17

Turn

902 – 904

3

Helix

907 – 931

25

Beta strand

936 – 939

4

Helix

940 – 957

18

Helix

969 – 973

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: BA93F931E92E9E0D	FASTA	977	110,397
	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
	Isoform 2 [UniParc]. Checksum: 5C704137B4C4F075	FASTA	965	109,215
	10 20 30 40 50 60 MASSHSSSPV PQGSSSDVFF KKEVDPTKHI RPVQSLPDVC PKEPTVTDQH RWTVYHSKVN 70 80 90 100 110 120 LPAALNDPTL AKRESDFFTK TWGLDFVDTE VIPSLYLPQI SKENFIAYQQ EISQREKIHE 130 140 150 160 170 180 RCKNICPPKD TFDRTLLHIH DKSRTDLEQV PKIFMKPDFA LDDSLTFNSV LPWSHFNTAG 190 200 210 220 230 240 GKGSRDAASS KLLQEKLSHY LDIVEVNIAH QISLRSEAFF HAMTSQHELQ DYLKKTTQAV 250 260 270 280 290 300 KMLRDKIAQI DKVMCEGSLQ ILRLALTRNN CVKVYNKLKL MATVHQTQPT VQVLLSTSEF 310 320 330 340 350 360 VGALDLIATT QEVLQQELQG IHSFRHLGSQ LCELEKLIDK MMIAEFSTYS HSDLNRPLEG 370 380 390 400 410 420 ECQVLEEERL VSLVFGLLKQ RKLNFLEIYG EEMIITAKNI IKERVINKVS QIEEIDTDVV 430 440 450 460 470 480 VKLADQMRML NFPQWIDLLK DIFSKFTVFL QRVKATLNII HSVVLSVLEK SQRTRELEEI 490 500 510 520 530 540 PQQRSAGKDS SLDTDVAYLT HEGWFISDAF SEGEPASAAV DTTSQRNTSP HSEPCSSDSV 550 560 570 580 590 600 SEPECTTDSS SSKEQTSACA PPGGIEIIVS EDMRLTDLEL GKLASNIQEL LCNASDVCHD 610 620 630 640 650 660 RAVKFLMSRA KDGFLEKLNS TEFIALSRLM ETFIVDTEQI CGRKSTSLLG ALQSQANKFV 670 680 690 700 710 720 NRFHEERRTK LSLLLDNERW KQADVPAEFQ DLVDSIADGK IALPEKKPVV TEERKPADVL 730 740 750 760 770 780 VVEGHQYAVV GTVLLLIRII LEYCQCVDNI PSVTTDMLTR LTDLLKYFNS RSCQLVLGAG 790 800 810 820 830 840 ALQVVGLKTI TTKNLALSSR CLQLIVHYIP VIRAHFEARL PPKQWSMLRH FDHITKDYHD 850 860 870 880 890 900 HIAEISAKLV AIMDSLFDKL LSKYEVKAPV PSPCFRNICK QMTKMHEAIF DLLPEEQTQM 910 920 930 940 950 960 LFLRINASYK LHLKKQLSHL NVINDGGPQN GLVTADVAFY TGNLQALKGL KDLDLNMAEI WEQKR

References

	« Hide 'large scale' referencesShow '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. , 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. , 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]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-541, MASS SPECTROMETRY. Tissue: Liver.
[7]	"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.

IPI

IPI00556732.
IPI00556779.

RefSeq

NP_620692.3. NM_139061.4.

UniGene

Mm.170103.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q5SPW0.

SMR

Q5SPW0. Positions 836-974.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-59351N.

PTM databases

PhosphoSite

Q5SPW0.

Proteomic databases

PaxDb

Q5SPW0.

PRIDE

Q5SPW0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000006221; ENSMUSP00000006221; ENSMUSG00000020128.
ENSMUST00000109578; ENSMUSP00000105206; ENSMUSG00000020128.

GeneID

245944.

KEGG

mmu:245944.

UCSC

uc007ido.2. mouse.
uc007idp.2. mouse.

Organism-specific databases

CTD

51542.

MGI

MGI:2178798. Vps54.

Phylogenomic databases

eggNOG

NOG285553.

GeneTree

ENSGT00390000000583.

HOGENOM

HOG000045110.

HOVERGEN

HBG068681.

InParanoid

Q5SPW0.

OMA

HSFRHLG.

OrthoDB

EOG4W3SMB.

Gene expression databases

ArrayExpress

Q5SPW0.

Bgee

Q5SPW0.

CleanEx

MM_VPS54.

Genevestigator

Q5SPW0.

GermOnline

ENSMUSG00000020128. Mus musculus.

Family and domain databases

InterPro

IPR019515. Vacuolar_sorting-assoc_54.
IPR012501. Vps54.
[Graphical view]

Pfam

PF10475. DUF2450. 1 hit.
PF07928. Vps54. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

VPS54. mouse.

EvolutionaryTrace

Q5SPW0.

NextBio

387018.

SOURCE

Search...

Entry information

Entry name

VPS54_MOUSE

Accession

Primary (citable) accession number: Q5SPW0
Secondary accession number(s): Q8BPB3 , Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	December 21, 2004
Last modified:	April 3, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program