VPS41_DANRE
ID VPS41_DANRE Reviewed; 854 AA.
AC E7F590;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=Vacuolar protein sorting-associated protein 41 homolog;
GN Name=vps41 {ECO:0000312|ZFIN:ZDB-GENE-030131-6671};
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 FUNCTION, SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=33764426; DOI=10.1093/brain/awaa459;
RA Sanderson L.E., Lanko K., Alsagob M., Almass R., Al-Ahmadi N., Najafi M.,
RA Al-Muhaizea M.A., Alzaidan H., AlDhalaan H., Perenthaler E.,
RA van der Linde H.C., Nikoncuk A., Kuehn N.A., Antony D., Owaidah T.M.,
RA Raskin S., Vieira L.G.D.R., Mombach R., Ahangari N., Silveira T.R.D.,
RA Ameziane N., Rolfs A., Alharbi A., Sabbagh R.M., AlAhmadi K., Alawam B.,
RA Ghebeh H., AlHargan A., Albader A.A., Binhumaid F.S., Goljan E., Monies D.,
RA Mustafa O.M., Aldosary M., AlBakheet A., Alyounes B., Almutairi F.,
RA Al-Odaib A., Aksoy D.B., Basak A.N., Palvadeau R., Trabzuni D.,
RA Rosenfeld J.A., Karimiani E.G., Meyer B.F., Karakas B., Al-Mohanna F.,
RA Arold S.T., Colak D., Maroofian R., Houlden H., Bertoli-Avella A.M.,
RA Schmidts M., Barakat T.S., van Ham T.J., Kaya N.;
RT "Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia
RT and abnormal membrane trafficking.";
RL Brain 144:769-780(2021).
CC -!- FUNCTION: Plays a role in vesicle-mediated protein trafficking to
CC lysosomal compartments including the endocytic membrane transport and
CC autophagic pathways. Believed to act as a core component of the
CC putative HOPS and CORVET endosomal tethering complexes.
CC {ECO:0000269|PubMed:33764426}.
CC -!- SUBUNIT: Core component of at least two putative endosomal tethering
CC complexes, the homotypic fusion and vacuole protein sorting (HOPS)
CC complex and the class C core vacuole/endosome tethering (CORVET)
CC complex. {ECO:0000269|PubMed:33764426}.
CC -!- SUBCELLULAR LOCATION: Endosome membrane {ECO:0000250|UniProtKB:P49754};
CC Peripheral membrane protein {ECO:0000250|UniProtKB:P49754}. Late
CC endosome membrane {ECO:0000250|UniProtKB:P49754}; Peripheral membrane
CC protein {ECO:0000250|UniProtKB:P49754}. Early endosome membrane
CC {ECO:0000250|UniProtKB:P49754}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:P49754}. Lysosome membrane
CC {ECO:0000250|UniProtKB:P49754}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:P49754}. Golgi apparatus, trans-Golgi network
CC {ECO:0000250|UniProtKB:P49754}. Cytoplasmic vesicle, clathrin-coated
CC vesicle {ECO:0000250|UniProtKB:P49754}. Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:P49754}.
CC -!- DISRUPTION PHENOTYPE: Disruption of the gene results in melanocyte
CC pigmentation defects, decreased body length, and bladder defects
CC associated with abnormalities in surfactant production or distribution,
CC consistent with abnormalities of lysosome-related organelles. Mutant
CC animals also have defects in the optokinetic response and eye movement
CC control system, suggesting cerebellar dysfunction. Microglia from
CC mutant fish show morphologic abnormalities, with larger or more
CC numerous lysosomal compartments and increased expression of acidic
CC lysosomal markers compared to controls. {ECO:0000269|PubMed:33764426}.
CC -!- SIMILARITY: Belongs to the VPS41 family. {ECO:0000305}.
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DR EMBL; BX571690; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BX571823; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_691671.2; XM_686579.6.
DR PeptideAtlas; E7F590; -.
DR Ensembl; ENSDART00000092975; ENSDARP00000087407; ENSDARG00000063573.
DR GeneID; 563215; -.
DR KEGG; dre:563215; -.
DR CTD; 27072; -.
DR ZFIN; ZDB-GENE-030131-6671; vps41.
