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Protein

Vacuolar protein sorting-associated protein 53 homolog

Gene

Vps53

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). 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. Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane.By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

ReactomeiR-MMU-6811440. Retrograde transport at the Trans-Golgi-Network.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 53 homolog
Gene namesi
Name:Vps53
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1915549. Vps53.

Subcellular locationi

  • Golgi apparatustrans-Golgi network membrane By similarity; Peripheral membrane protein By similarity
  • Endosome membrane By similarity; Peripheral membrane protein By similarity
  • Recycling endosome By similarity

  • Note: Localizes to the trans-Golgi network as part of the GARP complex, while it localizes to recycling endosomes as part of the EARP complex.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 832832Vacuolar protein sorting-associated protein 53 homologPRO_0000215190Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei110 – 1101N6-acetyllysineBy similarity
Modified residuei360 – 3601N6-acetyllysineBy similarity
Modified residuei377 – 3771PhosphoserineCombined sources
Modified residuei391 – 3911PhosphothreonineCombined sources
Modified residuei580 – 5801PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ8CCB4.
MaxQBiQ8CCB4.
PaxDbiQ8CCB4.
PeptideAtlasiQ8CCB4.
PRIDEiQ8CCB4.

PTM databases

iPTMnetiQ8CCB4.
PhosphoSiteiQ8CCB4.

Expressioni

Gene expression databases

BgeeiQ8CCB4.
CleanExiMM_VPS53.
ExpressionAtlasiQ8CCB4. baseline and differential.
GenevisibleiQ8CCB4. MM.

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. Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin.By similarity

Protein-protein interaction databases

BioGridi212792. 1 interaction.
MINTiMINT-4997697.
STRINGi10090.ENSMUSP00000061317.

Structurei

3D structure databases

ProteinModelPortaliQ8CCB4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili55 – 14288Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the VPS53 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2180. Eukaryota.
ENOG410XNMT. LUCA.
GeneTreeiENSGT00390000015165.
HOGENOMiHOG000265899.
HOVERGENiHBG092351.
InParanoidiQ8CCB4.
OMAiCMTERIS.
OrthoDBiEOG70PBWZ.
PhylomeDBiQ8CCB4.
TreeFamiTF106150.

Family and domain databases

InterProiIPR007234. Vps53_N.
[Graphical view]
PfamiPF04100. Vps53_N. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8CCB4-1) [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
MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDQA DFNAVEYINT
60 70 80 90 100
LFPTEQSLAN IDDVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA
110 120 130 140 150
QKAIQQLFGK IKDIKDKAEK SEQMVKEITR DIKQLDHAKR HLTTSITTLN
160 170 180 190 200
HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG VMNVLEHFHK YMGIPQIRQL
210 220 230 240 250
SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD ACLVANILDP
260 270 280 290 300
RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW VKRQLVDYEE
310 320 330 340 350
KYGRMFPREW CMTERISVEF CHVTRAELSK IMRARAKEIE VKLLLFAIQR
360 370 380 390 400
TTNFEGFLAK RFSGCTLTDG TLKKLESPPP STNPFLEDET TPEMEELALE
410 420 430 440 450
KGELEQPKKP KAPDNPFHGI VSKCFEPHLY VYIESQDKNL SELIDRFVAD
460 470 480 490 500
FKAQGPPKPN TDEGGAVLPS CADLFVYYKK CMVQCSQLST GEPMIALTTI
510 520 530 540 550
FQKYLREYAW KILSGNLPKT SSSSGGLTIS SLLKEKEGSE VARFTLEELC
560 570 580 590 600
LICSILSTAE YCLATTQQLE EKLKEKVDVS LTERINLTGE MDTFSTVISS
610 620 630 640 650
SIQLLVQDLD AACDPALIAM SKMPWQNVEH VGDQSPYVTS VILHIKQNVP
660 670 680 690 700
IIRDNLASTR KYFTQFCIKF ANSFIPKFIT HLFKCKPISM VGAEQLLLDT
710 720 730 740 750
HSLKMVLLDL PSIGSQVVRK APASYTKIVV KGMTRAEMIL KVVMAPHEPL
760 770 780 790 800
VVFVDNYIKL LTDCNSETFQ KILDMKGLKR SEQSSMLELL RQRLPAPPSG
810 820 830
TEGSSTLSLI APTPEQESSR IRKLEKLIKK RL
Length:832
Mass (Da):94,423
Last modified:March 1, 2003 - v1
Checksum:i7B9C9FFA702EE88E
GO
Isoform 2 (identifier: Q8CCB4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     230-406: Missing.

