D1039_DICDI
ID D1039_DICDI Reviewed; 715 AA.
AC Q54Q40; O15731;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=Probable ubiquitin thioesterase DG1039;
DE EC=3.4.19.-;
DE AltName: Full=Developmental gene 1039 protein;
GN Name=DG1039; ORFNames=DDB_G0284037;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 271-715.
RC STRAIN=AX4;
RA Loomis W.F., Iranfar N.;
RL Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: May be a zinc metalloprotease that specifically cleaves
CC ubiquitin chains. {ECO:0000250}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250};
CC -!- DOMAIN: The JAMM motif is essential for the protease activity.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the peptidase M67C family. {ECO:0000305}.
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DR EMBL; AAFI02000063; EAL65359.1; -; Genomic_DNA.
DR EMBL; AF018638; AAB82533.1; -; Genomic_DNA.
DR RefSeq; XP_638757.1; XM_633665.1.
DR AlphaFoldDB; Q54Q40; -.
DR SMR; Q54Q40; -.
DR STRING; 44689.DDB0191462; -.
DR MEROPS; M67.A15; -.
DR PaxDb; Q54Q40; -.
DR EnsemblProtists; EAL65359; EAL65359; DDB_G0284037.
DR GeneID; 8624428; -.
DR KEGG; ddi:DDB_G0284037; -.
DR dictyBase; DDB_G0284037; -.
DR eggNOG; KOG2880; Eukaryota.
DR HOGENOM; CLU_386589_0_0_1; -.
DR InParanoid; Q54Q40; -.
DR OMA; HQLKQGY; -.
DR Reactome; R-DDI-5689901; Metalloprotease DUBs.
DR PRO; PR:Q54Q40; -.
DR Proteomes; UP000002195; Chromosome 4.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0070122; F:isopeptidase activity; IEA:InterPro.
DR GO; GO:0061578; F:Lys63-specific deubiquitinase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140492; F:metal-dependent deubiquitinase activity; IEA:InterPro.
DR GO; GO:0070536; P:protein K63-linked deubiquitination; IBA:GO_Central.
DR CDD; cd08066; MPN_AMSH_like; 1.
DR InterPro; IPR000555; JAMM/MPN+_dom.
DR InterPro; IPR037518; MPN.
DR InterPro; IPR044098; STAMBP/STALP-like_MPN.
DR InterPro; IPR015063; USP8_dimer.
DR Pfam; PF01398; JAB; 1.
DR Pfam; PF08969; USP8_dimer; 1.
DR SMART; SM00232; JAB_MPN; 1.
DR PROSITE; PS50249; MPN; 1.
PE 3: Inferred from homology;
KW Coiled coil; Hydrolase; Metal-binding; Metalloprotease; Protease;
KW Reference proteome; Ubl conjugation pathway; Zinc.
FT CHAIN 1..715
FT /note="Probable ubiquitin thioesterase DG1039"
FT /id="PRO_0000388781"
FT DOMAIN 537..666
FT /note="MPN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT REGION 287..367
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 398..450
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 502..527
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 86..302
FT /evidence="ECO:0000255"
FT MOTIF 615..628
FT /note="JAMM motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT COMPBIAS 322..353
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 502..525
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 615
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 617
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 628
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 630
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 672
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 678
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 680
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT SITE 560
FT /note="Indirect zinc-binding"
FT /evidence="ECO:0000250"
SQ SEQUENCE 715 AA; 83674 MW; 3AAA55BEC3DCC456 CRC64;
MAAELPFYIA SSVEELVKKH VEGVEVDKNY SIFHYLSTCN NLVKQADIYK SEGDIERTYI
YSLRFCILIF EKLQKHPDFN KESFTKSRNE IKRKAELKLK ELEGLKETLK KGYERIQHKK
EEERKRIERE KEKERIFKQE KLKLEREQQL LREEEEQRKR EDLELESEIQ RLKEVEDFEN
RKLQAQKNIK RATSARTFEL LRQEALLEER KRLQGIETEK KRILAEKQEA LEKEFQQQLF
EQQEKERLEK ERLEKEEQLR LASLPPPPPD YSSFDSDQLL NLIENNNKKL ENNNQTDDKL
DNEFLLDPSF LPPPPPIITQ PSPSQEKKDN NNNNNNKNTT AQLPLSITQP PHMPNNEKKL
PPIYNSTSPI QFGYPSLNNS VNNPPSFSLQ NNTPLIQQYK QQQQQQPIQS PTNNINRPNI
PQYNNYNAKP LSSNLNPLPP QYQPQQQQQY QQQQQQQQYQ QQQQYQQQQQ QQQQQQQQQQ
HQLPKLPQYQ PIENKSISAN GLAQSPAVNT PSITPTTNKP NIDSSEASKK YSKLRKIIVH
GEVFQEFMRL AENNTKRSIE TCGILSGTLS NDVFRITTII IPKQEGTTDT CNTIEEHEIF
EYQLENDLLT LGWIHTHPTQ DCFLSAVDVH THCSYQYLLQ EAIAVVISPM ANPNFGIFRL
TDPPGLETVQ KCKLKSFHPH PPVNGIPIYT KVDHVDLIWG KKSDSKVVDL RFLKK
