This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Dioxygenase 3D structures

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:15, 29 January 2023) (edit) (undo)
 
(One intermediate revision not shown.)
Line 75: 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 90: 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 />
Line 129: Line 130:
**[[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 />
+
**[[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 135: 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 145: 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 150: 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]] – 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 188:
**[[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 />
 +
 +
* 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 188: Line 225:
**[[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]] – CcTET + DNA – ''Coprinopsis cinerea''<br />
 +
**[[7vpn]] – CcTET + oxalylglycine + Mn<br />
*'''Dioxygenase extradiol family'''
*'''Dioxygenase extradiol family'''
Line 227: Line 267:
**[[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]] - 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 263: 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 304: Line 347:
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
-
**[[6a4i]] – hTDO + heme + Trp + inhibitor<br />
+
**[[6a4i]], [[7lu7]] – hTDO + heme + Trp + inhibitor<br />
**[[6ud5]] – hTDO + heme + Trp + CO<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 + Trp <br />
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + Trp <br />
Line 327: Line 371:
**[[6u4s]], [[6u4v]] – rCysDO + Fe+3 <br />
**[[6u4s]], [[6u4v]] – rCysDO + Fe+3 <br />
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]], [[6u1m]], [[6u4l]] – rCysDO (mutant) + 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 341: 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]], [[6j63]] – 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]] – AtHPPD + Co+2 + 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 356: Line 405:
*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]] – QDO + Fe+3 – ''Bacillus subtilis''<br />
Line 391: 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 />
-
**[[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 455:
**[[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 512:
**[[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 481: Line 545:
**[[6azu]], [[7a62]] – hIAD + heme <br />
**[[6azu]], [[7a62]] – hIAD + heme <br />
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
-
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]], [[7ah4]], [[7ah5]], [[7ah6]] – 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]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]] – hIAD + inhibitor<br />
**[[6azw]], [[6azv]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]] – hIAD + inhibitor<br />
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
-
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]] – hIAD + heme + 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 />
**[[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 />
Line 502: 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 521: Line 587:
**[[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 />
 +
**[[2ckf]] – SphRCD + Fe+3 + Fe2S2 - ''Sphingomonas'' <br />
*L-dopa dioxygenase (LDD)
*L-dopa dioxygenase (LDD)
Line 529: Line 598:
*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 606:
**[[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]] – 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

Retrieved from "http://52.214.119.220/wiki/index.php/Dioxygenase_3D_structures"
Personal tools