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Dioxygenase 3D structures

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(New page: ==3D structures of dioxygenase== Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *'''Dioxygenase Intradiol family''...)
Current revision (11:15, 29 January 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 50: Line 50:
**[[2xsu]] – ArCTD + Fe+3 + phosphoinositol derivative – ''Acinetobacter radioresistens''<br />
**[[2xsu]] – ArCTD + Fe+3 + phosphoinositol derivative – ''Acinetobacter radioresistens''<br />
**[[2xsv]], [[2xsr]] – ArCTD + Fe+3 + phosphoinositol derivative <br />
**[[2xsv]], [[2xsr]] – ArCTD + Fe+3 + phosphoinositol derivative <br />
 +
 +
*Catechol 2,3-dioxygenase (CT23D)
 +
 +
**[[5zsz]] – DiCT23D + Fe+3 - ''Diaphorobacter''<br />
 +
**[[5znh]], [[5zsx]] – DiCTD + Fe+3 + catechol derivative<br />
*Chlorocatechol 1,2-dioxygenase (CCTD)
*Chlorocatechol 1,2-dioxygenase (CCTD)
Line 70: Line 75:
**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
 +
**[[3n9t]] – PpHQD + Fe+3 <br />
*Nitrobenzene dioxygenase (NBDO)
*Nitrobenzene dioxygenase (NBDO)
Line 85: Line 91:
**[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
**[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
**[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
**[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
-
**[[4jht]] – EcAlkb + Mn+2 + quinoline derivative <br />
+
**[[4jht]], [[7nro]] – EcAlkb + Mn+2 + inhibitor<br />
**[[4rfr]] – EcAlkb + Mn+2 + rhein<br />
**[[4rfr]] – EcAlkb + Mn+2 + rhein<br />
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
 +
**[[6ypv]] – EcAlkb + Fe+3 + oxoglutarate <br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
 +
**[[6y0q]] – EcAlkb + Fe+3 + oxoglutarate + pyrimidine derivative<br />
 +
**[[6f9p]] – FlAlkb + Re+2 - ''Flavobacterium''<br />
 +
**[[6exf]] – FlAlkb + Fe+3 + lysine <br />
 +
**[[6eur]] – FlAlkb + Fe+3 + oxoglutarate <br />
 +
**[[6euo]] – FlAlkb + Fe+3 + succinate <br />
 +
**[[6exh]] – FlAlkb + Fe+3 + succinate + hydroxylysine <br />
 +
**[[6f6e]], [[6p77]] – CaAlkb – ''Catenulispora acidiphila''<br />
 +
**[[6f2b]] – CaAlkb + Fe+2 + oxoglutarate <br />
 +
**[[6f2a]] – CaAlkb + Fe+2 + lysine <br />
 +
**[[6f6j]] – CaAlkb + Fe+3 + succinate + hydroxylysine <br />
*''Alkb complex with DNA''
*''Alkb complex with DNA''
Line 110: Line 127:
*α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
*α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
 +
**[[6ima]] – hAlkbh1 catalytic domain 37-369<br />
 +
**[[6ie3]] – hAlkbh1 + Mn <br />
 +
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
 +
**[[6imc]] – hAlkbh1 catalytic domain + Mn + oxalylglycine <br />
 +
**[[6ksf]] – mAlkbh1 catalytic domain 4-384 + succinate + DNA<br />
 +
**[[6l94]] – mAlkbh1 catalytic domain + Fe+2<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
Line 115: Line 138:
**[[4nro]] – hAlkbh5 residues 66-292 + Mn + ketoglutarate <br />
**[[4nro]] – hAlkbh5 residues 66-292 + Mn + ketoglutarate <br />
**[[4oct]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate <br />
**[[4oct]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate <br />
 +
