DOP_ACIC1
ID DOP_ACIC1 Reviewed; 503 AA.
AC A0LU48;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 12-DEC-2006, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Depupylase;
DE EC=3.4.-.-;
GN Name=dop; OrderedLocusNames=Acel_1186;
OS Acidothermus cellulolyticus (strain ATCC 43068 / DSM 8971 / 11B).
OC Bacteria; Actinobacteria; Acidothermales; Acidothermaceae; Acidothermus.
OX NCBI_TaxID=351607;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43068 / DSM 8971 / 11B;
RX PubMed=19270083; DOI=10.1101/gr.084848.108;
RA Barabote R.D., Xie G., Leu D.H., Normand P., Necsulea A., Daubin V.,
RA Medigue C., Adney W.S., Xu X.C., Lapidus A., Parales R.E., Detter C.,
RA Pujic P., Bruce D., Lavire C., Challacombe J.F., Brettin T.S., Berry A.M.;
RT "Complete genome of the cellulolytic thermophile Acidothermus
RT cellulolyticus 11B provides insights into its ecophysiological and
RT evolutionary adaptations.";
RL Genome Res. 19:1033-1043(2009).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 1-501 OF APOENZYME AND IN COMPLEX
RP WITH ATP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, AND
RP MUTAGENESIS OF GLU-8; GLU-10; TYR-92; ASP-94; HIS-97; GLN-139; HIS-155;
RP ARG-205; ARG-221; HIS-241 AND ARG-400.
RC STRAIN=ATCC 43068 / DSM 8971 / 11B;
RX PubMed=22910360; DOI=10.1038/ncomms2009;
RA Ozcelik D., Barandun J., Schmitz N., Sutter M., Guth E., Damberger F.F.,
RA Allain F.H., Ban N., Weber-Ban E.;
RT "Structures of Pup ligase PafA and depupylase Dop from the prokaryotic
RT ubiquitin-like modification pathway.";
RL Nat. Commun. 3:1014-1014(2012).
CC -!- FUNCTION: Displays depupylase (DPUP) activity, removing conjugated Pup
CC from target proteins; is thus involved in the recycling of Pup and may
CC function similarly to deubiquitinases (DUBs) in eukaryotes to prevent
CC or promote proteasomal degradation of certain proteins. Is also able to
CC catalyze the deamidation of the C-terminal glutamine to glutamate in a
CC variant of the prokaryotic ubiquitin-like protein Pup; however, since
CC Pup from A.cellulolyticus possesses a C-terminal glutamate, this
CC deamidase activity may be of no significance in vivo.
CC {ECO:0000269|PubMed:22910360}.
CC -!- COFACTOR:
CC Name=ATP; Xref=ChEBI:CHEBI:30616; Evidence={ECO:0000250};
CC Note=ATP is required for the deamidation and depupylation reactions but
CC is not hydrolyzed during the reactions. {ECO:0000250};
CC -!- PATHWAY: Protein degradation; proteasomal Pup-dependent pathway.
CC -!- SUBUNIT: Likely interacts with the C-terminal half of the prokaryotic
CC ubiquitin-like protein Pup. {ECO:0000269|PubMed:22910360}.
CC -!- SIMILARITY: Belongs to the Pup ligase/Pup deamidase family. Pup
CC deamidase subfamily. {ECO:0000305}.
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DR EMBL; CP000481; ABK52958.1; -; Genomic_DNA.
DR PDB; 4B0R; X-ray; 2.60 A; A=1-501.
DR PDB; 4B0S; X-ray; 2.85 A; A=1-501.
DR PDB; 5LRT; X-ray; 1.85 A; A=1-502.
DR PDB; 7OXV; X-ray; 1.39 A; A=1-502.
DR PDB; 7OXY; X-ray; 1.65 A; A=1-502.
DR PDB; 7OY3; X-ray; 1.78 A; A=1-502.
DR PDB; 7OYF; X-ray; 1.88 A; A=1-502.
DR PDB; 7OYH; X-ray; 1.75 A; A=1-502.
DR PDBsum; 4B0R; -.
DR PDBsum; 4B0S; -.
DR PDBsum; 5LRT; -.
DR PDBsum; 7OXV; -.
DR PDBsum; 7OXY; -.
DR PDBsum; 7OY3; -.
DR PDBsum; 7OYF; -.
DR PDBsum; 7OYH; -.
DR AlphaFoldDB; A0LU48; -.
DR SMR; A0LU48; -.
DR STRING; 351607.Acel_1186; -.
DR MEROPS; U72.001; -.
