Dioxygenase 3D structures: Difference between revisions

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**[[1dlm]], [[1dlq]] – AcCTD + Fe+3 <br />
**[[1dlm]], [[1dlq]] – AcCTD + Fe+3 <br />
**[[2azq]] – PpCTD + Fe+3 <br />
**[[2azq]] – PpCTD + Fe+3 <br />
**[[5umh]] – CTD – ''Burkholderia multivorans''<br />
**[[5umh]], [[9dr5]], [[9dr6]] – BmCTD + Zn+2 – ''Burkholderia multivorans''<br />
**[[9dr8]] – BmCTD + Fe+2
**[[5td3]] – CTD – ''Burkholderia vietnamiensis''<br />
**[[5td3]] – CTD – ''Burkholderia vietnamiensis''<br />
**[[5vxt]] – BaCTD + Fe+3 + catechol – ''Burkholderia ambifaria''<br />
**[[5vxt]] – BaCTD + Fe+3 + catechol – ''Burkholderia ambifaria''<br />
Line 48: Line 49:
**[[3hj8]], [[3hjq]], [[3hjs]], [[3i4v]], [[3i4y]], [[3i51]] – RoCTD + Fe+3 + catechol derivative<br />
**[[3hj8]], [[3hjq]], [[3hjs]], [[3i4v]], [[3i4y]], [[3i51]] – RoCTD + Fe+3 + catechol derivative<br />
**[[3hhx]] – RoCTD + Fe+3 + pyrogallol<br />
**[[3hhx]] – RoCTD + Fe+3 + pyrogallol<br />
**[[9dra]] – BmCTD + Fe+3 + catechol derivative<br />
**[[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 />
Line 65: Line 67:
**[[2boy]] – RoCCTD + Fe+3 + benzhydroxamate<br />
**[[2boy]] – RoCCTD + Fe+3 + benzhydroxamate<br />


*Hydroxyquinol 1,2-dioxygenase (HQD)
*Hydroxyquinol 1,2-dioxygenase (HQX) or hydroquinone dioxygenase


**[[1tmx]] – PsiHQD + Fe+3 – ''Pimelobacter simplex''<br />
**[[1tmx]] – PsiHDX + Fe+3 – ''Pimelobacter simplex''<br />
**[[4zxd]] – PsHQD - ''Pseudomonas''<br />
**[[4zxd]] – PsHDX - ''Pseudomonas''<br />
**[[4zxa]] – PsHQD + Cd+2 + benzonitrile <br />
**[[4zxa]] – PsHDX + Cd+2 + benzonitrile <br />
**[[4zxc]] – PsHQD + Fe+3 <br />
**[[4zxc]] – PsHDX + Fe+3 <br />
**[[5m22]] – SpHQD + Fe+3 <br />
**[[5m22]] – SpHDX + Fe+3 <br />
**[[5m4o]] – SpHQD + Fe+3 + nitrophenol<br />
**[[5m4o]] – SpHDX + Fe+3 + nitrophenol<br />
**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
**[[5m26]] – SpHDX + Fe+3 + hydroquinone derivative<br />
**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
**[[5m21]] – SpHDX + Fe+3 + hydroxybenzoate<br />
**[[3n9t]] – PpHDX + Fe+3 <br />
**[[8r2w]] – HDX + Fe+3 + phosphatidylethanolamine – ''Trametes versicolor''<br />
**[[8r2v]] – HDX + Fe+3 + phosphatidylethanolamine – ''Gelatoporia subvermispora"<br />
**[[8r2x]] - RjHDX + Fe+3 + phosphatidylethanolamine - ''Rhodococcus jostii''<br />
**[[8z4q]] - AwHDX + Fe+3 – ''Aspergillus westerdijkiae''<br />
**[[8z4r]], [[8z4s]] - AwHDX + Fe+3 + substrate<br />