**[[7v4g]] – hAlkbh5 residues 66-292 + Mn + RNA<br />
 +
**[[7wkv]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate + RNA<br />
 +
**[[7wl0]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine + RNA<br />
**[[4nrp]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine <br />
**[[4nrp]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine <br />
**[[4nrq]] – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate <br />
**[[4nrq]] – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate <br />
**[[4npl]] – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish<br />
**[[4npl]] – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish<br />
**[[4npm]] – zfAlkbh5 residues 38-287 + Mn + succinate <br />
**[[4npm]] – zfAlkbh5 residues 38-287 + Mn + succinate <br />
 +
**[[7vjs]] – hAlkbh6 + Ni <br />
 +
**[[7vjv]] – hAlkbh6 + Mn + ketoglutarate <br />
**[[4qkb]], [[4qkd]] – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate <br />
**[[4qkb]], [[4qkd]] – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate <br />
**[[4qkf]] – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine <br />
**[[4qkf]] – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine <br />
Line 125: Line 153:
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
 +
**[[7ckk]] – hFto + inhibitor + oxalylglycine<br />
**[[4ie0]], [[4ie5]], [[4qho]] – hFto + Zn+2 + pyrimidine derivative<br />
**[[4ie0]], [[4ie5]], [[4qho]] – hFto + Zn+2 + pyrimidine derivative<br />
**[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
**[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
Line 130: Line 159:
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
 +
**[[6aej]], [[7e8z]] – hFto + Zn+2 + inhibitor<br />
 +
**[[6ak4]] – hFto (mutant) + Zn+2 + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
**[[4zs2]], [[4zs3]] – hFto + Mn+2 + oxoglutarate + fluorescin<br />
**[[4zs2]], [[4zs3]] – hFto + Mn+2 + oxoglutarate + fluorescin<br />
 +
**[[7wcv]] – hFto + Mn+2 + oxoglutarate <br />
**[[5zmd]] – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine<br />
**[[5zmd]] – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine<br />
-
**[[6eoz]] – EnFto + Ni+2 + cyclopeptin – Emericela nidulans<br />
+
**[[6eoz]] – EnFto + Ni+2 + cyclopeptin – ''Emericela nidulans''<br />
-
**[[5ybl]] – EnFto + Mn+2 + oxoglutarate <br />
+
**[[5y7t]], [[5y7r]] – EnFto + Fe+3 + oxoglutarate + cyclopeptin<br />
**[[5y7t]], [[5y7r]] – EnFto + Fe+3 + oxoglutarate + cyclopeptin<br />
**[[5oa8]], [[5oa7]], [[5oa4]] – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin<br />
**[[5oa8]], [[5oa7]], [[5oa4]] – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin<br />
Line 143: Line 174:
**[[5zm2]] – EvANDA – ''Emericella variicolor''<br />
**[[5zm2]] – EvANDA – ''Emericella variicolor''<br />
**[[5zm4]], [[5zm3]] – EvANDA + Fe+3 + oxoglutarate + preandiloid<br />
**[[5zm4]], [[5zm3]] – EvANDA + Fe+3 + oxoglutarate + preandiloid<br />
 +
 +
* α-ketoglutarate-dependent dioxygenase (DAO)
 +
 +
**[[6kun]] – DAO + oxoglutarate – rice<br />
 +
 +
* Iron/α-ketoglutarate-dependent dioxygenase (AsqJ)
 +
 +