DR GeneTree; ENSGT00390000000481; -.
DR OrthoDB; 722805at2759; -.
DR PhylomeDB; E7F590; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 24.
DR Bgee; ENSDARG00000063573; Expressed in spleen and 26 other tissues.
DR ExpressionAtlas; E7F590; baseline and differential.
DR GO; GO:0030136; C:clathrin-coated vesicle; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0031901; C:early endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
DR GO; GO:0030897; C:HOPS complex; IBA:GO_Central.
DR GO; GO:0005770; C:late endosome; 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:0009267; P:cellular response to starvation; IBA:GO_Central.
DR GO; GO:0034058; P:endosomal vesicle fusion; IBA:GO_Central.
DR GO; GO:0008333; P:endosome to lysosome transport; IMP:UniProtKB.
DR GO; GO:0016236; P:macroautophagy; IBA:GO_Central.
DR GO; GO:0006623; P:protein targeting to vacuole; IBA:GO_Central.
DR Gene3D; 1.25.40.10; -; 1.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR000547; Clathrin_H-chain/VPS_repeat.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR016902; VPS41.
DR InterPro; IPR045111; Vps41/Vps8.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR InterPro; IPR001841; Znf_RING.
DR PANTHER; PTHR12616; PTHR12616; 1.
DR Pfam; PF00637; Clathrin; 1.
DR PIRSF; PIRSF028921; VPS41; 1.
DR SMART; SM00299; CLH; 1.
DR SUPFAM; SSF48452; SSF48452; 1.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50236; CHCR; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW Autophagy; Coiled coil; Cytoplasm; Cytoplasmic vesicle; Endosome;
KW Golgi apparatus; Lysosome; Membrane; Metal-binding; Protein transport;
KW Reference proteome; Transport; Zinc; Zinc-finger.
FT CHAIN 1..854
FT /note="Vacuolar protein sorting-associated protein 41
FT homolog"
FT /id="PRO_0000454897"
FT REPEAT 568..712
FT /note="CHCR"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01006"
FT ZN_FING 791..839
FT /note="RING-type; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 854 AA; 99092 MW; E61307814A4BDE6D CRC64;
MAEVEEQGRK LSEESTDESE EEDTEEEPKL KYERLTNGVT EILQKDAASC MTVHDKFLAL
GTHFGKVFLL DIQGNVTQKF EISSVKINQI SLDESGDHVG ICSEDGKVQV FGLYTREGFH
ENFDCPIKVV ALHPQFSKSN NKQFVTGGNK LLLYERNWLN RWKTSVLHEG EGNITSVKWR
GNLIAWANNV GVKIYDIGSK QRITNVLRDN TSLRPDMYPC SLCWKDNTTL IIGWGCSVKI
CAVKERDPTE MRDLPSRYVE IVSAFETEFF ISGLAPLADQ LVTLYYVKEN SDHMEEEFRT
RPRLDIIQPL PEGCEEISSD ALTVRNFQEN QCRDYRLEHS EGESLFYIIS PKDIVVAKER
DQDDHIDWLL EKKKYEEALM AAEISFKNIK RHDVQKIGMA YINHLVEKGD YDTAARKCQK
VLGKNMDLWE NEVYRFKTIG QLKAISQYLP RGDLRLRPAI YEMILHDFLK TDYEGFATLI
REWPGELYNN MAIVQAVNEH LKKDPTNSIL LTTLAELYTY DQRYDRALEI YLRLRHKDVY
QLIHKHNLFS SIKDKIVLLM DFDKEKAVDM LLDNEDKISM DKVVEELKDR PELLHVYLHK
LFKRDHHKGQ KYHERQISLY AEFDRPNLLP FLRESMHCPL EKALEICQQR HFVEETVFLL
SRMGNCRRAL QMIMEELANV DKAIEFAKEQ DDRELWEDLI SYSIDKPPFI TGLLNNIGTH
VDPILLIHRI KEGMEIPNLR DSLVKILHDY NLQILLREGC KKILVADSLS LLQRMHRTQK
KGVRVDEENI CESCHTPILP SDTAQAFGVV VFHCRHMFHK ECLPSPGSIP GIQYCNICSA
KRRGPGSGIL EMKK