*Nitrobenzene dioxygenase (NBDO)
*Nitrobenzene dioxygenase (NBDO)
Line 90: Line 98:
**[[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 />
Line 129: Line 137:
**[[6ie3]] – hAlkbh1 + Mn <br />
**[[6ie3]] – hAlkbh1 + Mn <br />
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
**[[6ksf]] – mAlkbh1 catalytic domain + succinate + DNA<br />
**[[8k62]] – hAlkbh1 + Mn + inhibitor <br />
**[[6imc]] – hAlkbh1 catalytic domain + Mn + oxalylglycine <br />
**[[6ksf]] – mAlkbh1 catalytic domain 4-384 + succinate + DNA<br />
**[[6l94]] – mAlkbh1 catalytic domain + Fe+2<br />
**[[8jnk]], [[8jnr]] – hAlkbh3 + DNA <br />
**[[9ncz]] – hAlkbh3 + Mn + oxoglutarate <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 135: Line 149:
**[[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 144: Line 163:
* α-ketoglutarate-dependent dioxygenase (Fto)
* α-ketoglutarate-dependent dioxygenase (Fto)


**[[9kni]] – hFto + inhibitor <br />
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
**[[7ckk]] – hFto + inhibitor + oxalylglycine<br />
**[[8it9]] – hFto + inhibitor + Akg<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 150: Line 172:
**[[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]] – hFto + Zn+2 + inhibitor<br />
**[[6aej]], [[7e8z]] – hFto + Zn+2 + inhibitor<br />
**[[6ak4]] – hFto (mutant) + 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 179: Line 201:
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
**[[6jzm]], [[6k30]], [[6kd9]] – AnAsqJ + Fe+3 + cyclopeptin + succinate<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 />
**[[7v2u]], [[7v3o]], [[8hiv]] – SoBcmB + Fe+2 + Akg – ''Streptomyces ossamyceticus''<br />
**[[7v2t]], [[7v2x]], [[7v34]], [[7v36]], [[7v3e]] – SoBcmB + Fe+2 + Akg + inhibitor<br />
**[[7v3n]] – SoBcmB (mutant) + Fe+2 + Akg + inhibitor<br />
**[[7wpy]] – AsqJ (mutant) + Fe+3 – ''Aspergillus stellatus''<br />
* Fe(II)/(alpha)-ketoglutarate-dependent dioxygenase (PrhA)
**[[8s7b] – riHis1 + Mn+2 + oxoglutarate <br />
**[[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 />
**[[7vbq]], [[7vbr]] – TlxI – ''Talaromyces purpureogenus''<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 188: Line 244:


**[[6asd]] – hTET1 + DNA  <br />
**[[6asd]] – hTET1 + DNA  <br />
**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + 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]], [[8jkk]] – CcTET + DNA – ''Coprinopsis cinerea''<br />
**[[7vpn]] – CcTET + oxalylglycine + Mn<br />


*'''Dioxygenase extradiol family'''
*'''Dioxygenase extradiol family'''
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**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
**[[6l3w]] – MPC + Fe+3 - metagenome<br />
**[[6l3w]] – MPC + Fe+3 - metagenome<br />
**[[7q2a]] - RjMPC + Fe+3 + catechol derivative <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 263: Line 324:
**[[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 303: Line 365:
**[[4pw8]] - hTDO + Co+2  <br />
**[[4pw8]] - hTDO + Co+2  <br />
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
**[[8r5q]], [[8r5r]], [[8vug]], [[8vzv]], [[8w1h]], [[8w2k]], [[9at2]] – hTDO + inhibitor<br />
**[[6a4i]] – hTDO + heme + Trp + inhibitor<br />
**[[6pyy]], [[6pyz]], [[6vbn]], [[9b17]], [[9b1q]] – hTDO + heme + inhibitor<br />
**[[6a4i]], [[7lu7]] – hTDO + heme + Trp + inhibitor<br />
**[[6ud5]] – hTDO + heme + Trp + CO<br />
**[[6ud5]] – hTDO + heme + Trp + CO<br />
**[[7ui3]], [[8qv7]] – hTDO + Trp derivative<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[2nw7]] – XcTDO + heme <br />
**[[2nw7]] – XcTDO + heme <br />
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
**[[7p46]] – XcTDO + heme + kynurenine + Trp<br />
**[[4hka]] – DmTDO + heme – ''Drosophila melanogaster''<br />
**[[9foz]] – DmTDO + heme + inhibitor
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + Trp <br />
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + Trp <br />
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + Trp derivative<br />
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + Trp derivative<br />
**[[8vyy]] – StTDO + heme + Trp derivative<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />


*Cysteine dioxygenase type I (CysDO)
*Cysteine dioxygenase type I (CDO) or ergothioneine dioxygenase


**[[6bgm]], [[6bgf]], [[6e87]] – hCysDO + Fe+2 <br />
**[[6bgm]], [[6bgf]], [[6e87]] – hCDO + Fe+2 <br />
**[[2ic1]], [[6n42]] – hCysDO + Fe+2 + cysteine<br />
**[[2ic1]], [[6n42]] – hCDO + Fe+2 + cysteine<br />
**[[6cdh]], [[6bpw]], [[6bpu]], [[6bpt]] – hCysDO + Fe+2 + Tyr derivative<br />
**[[6cdh]], [[6bpw]], [[6bpu]], [[6bpt]] – hCDO + Fe+2 + Tyr derivative<br />
**[[6cdn]], [[6bpx]], [[6bpv]], [[6bps]] – hCysDO + Fe+2 + cysteine + Tyr derivative<br />
**[[6cdn]], [[6bpx]], [[6bpv]], [[6bps]] – hCDO + Fe+2 + cysteine + Tyr derivative<br />
**[[6bpr]] – hCysDO + Fe+3 + cysteine + Tyr derivative + NO<br />
**[[6bpr]] – hCDO + Fe+3 + cysteine + Tyr derivative + NO<br />
**[[6n43]] – hCysDO + Fe+3 + cysteine + NO<br />
**[[6n43]] – hCDO + Fe+3 + cysteine + NO<br />
**[[2gh2]], [[4ieo]], [[4iep]], [[4ieq]], [[4ier]], [[4ies]], [[4iet]], [[4ieu]], [[4iev]], [[4iew]], [[4iex]], [[4iey]], [[4iez]], [[4jtn]], [[4jto]], [[4kwj]], [[4kwk]], [[4kwl]], [[2b5h]] – rCysDO + Fe+2 – rat <br />
**[[8vl9]], [[8vlb]] – hCDO + Fe+3 + VHL + elongin b,c<br />
**[[4ubg]], [[4ubh]], [[5ezw]], [[5efu]], [[4ysf]], [[4yyo]] – rCysDO (mutant) + Fe+2  <br />
**[[2gh2]], [[4ieo]], [[4iep]], [[4ieq]], [[4ier]], [[4ies]], [[4iet]], [[4ieu]], [[4iev]], [[4iew]], [[4iex]], [[4iey]], [[4iez]], [[4jtn]], [[4jto]], [[4kwj]], [[4kwk]], [[4kwl]], [[2b5h]] – rCDO + Fe+2 – rat <br />
**[[5fdb]] – rCysDO (mutant)  <br />
**[[4ubg]], [[4ubh]], [[5ezw]], [[5efu]], [[4ysf]], [[4yyo]] – rCDO (mutant) + Fe+2  <br />
**[[4yni]] – rCysDO <br />
**[[5fdb]] – rCDO (mutant)  <br />
**[[6u4s]], [[6u4v]] – rCysDO + Fe+3  <br />
**[[4yni]] – rCDO <br />
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]], [[6u1m]], [[6u4l]] – rCysDO (mutant) + Fe+3  <br />
**[[6u4s]], [[6u4v]] – rCDO + Fe+3  <br />
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]], [[6u1m]], [[6u4l]] – rCDO (mutant) + Fe+3  <br />
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
**[[4pjy]] – rCDO + Fe+3 + N3 <br />
**[[5i0u]], [[5i0t]], [[5i0s]], [[4xf4]], [[4xf9]], [[4xfa]], [[4piz]] – rCysDO + Fe+3 + cysteine derivative<br />
**[[3eln]] – rCDO + Fe+2 + cysteine derivative<br />
**[[4xf0]], [[4xf1]], [[4xfg]], [[4xfh]], [[4xfi]], [[4piy]] – rCysDO (mutant) + Fe+3 + cysteine derivative<br />
**[[4z82]] – rCDO (mutant) + Fe+2 + cysteine derivative<br />
**[[4xez]], [[4xff]] – rCysDO (mutant) + Fe+3 + inhibitor <br />
**[[5i0u]], [[5i0t]], [[5i0s]], [[4xf4]], [[4xf9]], [[4xfa]], [[4piz]] – rCDO + Fe+3 + cysteine derivative<br />
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[4xf0]], [[4xf1]], [[4xfg]], [[4xfh]], [[4xfi]], [[4piy]] – rCDO (mutant) + Fe+3 + cysteine derivative<br />
**[[2q4s]], [[2atf]] – mCysDO + Ni+2  <br />
**[[4xez]], [[4xff]] – rCDO (mutant) + Fe+3 + inhibitor <br />
**[[6xb9]] – AvCysDO + Fe+3 + hydroxyl propionic acid – ''Azotobacter vinelandii''  <br />
**[[4xf3]] – rCDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[7kov]] – AvCysDO + Fe+3 + SCN<br />
**[[2q4s]], [[2atf]] – mCDO + Ni+2  <br />
**[[6xb9]] – AvCDO + Fe+3 + hydroxyl propionic acid – ''Azotobacter vinelandii''  <br />
**[[7kov]] – AvCDO + Fe+3 + SCN<br />
**[[8qfm]], [[8qfn]], [[8qfp]] – TtCDO + Mn+2 – ''Thermocatellispora tenchongensis''<br />
**[[8qfo]], [[8qfq]] – TtCDO (mutant) + Mn+2 <br />
**[[8qfl]] – TtCDO + Fe+3 <br />
**[[8qfr]] – TtCDO + Ni+2 + inhibitor <br />