**[[5dav]] – AnAsqJ + Ni+2 + cyclopeptin – ''Aspergillus nidulans''<br />
 +
**[[5oa4]], [[5oa7]], [[5oa8]], [[6eoz]] – AnAsqJ (mutant) + Ni+2 + cyclopeptin <br />
 +
**[[5dap]] – AnAsqJ + Ni+2 + oxoglutarate<br />
 +
**[[5daq]], [[5daw]], [[5dax]], [[5y7r]], [[5y7t]] – AnAsqJ + Fe+3 + cyclopeptin + oxoglutarate<br />
 +
**[[6k0e]] – AnAsqJ + Fe+3 + O2 + cyclopeptin + oxoglutarate<br />
 +
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
 +
**[[6jzm]], [[6k30]], [[6kd9]] – AnAsqJ + Fe+3 + cyclopeptin + succinate<br />
 +
**[[7eyt]], [[7eyu]], [[7eyw]] – AnAsqJ (mutant) + Fe+2 + terpenoid<br />
 +
**[[7olk]] – EnAsqJ + Ni+2 + inhibitor<br />
 +
**[[7oll]], [[7olm]], [[7olo]], [[7olq]] – EnAsqJ (mutant) + Ni+2 + inhibitor<br />
 +
**[[7olt]] – EnAsqJ + Ni+2 + cyclopeptin<br />
 +
**[[7olr]] – EnAsqJ + Ni+2 + oxoglutarate + cyclopeptin<br />
 +
 +
* Fe(II)/(alpha)-ketoglutarate-dependent dioxygenase (PrhA)
 +
 +
**[[5ybm]] – PbPrhA – ''Penicillium brasilianum''<br />
 +
**[[5ybn]], [[7olp]] – PbPrhA + Fe+3 + oxoglutarate + cyclopeptin <br />
 +
**[[5ybs]], [[5ybt]] – PbPrhA (mutant) + Fe+3 + oxoglutarate + berkeleyone <br />
 +
**[[5ybo]], [[5ybp]], [[5ybq]], [[5ybr]] – PbPrhA (mutant) + Fe+3 + oxoglutarate + preaustinoid <br />
 +
**[[7qtf]] – StPlaO1 + succinate - Streptomyces<br />
 +
**[[7qtg]] – StPlaO1 + Fe+2<br />
 +
**[[7qtd]] – StPlaO1 + Fe+2 + oxoglutarate <br />
 +
**[[7qte]] – StPlaO1 + Co + succinate <br />
 +
**[[5ybl]] – EnAusE + Mn+2 + oxoglutarate <br />
 +
 +
* Gamma-butyrobetaine dioxygenase
 +
 +
**[[4bhf]] – hGBBD + inhibitor <br />
 +
**[[3n6w]] – hGBBD + Zn <br />
 +
**[[3o2g]] – hGBBD + Zn + oxalylglycine <br />
 +
**[[3ms5]] – hGBBD + Ni + Zn + oxalylglycine <br />
 +
**[[4bg1]], [[4bgk]], [[4bgm]], [[4bhf]], [[4bhi]] – hGBBD + Zn + inhibitor<br />
 +
**[[4c8r]] – hGBBD + Ni + Zn + inhibitor<br />
 +
**[[4bhg]], [[4c5w]] – hGBBD + Zn + oxalylglycine + inhibitor<br />
 +
**[[4cwd]] – hGBBD + Ni + Zn + oxalylglycine + inhibitor<br />
*Leucoanthocyanidin dioxygenase (LACD)
*Leucoanthocyanidin dioxygenase (LACD)
Line 151: Line 224:
*Methylcytosine dioxygenase (TET)
*Methylcytosine dioxygenase (TET)
-
**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + DNA <br />
+
**[[6asd]] – hTET1 + DNA <br />
 +
**[[5d9y]], [[5deu]], [[4nm6]], [[7ne6]] – hTET2 + DNA <br />
 +
**[[7ne3]] – hTET2 (mutant) + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
**[[5exh]] – mTET3 + DNA – mouse <br />
**[[5exh]] – mTET3 + DNA – mouse <br />
 +
**[[7w5p]] – CcTET + DNA – ''Coprinopsis cinerea''<br />
 +
**[[7vpn]] – CcTET + oxalylglycine + Mn<br />
*'''Dioxygenase extradiol family'''
*'''Dioxygenase extradiol family'''
Line 189: Line 266:
**[[5zsz]] – DiMPC + Fe+3 - ''Diaphorobacter''<br />
**[[5zsz]] – DiMPC + Fe+3 - ''Diaphorobacter''<br />
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
 +
**[[6l3w]] – MPC + Fe+3 - metagenome<br />
 +
**[[7q2a]] - MPC + Fe+3 + catechol derivative - ''Rhodococcus jostii''<br />
*Naphthalene 1,2-dioxygenase (NDO)
*Naphthalene 1,2-dioxygenase (NDO)
-
**[[1ndo]], [[1o7h]], [[1o7w]] – PpNDO + Fe+3 + Fe2S2<br />
+
**[[2qpz]] – PpNDO ferredoxin subunit 1-104 + Fe2S2<br />
-
**[[2hmj]] – PpNDO (mutant) + Fe+3 + Fe2S2 <br />
+
