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Dioxygenase 3D structures

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Current revision (11:15, 29 January 2023) (edit) (undo)
 
Line 267: 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 303: 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 344: 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 367: 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 381: 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 396: 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 431: 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 438: 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 488: 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 521: 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 542: 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 561: 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 569: 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 577: 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

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