CALYP_DROME
ID CALYP_DROME Reviewed; 471 AA.
AC Q7K5N4;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase calypso;
DE EC=3.4.19.12;
DE AltName: Full=BAP1 homolog;
GN Name=calypso; ORFNames=CG8445;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley; TISSUE=Head;
RX PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
RA Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A.,
RA Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M.,
RA Celniker S.E.;
RT "A Drosophila full-length cDNA resource.";
RL Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=17717194; DOI=10.1534/genetics.107.075739;
RA Gaytan de Ayala Alonso A., Gutierrez L., Fritsch C., Papp B., Beuchle D.,
RA Muller J.;
RT "A genetic screen identifies novel polycomb group genes in Drosophila.";
RL Genetics 176:2099-2108(2007).
RN [5]
RP FUNCTION, IDENTIFICATION IN THE PR-DUB COMPLEX, INTERACTION WITH ASX,
RP MUTAGENESIS OF CYS-131, AND DISRUPTION PHENOTYPE.
RX PubMed=20436459; DOI=10.1038/nature08966;
RA Scheuermann J.C., de Ayala Alonso A.G., Oktaba K., Ly-Hartig N.,
RA McGinty R.K., Fraterman S., Wilm M., Muir T.W., Muller J.;
RT "Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-
RT DUB.";
RL Nature 465:243-247(2010).
CC -!- FUNCTION: Polycomb group (PcG) protein. Catalytic component of the PR-
CC DUB complex, a complex that specifically mediates deubiquitination of
CC histone H2A monoubiquitinated at 'Lys-118' (H2AK118ub1). Does not
CC deubiquitinate monoubiquitinated histone H2B. Required to maintain the
CC transcriptionally repressive state of homeotic genes throughout
CC development. The PR-DUB complex has weak or no activity toward 'Lys-
CC 48'- and 'Lys-63'-linked polyubiquitin chains.
CC {ECO:0000269|PubMed:20436459}.
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;
CC -!- SUBUNIT: Component of the PR-DUB complex, at least composed of calypso
CC and Asx. {ECO:0000269|PubMed:20436459}.
CC -!- INTERACTION:
CC Q7K5N4; Q9V727: Asx; NbExp=2; IntAct=EBI-15851838, EBI-103394;
CC -!- SUBCELLULAR LOCATION: Nucleus. Note=Localizes to PcG response elements
CC (PREs).
CC -!- DISRUPTION PHENOTYPE: Polycomb phenotype leading to lethality, probably
CC due to misexpression of homeotic genes. {ECO:0000269|PubMed:17717194,
CC ECO:0000269|PubMed:20436459}.
CC -!- SIMILARITY: Belongs to the peptidase C12 family. BAP1 subfamily.
CC {ECO:0000305}.
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DR EMBL; AE013599; AAF58046.1; -; Genomic_DNA.
DR EMBL; AE013599; AAO41384.1; -; Genomic_DNA.
DR EMBL; AY047515; AAK77247.1; -; mRNA.
DR RefSeq; NP_611096.1; NM_137252.3.
DR RefSeq; NP_788374.1; NM_176194.2.
DR PDB; 6CGA; X-ray; 3.50 A; A/C=43-404.
DR PDB; 6HGC; X-ray; 3.02 A; A/B=43-306, A=334-404, B=334-373.
DR PDBsum; 6CGA; -.
DR PDBsum; 6HGC; -.
DR AlphaFoldDB; Q7K5N4; -.
DR SMR; Q7K5N4; -.
DR BioGRID; 62514; 29.
DR DIP; DIP-59274N; -.
DR IntAct; Q7K5N4; 1.
DR STRING; 7227.FBpp0086383; -.
DR MEROPS; C12.A09; -.
DR PaxDb; Q7K5N4; -.
DR DNASU; 36794; -.
DR EnsemblMetazoa; FBtr0087245; FBpp0086383; FBgn0262166.
DR EnsemblMetazoa; FBtr0087246; FBpp0086384; FBgn0262166.
DR GeneID; 36794; -.
DR KEGG; dme:Dmel_CG8445; -.