**[[1ndo]], [[1o7h]], [[1o7w]] – PpNDO alpha+beta subunits + Fe+3 + Fe2S2<br />
-
**[[2b1x]] – RoNDO + Fe+3 + Fe2S2<br />
+
**[[2hmj]] – PpNDO (mutant) alpha+beta subunits + Fe+3 + Fe2S2 <br />
 +
**[[2b1x]] – RoNDO alpha+beta subunits + Fe+3 + Fe2S2<br />
*''NDO complex with aromatic compound''
*''NDO complex with aromatic compound''
Line 225: Line 305:
**[[1kwb]] – PsDHBP (mutant) <br />
**[[1kwb]] – PsDHBP (mutant) <br />
**[[1han]], [[1kmy]] – BxDHBP (mutant) + Fe+3 – ''Burkholderia xenovorans''<br />
**[[1han]], [[1kmy]] – BxDHBP (mutant) + Fe+3 – ''Burkholderia xenovorans''<br />
 +
**[[3huh]] – DHBP – ''Salmonella typhimurium'' <br />
*''DHBP complex with aromatic compound''
*''DHBP complex with aromatic compound''
Line 264: Line 345:
**[[4pw8]] - hTDO + Co+2 <br />
**[[4pw8]] - hTDO + Co+2 <br />
-
**[[5tia]], [[5ti9]] – hTDO + heme + tryptophan <br />
+
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
-
**[[6a4i]] – hTDO + heme + tryptophan + inhibitor<br />
+
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
 +
**[[6a4i]], [[7lu7]] – hTDO + heme + Trp + inhibitor<br />
 +
**[[6ud5]] – hTDO + heme + Trp + CO<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[2nw7]] – XcTDO + heme <br />
**[[2nw7]] – XcTDO + heme <br />
 +
**[[7p46]] – XcTDO + heme + kynurenine + Trp<br />
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
-
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + tryptophan <br />
+
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + Trp <br />
-
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + tryptophan derivative<br />
+
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + Trp derivative<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
Line 285: Line 369:
**[[5fdb]] – rCysDO (mutant) <br />
**[[5fdb]] – rCysDO (mutant) <br />
**[[4yni]] – rCysDO <br />
**[[4yni]] – rCysDO <br />
-
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]] – rCysDO (mutant) + Fe+3 <br />
+
**[[6u4s]], [[6u4v]] – rCysDO + Fe+3 <br />
 +
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]], [[6u1m]], [[6u4l]] – rCysDO (mutant) + Fe+3 <br />
 +
**[[4pjy]] – rCysDO + Fe+3 + N3 <br />
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
Line 293: Line 379:
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[2q4s]], [[2atf]] – mCysDO + Ni+2 <br />
**[[2q4s]], [[2atf]] – mCysDO + Ni+2 <br />
 +
**[[6xb9]] – AvCysDO + Fe+3 + hydroxyl propionic acid – ''Azotobacter vinelandii'' <br />
 +
**[[7kov]] – AvCysDO + Fe+3 + SCN<br />
*4-hydroxyphenylpyruvate dioxygenase (HPPD)
*4-hydroxyphenylpyruvate dioxygenase (HPPD)
Line 298: Line 386:
**[[3isq]], [[5ec3]] – hHPPD + Co+2 <br />
**[[3isq]], [[5ec3]] – hHPPD + Co+2 <br />
**[[1sqi]] – rHPPD + Fe+3 + inhibitor - rat<br />
**[[1sqi]] – rHPPD + Fe+3 + inhibitor - rat<br />
-
**[[1cjx]] – HPPD + Fe+2 – ''Pseudomonas fluorescens''<br />
+
**[[7x7l]] – HPPD + Co+2 + inhibitor - maize<br />
 +
**[[1cjx]] – PfHPPD + Fe+2 – ''Pseudomonas fluorescens''<br />
 +
**[[7xnt]] – PfHPPD + Co+2 + inhibitor <br />
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
-
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