DR PRIDE; A0LU48; -.
DR EnsemblBacteria; ABK52958; ABK52958; Acel_1186.
DR KEGG; ace:Acel_1186; -.
DR eggNOG; COG4122; Bacteria.
DR HOGENOM; CLU_040524_1_0_11; -.
DR OMA; YFRGRCL; -.
DR BRENDA; 3.5.1.119; 9545.
DR UniPathway; UPA00997; -.
DR Proteomes; UP000008221; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016811; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008233; F:peptidase activity; IEA:InterPro.
DR GO; GO:0019941; P:modification-dependent protein catabolic process; IEA:InterPro.
DR GO; GO:0010498; P:proteasomal protein catabolic process; IEA:InterPro.
DR DisProt; DP02322; -.
DR InterPro; IPR022366; Pup_deamidase.
DR InterPro; IPR004347; Pup_ligase/deamidase.
DR PANTHER; PTHR42307; PTHR42307; 1.
DR Pfam; PF03136; Pup_ligase; 1.
DR PIRSF; PIRSF018077; UCP018077; 1.
DR TIGRFAMs; TIGR03688; pupylate_PafA2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Hydrolase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..503
FT /note="Depupylase"
FT /id="PRO_0000424323"
FT ACT_SITE 94
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:22910360"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 92
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 99
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 101..102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 155
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 157
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 239
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:22910360"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 8
FT /note="E->A: Abolishes depupylation and deamidation
FT activities."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 10
FT /note="E->A: Abolishes depupylation and deamidation
FT activities."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 92
FT /note="Y->A: Reduces depupylation but not deamidation
FT activity."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 94
FT /note="D->A: Abolishes depupylation and deamidation
FT activities."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 97
FT /note="H->A: Reduces depupylation but not deamidation
FT activity."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 139
FT /note="Q->E: Abolishes depupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 155
FT /note="H->A: Abolishes depupylation but not deamidation
FT activity."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 205
FT /note="R->A: Impairs depupylation and significantly slows
FT deamidation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 221
FT /note="R->A: Abolishes depupylation and deamidation
FT activities."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 241
FT /note="H->A: Abolishes depupylation and deamidation
FT activities."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 400
FT /note="R->E: Abolishes depupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:7OXY"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 108..131
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4B0R"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 154..161
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 181..184
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 197..202
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 217..225
FT /evidence="ECO:0007829|PDB:7OXV"
FT TURN 234..236
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 251..269
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 279..281
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 282..290
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 309..328
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 329..331
FT /evidence="ECO:0007829|PDB:7OXY"
FT HELIX 334..352
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 354..357
FT /evidence="ECO:0007829|PDB:7OXV"
FT TURN 358..360
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 362..377
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 384..392
FT /evidence="ECO:0007829|PDB:7OXV"
FT TURN 398..400
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 402..408
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 418..424
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 430..432
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 434..443
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 445..447
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 448..452
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 455..458
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 467..470
FT /evidence="ECO:0007829|PDB:7OXV"
FT STRAND 476..478
FT /evidence="ECO:0007829|PDB:7OXY"
FT HELIX 479..488
FT /evidence="ECO:0007829|PDB:7OXV"
FT HELIX 492..499
FT /evidence="ECO:0007829|PDB:7OXV"
SQ SEQUENCE 503 AA; 56577 MW; B57F6E5A8943BBD2 CRC64;
MHRVMGIETE YGISVPHQPN ANAMAASSQV VNAYAPIGAP AQRQARWDFE EENPLRDARG
FEVAREAADP SQLTDEDLGL ANVILTNGAR LYVDHAHPEY STPEVTNPRD AVLWDKAGER
IMAEAARRAA DLPMGWTIQL YKNNTDNKGA SYGCHENYLM NRSTPFADIV RHLIPFFVTR
QVFCGAGRVG IGADGRGEGF QLSQRADFFE VEVGLETTLK RPIINTRDEP HADPEKYRRL
HVIIGDANMS EIATYLKLGT TALVLAMIED GFLSQDFSVE SPVGALRAVS HDPTLRYQLR
LHDGRRLTAV QLQMEYLEQA RKYVEDRFGT DVDDMTRDVL DRWETTLVRL ADDPMQLSRD
LDWVAKLSIL EGYRQRENLP WSAHKLQLVD LQYHDVRPDR GLYNRLVARG RMNLLVDEAA
VRTAMHEPPN DTRAYFRGRC LAKFGAEIAA ASWDSVIFDL PGRDSLQRVP TLEPLRGTRA
HVGDLLDRCR SATELVAALT GGR