DR UCSC; CG8445-RA; d. melanogaster.
DR CTD; 36794; -.
DR FlyBase; FBgn0262166; calypso.
DR VEuPathDB; VectorBase:FBgn0262166; -.
DR eggNOG; KOG2778; Eukaryota.
DR GeneTree; ENSGT00940000156388; -.
DR HOGENOM; CLU_018316_2_1_1; -.
DR InParanoid; Q7K5N4; -.
DR OMA; IAINEQH; -.
DR OrthoDB; 1363547at2759; -.
DR PhylomeDB; Q7K5N4; -.
DR Reactome; R-DME-5689603; UCH proteinases.
DR BioGRID-ORCS; 36794; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 36794; -.
DR PRO; PR:Q7K5N4; -.
DR Proteomes; UP000000803; Chromosome 2R.
DR Bgee; FBgn0262166; Expressed in eye disc (Drosophila) and 24 other tissues.
DR ExpressionAtlas; Q7K5N4; baseline and differential.
DR Genevisible; Q7K5N4; DM.
DR GO; GO:0000785; C:chromatin; IDA:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0035517; C:PR-DUB complex; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:UniProtKB.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0035522; P:monoubiquitinated histone H2A deubiquitination; IDA:UniProtKB.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0007385; P:specification of segmental identity, abdomen; IMP:FlyBase.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR DisProt; DP02890; -.
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; 2.
DR Pfam; PF01088; Peptidase_C12; 1.
DR Pfam; PF18031; UCH_C; 1.
DR PRINTS; PR00707; UBCTHYDRLASE.
DR SUPFAM; SSF54001; SSF54001; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Hydrolase; Nucleus; Protease;
KW Reference proteome; Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..471
FT /note="Ubiquitin carboxyl-terminal hydrolase calypso"
FT /id="PRO_0000395823"
FT REGION 307..326
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 412..471
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 311..326
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 412..450
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 454..471
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 131
FT /note="Nucleophile"
FT /evidence="ECO:0000305"
FT ACT_SITE 213
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT SITE 228
FT /note="Important for enzyme activity"
FT /evidence="ECO:0000250"
FT MUTAGEN 131
FT /note="C->S: Abolishes deubiquitinase activity without
FT affecting the interaction with Asx."
FT /evidence="ECO:0000269|PubMed:20436459"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 131..140
FT /evidence="ECO:0007829|PDB:6HGC"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 152..160
FT /evidence="ECO:0007829|PDB:6HGC"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:6CGA"
FT HELIX 166..174
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 189..194
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 213..219
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 221..227
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 246..257
FT /evidence="ECO:0007829|PDB:6HGC"
FT STRAND 267..275
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 278..306
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 335..372
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 377..389
FT /evidence="ECO:0007829|PDB:6HGC"
FT HELIX 393..399
FT /evidence="ECO:0007829|PDB:6HGC"
SQ SEQUENCE 471 AA; 51507 MW; B7C90121EF7716E5 CRC64;
MNAAGGGSGA QAAAVAAGNN SLSHNALLST ASGATTMPMA QLADGWLELE SDPGLFTLLL
KDFGCHDVQV EEVYDLQKPI ESPYGFIFLF RWIEERRARR KIVETTAEIF VKDEEAISSI
FFAQQVVPNS CATHALLSVL LNCNENNLQL GDTLSRLKTH TKGMSPENKG LAIGNTPELA
CAHNSHAMPQ ARRRLERTGA GVSSCRFTGE AFHFVSFVPI NGQLFELDGL KPYPMNHGGW
EDSEDWTDKF RRVMAERLGI ATGEQDIRFN LMAVVPDRRI AITHKLKMLR TNQAIVSGTL
QKLLKADEQG ESGNGDSQRP DTPTTLLEPS AFTARDLQSL LKNLDTEIAI NEQHLADEND
RRHMFKVDAS RRTHNYDKFI CTFLSMLAHQ GVLGELVSQH LLPSKKVSGQ GAANRISKQS
TTASAGGSTA AGTASTPKTQ QQQAAAAKNG KSPSKTPGRR RKGRNKCRKR K