Note: No experimental confirmation available.
Show »
Length:655
Mass (Da):73,703
Checksum:i46D07A8D48BF59E0
GO

Sequence cautioni

The sequence BAB26620.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti85 – 851G → V in BAB31707 (PubMed:16141072).Curated
Sequence conflicti524 – 5241S → G in BAB26620 (PubMed:16141072).Curated
Sequence conflicti614 – 6141D → E in BAB26620 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei230 – 406177Missing in isoform 2. 1 PublicationVSP_016239Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009970 mRNA. Translation: BAB26620.1. Different initiation.
AK019408 mRNA. Translation: BAB31707.1.
AK033495 mRNA. Translation: BAC28318.1.
AK049259 mRNA. Translation: BAC33641.1.
AL591129 Genomic DNA. Translation: CAI35098.1.
BC034371 mRNA. Translation: AAH34371.1.
CCDSiCCDS25060.1. [Q8CCB4-1]
RefSeqiNP_080940.2. NM_026664.3. [Q8CCB4-1]
UniGeneiMm.46397.

Genome annotation databases

EnsembliENSMUST00000056601; ENSMUSP00000061317; ENSMUSG00000017288. [Q8CCB4-1]
ENSMUST00000108419; ENSMUSP00000104057; ENSMUSG00000017288. [Q8CCB4-2]
GeneIDi68299.
KEGGimmu:68299.
UCSCiuc007kfa.1. mouse. [Q8CCB4-1]
uc011xzq.1. mouse. [Q8CCB4-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009970 mRNA. Translation: BAB26620.1. Different initiation.
AK019408 mRNA. Translation: BAB31707.1.
AK033495 mRNA. Translation: BAC28318.1.
AK049259 mRNA. Translation: BAC33641.1.
AL591129 Genomic DNA. Translation: CAI35098.1.
BC034371 mRNA. Translation: AAH34371.1.
CCDSiCCDS25060.1. [Q8CCB4-1]
RefSeqiNP_080940.2. NM_026664.3. [Q8CCB4-1]
UniGeneiMm.46397.

3D structure databases

ProteinModelPortaliQ8CCB4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212792. 1 interaction.
MINTiMINT-4997697.
STRINGi10090.ENSMUSP00000061317.

PTM databases

iPTMnetiQ8CCB4.
PhosphoSiteiQ8CCB4.

Proteomic databases

EPDiQ8CCB4.
MaxQBiQ8CCB4.
PaxDbiQ8CCB4.
PeptideAtlasiQ8CCB4.
PRIDEiQ8CCB4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000056601; ENSMUSP00000061317; ENSMUSG00000017288. [Q8CCB4-1]
ENSMUST00000108419; ENSMUSP00000104057; ENSMUSG00000017288. [Q8CCB4-2]
GeneIDi68299.
KEGGimmu:68299.
UCSCiuc007kfa.1. mouse. [Q8CCB4-1]
uc011xzq.1. mouse. [Q8CCB4-2]

Organism-specific databases

CTDi55275.
MGIiMGI:1915549. Vps53.

Phylogenomic databases

eggNOGiKOG2180. Eukaryota.
ENOG410XNMT. LUCA.
GeneTreeiENSGT00390000015165.
HOGENOMiHOG000265899.
HOVERGENiHBG092351.
InParanoidiQ8CCB4.
OMAiCMTERIS.
OrthoDBiEOG70PBWZ.
PhylomeDBiQ8CCB4.
TreeFamiTF106150.

Enzyme and pathway databases

ReactomeiR-MMU-6811440. Retrograde transport at the Trans-Golgi-Network.

Miscellaneous databases

ChiTaRSiVps53. mouse.
PROiQ8CCB4.
SOURCEiSearch...

Gene expression databases

BgeeiQ8CCB4.
CleanExiMM_VPS53.
ExpressionAtlasiQ8CCB4. baseline and differential.
GenevisibleiQ8CCB4. MM.

Family and domain databases

InterProiIPR007234. Vps53_N.
[Graphical view]
PfamiPF04100. Vps53_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "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] (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Colon and Head.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "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: Mammary gland.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-377 AND THR-391, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiVPS53_MOUSE
AccessioniPrimary (citable) accession number: Q8CCB4
Secondary accession number(s): Q8C7U0
, Q8CIA1, Q9CX82, Q9D6T7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: March 1, 2003
Last modified: July 6, 2016
This is version 103 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

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.