BAP1_DANRE
ID BAP1_DANRE Reviewed; 755 AA.
AC A1L2G3; Q1LXB5;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 2.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase BAP1;
DE EC=3.4.19.12 {ECO:0000250|UniProtKB:Q92560};
DE AltName: Full=BRCA1-associated protein 1;
GN Name=bap1; ORFNames=si:dkey-42i9.9;
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] OF 1-682.
RC TISSUE=Olfactory epithelium;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP DISRUPTION PHENOTYPE.
RX PubMed=20040115; DOI=10.1186/1471-2164-10-637;
RA Tse W.K., Eisenhaber B., Ho S.H., Ng Q., Eisenhaber F., Jiang Y.J.;
RT "Genome-wide loss-of-function analysis of deubiquitylating enzymes for
RT zebrafish development.";
RL BMC Genomics 10:637-637(2009).
CC -!- FUNCTION: Deubiquitinating enzyme that plays a key role in chromatin by
CC mediating deubiquitination of histone H2A. Catalytic component of the
CC PR-DUB complex, a complex that specifically mediates deubiquitination
CC of histone H2A monoubiquitinated at 'Lys-119' (H2AK119ub1) (By
CC similarity). {ECO:0000250|UniProtKB:Q92560}.
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:Q92560};
CC -!- SUBUNIT: Component of the PR-DUB complex.
CC {ECO:0000250|UniProtKB:Q92560}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q92560}. Nucleus
CC {ECO:0000250|UniProtKB:Q92560}. Note=Mainly nuclear. Binds to
CC chromatin. {ECO:0000250|UniProtKB:Q92560}.
CC -!- DISRUPTION PHENOTYPE: Neuronal hyperplasia, suggesting a role in Notch
CC signaling pathway. {ECO:0000269|PubMed:20040115}.
CC -!- SIMILARITY: Belongs to the peptidase C12 family. BAP1 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI29507.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
CC Sequence=CAK11034.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; BX465868; CAK11034.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC129506; AAI29507.1; ALT_SEQ; mRNA.
DR AlphaFoldDB; A1L2G3; -.
DR SMR; A1L2G3; -.
DR STRING; 7955.ENSDARP00000086210; -.
DR MEROPS; C12.004; -.
DR PaxDb; A1L2G3; -.
DR PeptideAtlas; A1L2G3; -.
DR PRIDE; A1L2G3; -.
DR ZFIN; ZDB-GENE-050208-492; bap1.
DR eggNOG; KOG2778; Eukaryota.
DR InParanoid; A1L2G3; -.
DR PhylomeDB; A1L2G3; -.
DR Reactome; R-DRE-5689603; UCH proteinases.
DR PRO; PR:A1L2G3; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0035517; C:PR-DUB complex; ISS:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:1904888; P:cranial skeletal system development; IMP:ZFIN.
DR GO; GO:0035522; P:monoubiquitinated histone H2A deubiquitination; ISS:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0007219; P:Notch signaling pathway; IMP:ZFIN.
DR GO; GO:0016579; P:protein deubiquitination; ISS:UniProtKB.
DR GO; GO:0071108; P:protein K48-linked deubiquitination; ISS:UniProtKB.
DR GO; GO:0051726; P:regulation of cell cycle; ISS:UniProtKB.
DR GO; GO:0001558; P:regulation of cell growth; ISS:UniProtKB.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.40.532.10; -; 1.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001578; Peptidase_C12_UCH.
DR InterPro; IPR036959; Peptidase_C12_UCH_sf.
DR InterPro; IPR041507; UCH_C.
DR PANTHER; PTHR10589; PTHR10589; 1.
DR Pfam; PF01088; Peptidase_C12; 1.
DR Pfam; PF18031; UCH_C; 1.
DR PRINTS; PR00707; UBCTHYDRLASE.
DR SUPFAM; SSF54001; SSF54001; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Cytoplasm; Hydrolase; Nucleus; Protease;
KW Reference proteome; Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..755
FT /note="Ubiquitin carboxyl-terminal hydrolase BAP1"
FT /id="PRO_0000395819"
FT REGION 270..354
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 368..415
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 469..535
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 593..652
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 729..755
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 743..748
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250|UniProtKB:Q92560"
FT COMPBIAS 281..296
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 305..319
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 469..530
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 593..640
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 730..755
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 91
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q92560"
FT ACT_SITE 169
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P09936"
FT SITE 184
FT /note="Important for enzyme activity"
FT /evidence="ECO:0000250|UniProtKB:P09936"
FT CONFLICT 54
FT /note="E -> G (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
FT CONFLICT 111
FT /note="T -> A (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
FT CONFLICT 443
FT /note="G -> D (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
FT CONFLICT 504
FT /note="S -> P (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
FT CONFLICT 617..619
FT /note="VEM -> AEI (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
FT CONFLICT 627
FT /note="S -> L (in Ref. 2; AAI29507)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 755 AA; 83777 MW; 6DE37B40D438B535 CRC64;
MNKGWLELES DPGLFTLLVE DFGVKGVQVE EIYDLQSKCQ SPVYGFIFLF KWIEERRSRR
KVSTLVDETS VIDDDIVNDM FFAHQLIPNS CATHALLSVL LNCSGVELGM TLSRMKAFTK
GFNPESKGYA IGNAPELAKA HNSHARPEPR HLPEKQNGIS AVRTMEAFHF VSYVPIKDRL
FELDGLKAYP IDHGPWGEDE EWTDKARRVI MERIGLATAG EPYHDIRFNL MAVVPDRRIK
YESKLDILKR NRQIILEGLQ QIREKKVIRM TQQESGQDRK QQDSSSSEDT PPVVKKEEVQ
ETPIPSGAEQ ATPTEAQEGA ASLPSPAGKV RSMAKPALPA GGAPPPAPLP APSTNTIVQR
LPAFLDNHNY AKSPMQEEED LAAGVGRSRP PQPPYSDDED DYDDEEEECS TAGVTNSRVR
RKLGLRTRTM SRTAVGGVAA MEGQLALSVL AEKLKKEVQR KDALATTGST PLNVRTEGRT
GGISITSACQ PSPTPSNEST DTASEIGSAF NSPLRSPARS QATTRPSSPV ASHVGRVLFG
EEEGLPRLDA RHNRAVRDLG VLVSSTQLQL QEDGVIFALP PTEALEGLKK VGGVDKKKKE
EASGPGGEEE VKEGPSVEMK AEDVKESVDV KPEKENLPTT DVENSTKPPG EKYTPKELLA
LLKYVEADIA NYEVYLKEEV EKRKKYKIDD QRRTHNYDEF ICTFISMLAQ EGMLASLVEQ
NISVRRRQGV SIGRLHKQRK PDRRKRSRPY KAKRQ
