VPS18_DANRE
ID VPS18_DANRE Reviewed; 974 AA.
AC P59015; Q5SPB8;
DT 19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2007, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Vacuolar protein sorting-associated protein 18 homolog;
GN Name=vps18;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND FUNCTION.
RC TISSUE=Embryo;
RX PubMed=12006978; DOI=10.1038/ng896;
RA Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., Chen W.,
RA Burgess S., Haldi M., Artzt K., Farrington S., Lin S.-Y., Nissen R.M.,
RA Hopkins N.;
RT "Insertional mutagenesis in zebrafish rapidly identifies genes essential
RT for early vertebrate development.";
RL Nat. Genet. 31:135-140(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Ovary;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16000385; DOI=10.1242/dev.01918;
RA Sadler K.C., Amsterdam A., Soroka C., Boyer J., Hopkins N.;
RT "A genetic screen in zebrafish identifies the mutants vps18, nf2 and foie
RT gras as models of liver disease.";
RL Development 132:3561-3572(2005).
CC -!- FUNCTION: Plays a role in vesicle-mediated protein trafficking to
CC lysosomal compartments including the endocytic membrane transport
CC pathways. Believed to act as a core component of the putative HOPS
CC endosomal tethering complex which is proposed to be involved in the
CC Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via
CC binding SNAREs and SNARE complexes to mediate tethering and docking
CC events during SNARE-mediated membrane fusion (By similarity). May be
CC involved in vesicle trafficking to the hepatocyte apical membrane and
CC play a role in development of the intra-hepatic biliary tree. May
CC target endosomes to the pigment granule in melanocytes. Essential for
CC early embryonic development. {ECO:0000250|UniProtKB:Q9P253,
CC ECO:0000269|PubMed:12006978, ECO:0000269|PubMed:16000385}.
CC -!- SUBUNIT: Component of the homotypic fusion and vacuole protein sorting
CC (HOPS) complex (By similarity). {ECO:0000250|UniProtKB:Q9P253}.
CC -!- SUBCELLULAR LOCATION: Late endosome membrane
CC {ECO:0000250|UniProtKB:Q9P253}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:Q9P253}; Cytoplasmic side
CC {ECO:0000250|UniProtKB:Q9P253}. Lysosome membrane
CC {ECO:0000250|UniProtKB:Q9P253}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:Q9P253}; Cytoplasmic side
CC {ECO:0000250|UniProtKB:Q9P253}. Note=Cytoplasmic, peripheral membrane
CC protein associated with early endosomes and late endosomes/lysosomes.
CC -!- DISRUPTION PHENOTYPE: Mutants display hepatomegaly associated with
CC large, vesicle-filled hepatocytes. They also have defects in
CC pigmentation with reduced numbers of melanophores and no iridophores.
CC {ECO:0000269|PubMed:16000385}.
CC -!- SIMILARITY: Belongs to the VPS18 family. {ECO:0000305}.
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DR EMBL; AL929049; CAI20654.1; -; Genomic_DNA.
DR EMBL; BX897725; CAI11898.1; -; Genomic_DNA.
DR EMBL; AF506204; AAM34648.1; -; mRNA.
DR EMBL; BC086828; AAH86828.1; -; mRNA.
DR RefSeq; NP_775352.2; NM_173245.2.
DR AlphaFoldDB; P59015; -.
DR SMR; P59015; -.
DR STRING; 7955.ENSDARP00000094129; -.
DR PaxDb; P59015; -.
DR Ensembl; ENSDART00000103352; ENSDARP00000094129; ENSDARG00000070433.
DR GeneID; 100005887; -.
DR KEGG; dre:100005887; -.
DR CTD; 57617; -.
DR ZFIN; ZDB-GENE-020419-33; vps18.
DR eggNOG; KOG2034; Eukaryota.
DR GeneTree; ENSGT00940000153635; -.
DR HOGENOM; CLU_003488_1_0_1; -.
DR InParanoid; P59015; -.
DR OMA; HVQRESR; -.
DR OrthoDB; 87842at2759; -.
DR PhylomeDB; P59015; -.
DR TreeFam; TF105704; -.
DR PRO; PR:P59015; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000070433; Expressed in cleaving embryo and 29 other tissues.
DR ExpressionAtlas; P59015; baseline.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0030897; C:HOPS complex; IBA:GO_Central.
DR GO; GO:0031902; C:late endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005765; C:lysosomal membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030674; F:protein-macromolecule adaptor activity; IBA:GO_Central.
DR GO; GO:0045176; P:apical protein localization; IMP:ZFIN.
DR GO; GO:0015721; P:bile acid and bile salt transport; IMP:ZFIN.