+
**[[1sqd]], [[1sp9]], [[6j63]] – AtHPPD + Fe+3 <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
 +
**[[6jx9]], [[6lgt]], [[6m6d]], [[7cjk]], [[7cqr]], [[7cqs]], [[7ezq]], [[7vo8]], [[7v6x]], [[7vc8]], [[7wjj]], [[7x5r]], [[7x5s]], [[7x5u]], [[7x5w]], [[7x5x]], [[7x5y]], [[7x5z]], [[7x62]], [[7x67]], [[7x69]], [[7x6m]], [[7x6n]], [[7x8e]], [[7x8h]], [[8how]] – AtHPPD + Co+2 + inhibitor <br />
 +
**[[7x8c]], [[7x8d]] – AtHPPD + Co + phenylpyruvate <br />
 +
**[[7e0x]] – AtHPPD + Co + phenylacetate <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
Line 310: Line 403:
**[[5hmq]] – PpHPPD + Mg+2 <br />
**[[5hmq]] – PpHPPD + Mg+2 <br />
-
*Quercetin 2,3-dioxygenase (QDO)
+
*Quercetin 2,3-dioxygenase (QDO) or pirin
 +
**[[4ewa]], [[4gul]] – hQDO + Fe+3<br />
 +
**[[1j1l]] – hQDO + Fe+2<br />
 +
**[[4ero]] – hQDO + Co<br />
 +
**[[4ewd]], [[4ewe]] – hQDO + Mn<br />
 +
**[[4hlt]] – hQDO (mutant) + Fe+2<br />
 +
**[[5jct]], [[6h1h]], [[6h1i]], [[6n0j]], [[6n0k]] – hQDO + Fe+3 + inhibitor<br />
 +
**[[3acl]] – hQDO + Fe+2 + inhibitor<br />
**[[1juh]] – AjQDO + Cu+2 – ''Aspergillus japonicus''<br />
**[[1juh]] – AjQDO + Cu+2 – ''Aspergillus japonicus''<br />
**[[2h0v]] – QDO + Fe+3 – ''Bacillus subtilis''<br />
**[[2h0v]] – QDO + Fe+3 – ''Bacillus subtilis''<br />
Line 317: Line 417:
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
**[[1h1m]] – AjQDO + Cu+2 + kaempferol<br />
**[[1h1m]] – AjQDO + Cu+2 + kaempferol<br />
 +
**[[6d0g]], [[6d0p]] – QDO + Mn+2 – ''Acinetobacter baumannii''<br />
 +
**[[6uts]] – EcQDO + Ni+2 <br />
*Taurine/α-ketoglutarate dioxygenase (TauD)
*Taurine/α-ketoglutarate dioxygenase (TauD)
**[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
**[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
 +
**[[6edh]] – EcTauD + VO+2 + taurine + succinate <br />
**[[1otj]] – EcTauD + taurine <br />
**[[1otj]] – EcTauD + taurine <br />
**[[3pvj]], [[3v15]] – PpTauD <br />
**[[3pvj]], [[3v15]] – PpTauD <br />
Line 327: Line 430:
**[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
**[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
**[[3swt]] – HAD + Fe+3 – ''Mycobacterium marinum''<br />
**[[3swt]] – HAD + Fe+3 – ''Mycobacterium marinum''<br />
 +
**[[6l86]] – HAD + Fe+3 + malate – S''treptomyces thioluteus''<br />
**[[5keu]] – BxHAD + Mg+2<br />
**[[5keu]] – BxHAD + Mg+2<br />
**[[5vn6]] – BaHAD + Mg+2<br />
**[[5vn6]] – BaHAD + Mg+2<br />
Line 337: Line 441:
**[[3fe5]] – HAD + Fe+3 - bovine<br />
**[[3fe5]] – HAD + Fe+3 - bovine<br />
**[[1zvf]] – HAD + Ni+2 - yeast<br />
**[[1zvf]] – HAD + Ni+2 - yeast<br />
-
**[[5v28]], [[4r52]] – CmHAD + Fe+2 – ''Cupriavidus metallidurans''<br />
+
**[[5v28]], [[4r52]], [[6vi5]] – CmHAD + Fe+2 – ''Cupriavidus metallidurans''<br />
**[[5v27]], [[5v26]], [[6d60]], [[6bvr]], [[6bvp]] – CmHAD (mutant) + Fe+2 <br />
**[[5v27]], [[5v26]], [[6d60]], [[6bvr]], [[6bvp]] – CmHAD (mutant) + Fe+2 <br />
**[[1yfu]], [[4hvq]], [[4hvr]], [[4i3p]], [[4l2n]] – CmHAD + Fe+3<br />
**[[1yfu]], [[4hvq]], [[4hvr]], [[4i3p]], [[4l2n]] – CmHAD + Fe+3<br />
Line 343: Line 447:
**[[1yfw]] – CmHAD + Fe+3 + O2 + hydroxyanthranilate<br />
**[[1yfw]] – CmHAD + Fe+3 + O2 + hydroxyanthranilate<br />
**[[1yfx]] – CmHAD + Fe+3 + NO + hydroxyanthranilate<br />
**[[1yfx]] – CmHAD + Fe+3 + NO + hydroxyanthranilate<br />
 +
**[[4hsj]] – CmHAD + Fe+2 + picolinic acid<br />
 +
**[[4hsl]], [[6vi7]] – CmHAD + Fe+2 + hydroxyanthranilate<br />
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
 +
**[[6vi6]], [[6vi8]], [[6vi9]], [[6vib]], [[6x11]] – CmHAD + Fe+2 + inhibitor<br />
 +
**[[6via]] – CmHAD + Fe+2 + Fe+3 + OH + dihydroxepine derivative<br />
**[[4wzc]] – HAD + Fe+2 + enedioate derivative – ''Ralstonia metallidurans''<br />
**[[4wzc]] – HAD + Fe+2 + enedioate derivative – ''Ralstonia metallidurans''<br />
-
*Carbazole 1,9a-dioxygenase (CDO)
+
*Carbazole 1,9a-dioxygenase (CDO); Domains – ferredoxin 1-115; terminal oxygenase 1-384
**[[1vck]] – CDO ferredoxin component + Fe+3 + Fe2S2 – ''Pseudomonas resinovorans''<br />
**[[1vck]] – CDO ferredoxin component + Fe+3 + Fe2S2 – ''Pseudomonas resinovorans''<br />
-
**[[2de5]], [[2de6]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 – ''Janthinobacterium''<br />
+
**[[2de5]], [[2de6]], [[6llf]], [[6llh]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 – ''Janthinobacterium''<br />
**[[2de7]], [[3vmg]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole<br />
**[[2de7]], [[3vmg]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole<br />
 +
**[[7c3b]] – JaCDO ferredoxin reductase component + Ni + Fe2S2 <br />
 +
**[[7c3a]] – JaCDO ferredoxin reductase component + Ni + Fe2S2 + FAD<br />
 +
**[[1ww9]], [[6llk]], [[7bug]] – JaCDO terminal oxygenase component + Fe+2 + Fe2S2 <br />
 +
**[[6ll1]] – JaCDO terminal oxygenase component + O2 + Fe2S2 <br />
 +
**[[6ll0]], [[6ll4]] – JaCDO terminal oxygenase component + Fe+2 + Fe2S2 + carbazole derivative<br />
 +
**[[7bui]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 <br />
**[[3vmh]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + O2<br />
**[[3vmh]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + O2<br />
**[[4nb8]], [[4nb9]], [[4nba]], [[4nbb]], [[4nbc]], [[4nbd]], [[4nbe]], [[4nbf]], [[4nbg]], [[4nbh]] – JaCDO ferredoxin and terminal oxygenase components (mutant) + Fe+2 + Fe2S2 <br />
**[[4nb8]], [[4nb9]], [[4nba]], [[4nbb]], [[4nbc]], [[4nbd]], [[4nbe]], [[4nbf]], [[4nbg]], [[4nbh]] – JaCDO ferredoxin and terminal oxygenase components (mutant) + Fe+2 + Fe2S2 <br />
**[[3vmi]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole + O2<br />
**[[3vmi]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole + O2<br />
**[[3gcf]] – CDO terminal oxygenase component + Fe+2 + Fe2S2 – ''Nocardioides aromaticivorans''<br />
**[[3gcf]] – CDO terminal oxygenase component + Fe+2 + Fe2S2 – ''Nocardioides aromaticivorans''<br />
-
**[[3gkq]] – SpCDO terminal oxygenase component + Fe+2 + Fe2S2 <br />
+
**[[3gce]] – NaCDO ferredoxin component + Fe+2 + Fe2S2 <br />
 +
**[[3gkq]] –Na SpCDO terminal oxygenase component + Fe+2 + Fe2S2 <br />
*Homogentisate 1,2-dioxygenase (HGDO)
*Homogentisate 1,2-dioxygenase (HGDO)
Line 397: Line 512:
**[[4qb5]] – GBD – ''Albidiferax ferrireducens''<br />
**[[4qb5]] – GBD – ''Albidiferax ferrireducens''<br />
**[[4rt5]] – GBD – ''Planctomyces limnophilus''<br />
**[[4rt5]] – GBD – ''Planctomyces limnophilus''<br />
-