*4-hydroxyphenylpyruvate dioxygenase (HPPD)
*4-hydroxyphenylpyruvate dioxygenase (HPPD) or Acmp1


**[[3isq]], [[5ec3]] – hHPPD + Co+2 <br />
**[[3isq]], [[5ec3]] – hHPPD + Co+2 <br />
**[[1sqi]] – rHPPD + Fe+3 + inhibitor - rat<br />
**[[8im2]] – hHPPD + Co+2 + inhibitor<br />
**[[1cjx]] – HPPD + Fe+2 – ''Pseudomonas fluorescens''<br />
**[[1sqi]] – rHPPD + Fe+3 + inhibitor <br />
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[7x7l]] – HPPD + Co+2 + inhibitor - maize<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
**[[6jx9]], [[6lgt]], [[6m6d]], [[7cjk]], [[7cqr]], [[7cqs]], [[7ezq]], [[7vo8]], [[7v6x]], [[7vc8]], [[7wj8]], [[7wjj]], [[7wjk]], [[7x5r]], [[7x5s]], [[7x5u]], [[7x5w]], [[7x5x]], [[7x5y]], [[7x5z]], [[7x62]], [[7x64]], [[7x67]], [[7x69]], [[7x6m]], [[7x6n]], [[7x8e]], [[7x8h]], [[7x8i]], [[7xvh]], [[8gwd]], [[8h6a]], [[8h6b]], [[8how]], [[8hwr]], [[8hx2]], [[8hx4]], [[8hxf]], [[8hxg]], [[8hxh]], [[8hym]], [[8hyo]], [[8hyp]], [[8hys]], [[8hz6]], [[8hz7]], [[8hz9]], [[8hza]], [[8hzu]], [[8i0g]], [[8i0y]], [[8i2u]], [[8i15]], [[8i2p]], [[8i2s]], [[8i36]], [[8im3]], [[8iok]], [[8j3c]], [[8j8w]], [[8j8x]], [[8who]], [[8whp]], [[8whq]], [[8wi6]], [[8wl0]], [[8wpc]], [[8wpd]], [[8wqm]], [[8x42]]. [[8x5c]], [[8x68]], [[8x69]], [[8x6a]], [[8x6c]], [[8xhj]], [[8xib]], [[8xii]], [[8xin]], [[8xlw]], [[8xlx]], [[8xqv]], [[8xqz]], [[8xqy]], [[8xr0]], [8xtv]], [[8xu9]], [[8xuc]], [[8xue]], [[8xug]] – AtHPPD + Co+2 + inhibitor<br />
**[[1sqd]], [[1sp9]], [[6j63]] – AtHPPD + Fe+3 <br />
**[[8wjz]], [[8wk2]] – AtHPPD (mutant) + Co+2 + inhibitor<br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
**[[8xly]] – AtHPPD + Co+2 + Phe<br />
**[[6jx9]], [[6lgt]], [[6m6d]] – AtHPPD + Co+2 + inhibitor <br />
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] – AtHPPD + Fe+3 + 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 />
**[[5dhw]], [[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
**[[5yy7]], [[5yy6]], [[5ywk]] – AtHPPD + Co+2 + benquitrione <br />  
**[[5yy7]], [[5yy6]], [[5ywk]] – AtHPPD + Co+2 + benquitrione <br />  
**[[5ywi]] – AtHPPD (mutant) + Co+2 + NTBC <br />
**[[5ywi]] – AtHPPD (mutant) + Co+2 + NTBC <br />  
**[[1sp8]] – HPPD + Fe+2 – corn<br />
**[[1sp8]] – HPPD + Fe+2 – corn<br />
**[[7yvv]] – HPPD + Fe+3 - ''Amycoaltopsis'' <br />
**[[1cjx]] – PfHPPD + Fe+2 – ''Pseudomonas fluorescens''<br />
**[[7xnt]] – PfHPPD + Co+2 + inhibitor <br />
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
**[[5hmq]] – PpHPPD + Mg+2 <br />
**[[5hmq]] – PpHPPD + Mg+2 <br />
**[[8jbw]] – HPPD + Co+2 + usnic acid – ''Zymoseptoria tritici''<br />