DR GO; GO:0007032; P:endosome organization; IBA:GO_Central.
DR GO; GO:0008333; P:endosome to lysosome transport; IMP:ZFIN.
DR GO; GO:0043485; P:endosome to pigment granule transport; IMP:ZFIN.
DR GO; GO:0048069; P:eye pigmentation; IMP:ZFIN.
DR GO; GO:0006886; P:intracellular protein transport; IEA:InterPro.
DR GO; GO:0007040; P:lysosome organization; IBA:GO_Central.
DR GO; GO:0060036; P:notochord cell vacuolation; IMP:ZFIN.
DR GO; GO:0007634; P:optokinetic behavior; IMP:ZFIN.
DR GO; GO:0048284; P:organelle fusion; IBA:GO_Central.
DR GO; GO:0048757; P:pigment granule maturation; IMP:ZFIN.
DR GO; GO:0007033; P:vacuole organization; IBA:GO_Central.
DR GO; GO:0006904; P:vesicle docking involved in exocytosis; IBA:GO_Central.
DR InterPro; IPR000547; Clathrin_H-chain/VPS_repeat.
DR InterPro; IPR007810; Pep3_Vps18.
DR Pfam; PF00637; Clathrin; 1.
DR Pfam; PF05131; Pep3_Vps18; 1.
DR PROSITE; PS50236; CHCR; 1.
PE 2: Evidence at transcript level;
KW Coiled coil; Developmental protein; Endosome; Lysosome; Membrane;
KW Metal-binding; Protein transport; Reference proteome; Transport; Zinc;
KW Zinc-finger.
FT CHAIN 1..974
FT /note="Vacuolar protein sorting-associated protein 18
FT homolog"
FT /id="PRO_0000055904"
FT REPEAT 618..772
FT /note="CHCR"
FT ZN_FING 853..948
FT /note="RING-type"
FT REGION 905..930
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 461..481
FT /evidence="ECO:0000255"
FT COILED 799..852
FT /evidence="ECO:0000255"
FT COMPBIAS 910..924
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 258..260
FT /note="FQE -> SRN (in Ref. 2; AAM34648)"
FT /evidence="ECO:0000305"
FT CONFLICT 745
FT /note="P -> S (in Ref. 2; AAM34648)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 974 AA; 113267 MW; 05B5AE0D853BEC74 CRC64;
MASILDQYED SQNIRQHSRM STANIGITHS GFVNVRLEEE KPIFTKQRID FSPPEKINQF
SVCNNQLCMS LGKDTLLRID LGKPDQPNQI ELGRKDDSKV HRLFLDPTGS HLVICLTTNE
CVYLNRNTQK VRGLSRWRGH LIESIGWNKL IGSETNTGPI LVGTSQGIIF EAEISASEGS
LFNTNPDQYF RQVHYLEEDG KPAPVCCLEV ERGLETKYFI IATTRKRLFQ FVGKLAEGSE
QQGFSSIFAQ NQDLLPSFQE FPVNMGYSEI TFYTSKLRSR PKTFAWMMGN GVLYGQLDYV
RPDSLLSDVQ VWEYTQDIDL NFVKPISIVL TQFHFLLLLP DRVRGICTLN GQVVHEDVFP
EKFGTLQKMI KDPITGLVWI YTEKAVFRYH IQKEARDVWQ MYMNMNKFDL AKEYCKDRPE
CLDMVLAKEA EHCFQNKRYL ESAKCYALTQ NYFEEIALKF IEAKQEEALK EFLIKKLVNL
KPSEKTQITL LVTWLTELYL NRLGQLEADE GKQHLFLETR EEFRTFLKSP KHKDCFYNNR
STIYDLLASH GDVDNMVYFS VIMQDYERVI SHYCQHDDYS AALDVLSKHC DDKLFYKFSP
VLMQHIPKKV VDAWIQMGNR LDPKNLIPAL VNYSQMGSMQ QINETIRYME FCVYELDVKE
EAIHNYLLSL YAKHKPDALL WYLEQAGTHV SDIHYDLKYA LRLCSEHGYL QACVLVYKIM
ELYEEAVDLA LKVDVDLAKS CADLPEDDEE LRKKLWLKIA RHVVQEEKDV KKAMNCLSSC
NLLKIEDILP FFPDFVTIDH FKEAICSSLE EYNKHIEELK QEMEEATESA KRIREDIQEM
RNKYGVVESQ EKCATCDFPL LNRPFYLFLC GHMFHYDCLL QEVIPHLSVY KQNKLDELQK
KLAATTQTTK ARHKPREEDT VSLGKGQGSR EQIKSDIDDI IACECVYCGE LMIKSIDKPF
IDPQKFDQEM SSWL