**[[5uhj]], [[5ujp]] – GBD + Ni+2 – ''Streptomyces''<br />
+
**[[2np9]], [[5ump]], [[5umq]] – StGBD – ''Streptomyces''<br />
 +
**[[5uhj]], [[5ujp]] – GBD + Ni+2 <br />
 +
**[[6bbx]] – StGBD + inhibitor <br />
 +
**[[5umw]], [[5umx]], [[5umw]] – StGBD + riboflavin<br />
 +
**[[5umy]], [[5w27]] – StGBD + antibiotics<br />
**[[5c4p]], [[5c68]], [[5cb9]] – TcGBD + Ni+2 – ''Thermomonospora curvata''<br />
**[[5c4p]], [[5c68]], [[5cb9]] – TcGBD + Ni+2 – ''Thermomonospora curvata''<br />
**[[5c6x]] – TcGBD + Co+2 <br />
**[[5c6x]] – TcGBD + Co+2 <br />
-
**[[4z04]] – GBD + Zn+2 + glutathione – ''Brucella abortu''s <br />
+
**[[5v0f]] – TcGBD + Fe+3 + roxasone <br />
 +
**[[4z04]] – GBD + Zn+2 + glutathione – ''Brucella abortus'' <br />
 +
**[[6a4x]] – GBD + Fe+2 – ''Streptomyces curacoi''<br />
* Procollagen-proline dioxygenase (PPD)
* Procollagen-proline dioxygenase (PPD)
Line 406: Line 527:
**[[5iat]] – BaPDD – ''Bacillus anthracis''<br />
**[[5iat]] – BaPDD – ''Bacillus anthracis''<br />
**[[5iax]] – BaPDD + Co+2 + oxoglutarate <br />
**[[5iax]] – BaPDD + Co+2 + oxoglutarate <br />
 +
**[[5v7y]] – BaPDD + Co+2 + oxoglutarate + imidazole<br />
**[[5iav]] – BaPDD + Co+2 + malonate<br />
**[[5iav]] – BaPDD + Co+2 + malonate<br />
* 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
* 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
 +
**[[7jxg]] – hKMTPD + Fe+2<br />
 +
**[[4qgn]] – hKMTPD + Fe+3<br />
**[[5i8s]] – mKMTPD + Ni+2 + pentanoate + valerate<br />
**[[5i8s]] – mKMTPD + Ni+2 + pentanoate + valerate<br />
**[[5i8t]] – mKMTPD + Ni+2 + lactate <br />
**[[5i8t]] – mKMTPD + Ni+2 + lactate <br />
Line 415: Line 539:
**[[5i91]] – mKMTPD + Ni+2 + keto-methylthio-butyrate<br />
**[[5i91]] – mKMTPD + Ni+2 + keto-methylthio-butyrate<br />
**[[5i93]] – mKMTPD + Ni+2 + keto-pentanoate<br />
**[[5i93]] – mKMTPD + Ni+2 + keto-pentanoate<br />
-
**[[4qgn]] – hKMTPD + Fe+3<br />
 
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
* Indoleamine 2,3-dioxygenase 1 (IAD)
* Indoleamine 2,3-dioxygenase 1 (IAD)
-
**[[6azu]] – hIAD + heme <br />
+
**[[6azu]], [[7a62]] – hIAD + heme <br />
-
**[[6e45]], [[6e44]] – hIAD 1 (mutant) + heme <br />
+
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
-
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]] – hIAD + heme + imidazole derivative<br />
+
**[[2d0t]], [[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]], [[7ah4]], [[7ah5]], [[7ah6]] – hIAD + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
-
**[[6azw]], [[6azv]] – hIAD + inhibitor<br />
+
**[[6azw]], [[6azv]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]] – hIAD + inhibitor<br />
-
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]] – hIAD + heme + inhibitor<br />
+
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
 +
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]], [[7e0o]], [[7e0p]], [[7e0q]], [[7e0s]], [[7e0t]], [[7e0u]], [[7m63]], [[7m7d]], [[7rrb]], [[7rrc]], [[7rrd]], [[7zv3]], [[8abx]] – hIAD + heme + inhibitor<br />
 +
**[[6ubp]] – hIAD 1 + heme + CO + Trp<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
 +