*Quercetin 2,3-dioxygenase (QDO) or pirin
*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]] – BsQDO + Fe+3 – ''Bacillus subtilis''<br />
**[[8hfb]] – BsQDO (mutant) + Ni+2 <br />
**[[1gqg]], [[1gqh]] – AjQDO + Cu+2 + inhibitor<br />
**[[1gqg]], [[1gqh]] – AjQDO + Cu+2 + inhibitor<br />
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
Line 391: Line 481:
**[[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 />
**[[6vi7]] – CmHAD + Fe+2 + 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 />  
Line 398: Line 489:
**[[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 448: Line 546:
**[[4qb5]] – GBD – ''Albidiferax ferrireducens''<br />
**[[4qb5]] – GBD – ''Albidiferax ferrireducens''<br />
**[[4rt5]] – GBD – ''Planctomyces limnophilus''<br />
**[[4rt5]] – GBD – ''Planctomyces limnophilus''<br />
**[[5ump]], [[5umq]] – StGBD – ''Streptomyces''<br />
**[[2np9]], [[5ump]], [[5umq]] – StGBD – ''Streptomyces''<br />
**[[5uhj]], [[5ujp]] – GBD + Ni+2 <br />
**[[5uhj]], [[5ujp]] – GBD + Ni+2 <br />
**[[6bbx]] – StGBD + inhibitor <br />
**[[6bbx]] – StGBD + inhibitor <br />
Line 477: Line 575:
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />


* Indoleamine 2,3-dioxygenase 1 (IAD)
* Indoleamine 2,3-dioxygenase 1 (IDO)


