MINY1_DANRE
ID MINY1_DANRE Reviewed; 520 AA.
AC A3KQS4;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase MINDY-1;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme MINDY-1;
DE AltName: Full=Protein FAM63A;
GN Name=mindy1; Synonyms=fam63a; ORFNames=si:ch211-210h11.5;
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).
CC -!- FUNCTION: Hydrolase that can specifically remove 'Lys-48'-linked
CC conjugated ubiquitin from proteins. May play a regulatory role at the
CC level of protein turnover. {ECO:0000250|UniProtKB:Q8N5J2}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12; Evidence={ECO:0000250|UniProtKB:Q8N5J2};
CC -!- SIMILARITY: Belongs to the MINDY deubiquitinase family. FAM63
CC subfamily. {ECO:0000305}.
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DR EMBL; BX927401; CAM56381.1; -; Genomic_DNA.
DR RefSeq; NP_001093481.1; NM_001100011.1.
DR RefSeq; XP_005159508.1; XM_005159451.3.
DR AlphaFoldDB; A3KQS4; -.
DR SMR; A3KQS4; -.
DR STRING; 7955.ENSDARP00000116319; -.
DR PaxDb; A3KQS4; -.
DR PeptideAtlas; A3KQS4; -.
DR Ensembl; ENSDART00000136502; ENSDARP00000117536; ENSDARG00000004866.
DR Ensembl; ENSDART00000147491; ENSDARP00000116319; ENSDARG00000004866.
DR GeneID; 563470; -.
DR KEGG; dre:563470; -.
DR CTD; 55793; -.
DR ZFIN; ZDB-GENE-070717-2; mindy1.
DR ZFIN; ZDB-GENE-070717-3; rfx5.
DR eggNOG; KOG2427; Eukaryota.
DR GeneTree; ENSGT00390000016607; -.
DR HOGENOM; CLU_022566_3_2_1; -.
DR InParanoid; A3KQS4; -.
DR OMA; NHEVPLG; -.
DR OrthoDB; 1601180at2759; -.
DR PhylomeDB; A3KQS4; -.
DR TreeFam; TF314589; -.
DR PRO; PR:A3KQS4; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 19.
DR Bgee; ENSDARG00000004866; Expressed in spleen and 27 other tissues.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0036435; F:K48-linked polyubiquitin modification-dependent protein binding; ISS:UniProtKB.
DR GO; GO:1990380; F:Lys48-specific deubiquitinase activity; IEA:InterPro.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR InterPro; IPR007518; MINDY.
DR InterPro; IPR033979; MINDY_domain.
DR PANTHER; PTHR18063; PTHR18063; 1.
DR Pfam; PF04424; MINDY_DUB; 1.
PE 3: Inferred from homology;
KW Hydrolase; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..520
FT /note="Ubiquitin carboxyl-terminal hydrolase MINDY-1"
FT /id="PRO_0000371435"
FT REGION 1..155
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 422..441
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 441..479
FT /note="Ubiquitin-binding domain (UBD)"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
FT REGION 467..520
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 36..53
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 61..118
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 426..441
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 471..504
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 505..520
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 189
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
FT ACT_SITE 371
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
FT SITE 465
FT /note="Ubiquitin-binding"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
FT SITE 468..469
FT /note="Ubiquitin-binding"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
FT SITE 472
FT /note="Ubiquitin-binding"
FT /evidence="ECO:0000250|UniProtKB:Q8N5J2"
SQ SEQUENCE 520 AA; 57366 MW; 504687F2EA54E275 CRC64;
MADSCADTVD GEIKGFSEGQ QLNITKNEDL EQTKPQKEAI ANTEESSACV SQIKQDLAPC
KDPPTTTTAS LEDDAKATSS ASVTSKSQDE SEVINSQSYT PSQSEATPSF SMASLEFSEE
NNGVPPDGPL SSAKSARDGN QVSVQENEGA VAGAMRPAEP TMPAYYFVKW ITWKEKKTAV
ITQSENGPCP LIAIMNILLL RWKVKFPAQT EVVTTEELMA HLGECVLSIK PREKAEGMEL
NFQQNMSDAM AVLPKLSTGL DVNVRFTGVS DFEYTPECIV FDLLDIPLYH GWLVDPQSPE
VVSAVGKLSY NQLVEKIIEF KHSTDSSQVS EGLIAEQFLE STATQLSYHG LCELNTTAKE
GELSVFFRNN HFSTMIKHKG HLYLLVTDQG FLQEESVVWE SLHNVEGDGN FCDSDFRLCH
PSQKPSAAAA QPSTQQQQQM QIDQDYLVAM SLQQEQGEAP GPLSDLELAR QLQQEEYQQP
QTQQQQQQQP SAGQMRGQAT SPQGGQRRRE KKEETDCCIL