**[[7nge]], [[7p0n]], [[7p0r]] – hIAD 1 (mutant) + heme + kynurenine + Trp<br />
**[[5wmv]] – hIAD + heme + CN + indole derivative + Trp<br />
**[[5wmv]] – hIAD + heme + CN + indole derivative + Trp<br />
**[[5wmx]] – hIAD (mutant) + heme + CN + indole derivative + Trp<br />
**[[5wmx]] – hIAD (mutant) + heme + CN + indole derivative + Trp<br />
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
**[[6e46]] – hIAD 1 + heme + Trp<br />
**[[6e46]] – hIAD 1 + heme + Trp<br />
-
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
 
* Thymine dioxygenase (TD)
* Thymine dioxygenase (TD)
Line 442: Line 567:
**[[5c3s]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative <br />
**[[5c3s]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative <br />
**[[5c3r]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative + uracil derivative<br />
**[[5c3r]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative + uracil derivative<br />
 +
**[[2xse]], [[8bbm]] – TD DBD – ''Leishmania tarentulae'' <br />
* 2,4’-dihydroxyacetophenone dioxygenase (APD)
* 2,4’-dihydroxyacetophenone dioxygenase (APD)
Line 457: Line 583:
**[[6d3m]] – ShFTTD + Co+2 + oxoglutarate + quinoxalin<br />
**[[6d3m]] – ShFTTD + Co+2 + oxoglutarate + quinoxalin<br />
**[[6d3i]], [[6d3h]] – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative<br />
**[[6d3i]], [[6d3h]] – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative<br />
 +
 +
*Ring-cleavage dioxygenase (RCD)
 +
 +
**[[5vg2]] – RCD + Fe+3 – spider mite<br />
 +
**[[5hl4]] – SmRCD + Fe+3 + Fe2S2 – ''Sinorhizobium melioli<''br />
 +
**[[3vcp]] – SmRCD + Fe+3 + Fe2S2 + Pro <br />
 +
**[[2ckf]] – SphRCD + Fe+3 + Fe2S2 - ''Sphingomonas'' <br />
 +
 +
*L-dopa dioxygenase (LDD)
 +
 +
**[[6on1]] – SsLDD + Fe+3 – ''Streptomyces sclerotialus''<br />
 +
**[[6on3]] – SsLDD + Fe+3 + Phe derivative<br />
 +
 +
*Kanamycin B dioxygenase (KBD)
 +
 +
**[[6s0r]], [[6s0t]], [[7cl2]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
 +
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
 +
**[[6s0w]], [[7cl3]] – SkKBD + Ni+2 + kanamycin<br />
 +
**[[6s0u]] – SkKBD + Ni+2 + oxoglutarate<br />
 +
**[[6s0s]] – SkKBD + Ni+2 + ribostamycin + oxoglutarate<br />
 +
**[[7cl4]] – SkKBD + Ni+2 + oxalylglycine<br />
 +
**[[7cl5]] – SkKBD + Ni+2 + oxalylglycine + kanamycin<br />
 +
**[[7cl6]] – SkKBD + Ni+2 + oxalylglycine + neamine<br />
 +
 +
*Phytanoyl-CoA dioxygenase or trans-3/4-proline-hydroxylase H11
 +
 +
**[[2opw]] – hPhyH <br />
 +
**[[2a1x]] – hPhyH + Fe+2 + oxoglutarate <br />
 +
**[[7e05]] – ubPhyH – uncultured bacteria <br />
 +
**[[7dzz]] – ubPhyH + Pro <br />
 +
**[[7e06]] – ubPhyH + Fe+3 + oxoglutarate <br />
 +
**[[7e01]], [[7e08]], [[7e09]] – ubPhyH + Pro derivative <br />
 +
**[[7e00]] – ubPhyH + oxoglutarate + Pro <br />
 +
**[[7e07]] – ubPhyH + Fe+3 + oxoglutarate + Pro <br />
 +
**[[7dt0]] – ubPhyH (mutant) + Fe+3 + oxoglutarate + Pro derivative <br />
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

3D structures of dioxygenase

Updated on 29-January-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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