**[[6azu]], [[7a62]] – hIAD + heme <br />
**[[6azu]], [[7a62]] – hIDO 1 + heme <br />
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
**[[6e45]], [[6e44]] – hIDO 1 (mutant) + heme <br />
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]], [[7ah4]], [[7ah5]], [[7ah6]] – hIAD + heme + imidazole derivative<br />
**[[2d0t]], [[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[4pk6]], [[5xe1]], [[5wn8]], [[7ah4]], [[7ah5]], [[7ah6]], [[8u5i]] – hIDO 1 + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIDO 1 (mutant) + heme + imidazole derivative<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
**[[7yxt]] – hIDO 1 (mutant) + heme + O2<br />
**[[6azw]], [[6azv]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]] – hIAD + inhibitor<br />
**[[6f0a]] – hIDO 1 + heme + imidazole derivative + Ala<br />
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
**[[6azw]], [[6azv]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]], [[[8i7l]], [8fur]], [[9ese]], [[9esg]], [[9etv]], [[9ew0]], [[9ezj]] – hIDO 1 + inhibitor<br />
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]] – hIAD + heme + inhibitor<br />
**[[6e43]] – hIDO 1 (mutant) + inhibitor<br />
**[[6ubp]] – hIAD 1 + heme + CO + Trp<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]] – hIDO 1 + heme + inhibitor<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[6ubp]] – hIDO 1 + heme + CO + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
**[[5wmu]], [[6e35]] – hIDO 1 + heme + CN + Trp<br />
**[[5wmv]] – hIAD + heme + CN + indole derivative + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIDO 1 (mutant) + heme + CN + Trp<br />
**[[5wmx]] – hIAD (mutant) + heme + CN + indole derivative + Trp<br />
**[[7z2l]] – hIDO 1 (mutant) + heme + kynurenine + O2<br />
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
**[[7nge]], [[7p0n]], [[7p0r]] – hIDO 1 (mutant) + heme + kynurenine + Trp<br />
**[[6e46]] – hIAD 1 + heme + Trp<br />
**[[5wmv]] – hIDO 1 + heme + CN + indole derivative + Trp<br />
**[[5wmx]] – hIDO 1 (mutant) + heme + CN + indole derivative + Trp<br />
**[[5whr]] – hIDO 1 + heme + pyrrolydine derivative <br />
**[[6e46]] – hIDO 1 + heme + Trp<br />
**[[9esd]], [[9esf]] – DmIDO + inhibitor<br />


* Thymine dioxygenase (TD)
* Thymine dioxygenase (TD)
Line 502: Line 604:
**[[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 521: Line 624:


**[[5vg2]] – RCD + Fe+3 – spider mite<br />
**[[5vg2]] – RCD + Fe+3 – spider mite<br />
**[[5hl4]] – SmRCD + Fe+3 + Fe2S2 – ''Sinorhizobium melioli''<br />
**[[3vcp]] – SmRCD + Fe+3 + Fe2S2 + Pro <br />
**[[6xma]] – SphRCD + Fe+3 - ''Sphingomonas''  <br />
**[[2ckf]] – SphRCD + Fe+3 + Fe2S2 <br />
**[[8t1t]], [[9chk]] – SoRCD + SAM + TP-methylase – ''Shewanella oneidensis'' <br />
**[[9ch0]], [[9ch1]], [[9ch2]], [[9ch3]], [[9ch5]], [[9ch7]] – SoRCD + SAH + TP-methylase <br />
**[[9cgw]] – SoRCD (mutant) + Zn+2 + TP-methylase <br />


*L-dopa dioxygenase (LDD)
*L-dopa dioxygenase (LDD)
Line 529: Line 639:
*Kanamycin B dioxygenase (KBD)
*Kanamycin B dioxygenase (KBD)


**[[6s0r]], [[6s0t]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
**[[6s0r]], [[6s0t]], [[7cl2]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
**[[6s0w]], [[7cl3]] – SkKBD + Ni+2 + kanamycin<br />
**[[6s0w]], [[7cl3]] – SkKBD + Ni+2 + kanamycin<br />
Line 537: Line 647:
**[[7cl5]] – SkKBD + Ni+2 + oxalylglycine + kanamycin<br />
**[[7cl5]] – SkKBD + Ni+2 + oxalylglycine + kanamycin<br />
**[[7cl6]] – SkKBD + Ni+2 + oxalylglycine + neamine<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]], [[8h7t]] – ubPhyH – uncultured bacteria <br />
**[[7dzz]], [[8h81]], [[8h85]] – ubPhyH + Pro <br />
**[[8h7v]] – ubPhyH + Akg <br />
**[[8h7y]] – ubPhyH + Akg + 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]]

Latest revision as of 16:25, 16 April 2025

3D structures of dioxygenase

Updated on 16-April-2025

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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