Dioxygenase

spinqualitylabelsall models Solved Crystal Structure of Hyperactive Catechol Dioxygenase Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Dioxygenases cleave the aromatic rings of their substrates by inserting two oxygen atoms, thus degrading these compounds. The dioxygenases are divided into 2 groups according to their mode of ring scission. The intradiol enzymes use Fe+3 as cofactor and cleave the substrate between 2 hydroxyl groups. The extradiol enzymes use Fe+2 as cofactor and cleave the substrate between a hydroxylated carbon and a non-hydroxylated one. Protocatechuate 3,4-dioxygenase (PCD), belongs to the intradiol family and catalyzes the oxygenation of dihydroxybenzoate (DHB) to 3-carboxy-muconate. PCD participates in the aromatic compound benzoate degredation and uses Fe as cofactor. PCD consists of 8 subunits each containing an Fe and a substrate binding site. Each of these subunits is composed of α and β chains. Hydroxyphenyl acetate is an inhibitor of PCD. Catechol 1,2-dioxygenase (CTD) cleaves the ring of catechol by insertion of 2 oxygen atoms to form muconic acid. Homoprotocatechuate 3,4-dioxygenase (HPCD), an extradiol cleaving enzyme cleaves the aromatic ring of its substrate, adds 2 oxygen atoms to form α-hydroxy-δ carboxymethyl muconic semialdehyde. Naphthalene 1,2-dioxygenase (NDO) catalyzes the conversion of naphthalene and O2 to dihydronaphthalene-diol. Glyoxalase/bleomycin resistant protein/dioxygenase (GBD) catalyzes the cleavage of S-lactoyl-glutathione to methylglyoxal and glutathione. Methylcytosine dioxygenase (TET) catalyzes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine to mediate DNA demethylation. For details see TET Enzymes. A Hyperactive Cobalt-Substituted Extradiol-Cleaving Catechol Dioxygenase       In most metalloenzyme mechanisms, O2 is reductively activated by direct electron transfer from the reduced metal ion. This implies that the rate of the reaction should be strongly dependent on the redox potential of the catalytic metal. We have proposed a different strategy for the Fe(II)-containing extradiol aromatic ring-cleaving dioxygenase family in which the activating electron is derived from the aromatic substrate rather the iron. When the aromatic substrate and the O2 are bound to the metal at the same time, the metal may serve as a conduit for the activating electron. Since there is no net change in metal oxidation state during this process, the impact of the redox potential of the metal on oxygen activation should be minimal, so long as it is low enough to allow formation of the initial O2 complex. This hypothesis is tested here by substituting Co(II) for Fe(II) in the Homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) from Brevibacterium fuscum.       2,3-HPCD catalyzes the cleavage of the C2-C3 bond of homoprotocatechuate (HPCA) with the incorporation of both oxygen atoms derived from O2 to form ring opened, 5-carboxymethyl-2-hydroxymuconic semialdehyde (5-CHMSA). Despite the significantly higher standard redox potential of Co(III/II) (1.92 V versus SHE) relative to that of the native metal Fe(II) (0.77 V), Co-HPCD was found to have more than twice the specific activity of Fe-HPCD under saturating O2 conditions, making Co-HPCD a hyper-active enzyme. The presence of Co in the active sites of Co-HPCD is illustrated by the 4 strong anomalous difference peaks determined from the X-ray diffraction data set collected at the cobalt K-edge (Figure 4A, 1.6050 Å, 7.725 keV), which shows cobalt coordinated via 2-His-1-Carboxylate facial triad. The structural comparison of the high-resolution X-ray crystal structures of Fe-HPCD (1.70 Å, 3ojt), Mn-HPCD (1.65 Å, 3ojn), and Co-HCPD (1.72 Å, 3ojj) shows no significant structural differences in the active site environment as indicated by the RMSD values of 0.10-0.14 Å for superposition of all atoms within 15 angstroms of the metal center. In addition, the presence of Co in the active site of HPCD has no structural consequences on either the mode of substrate binding or on the conformational integrity of the active site residues in the 1st or 2nd coordination sphere environment. The absence of any observable structural differences upon metal substitutions suggests that differential redox tuning of the metal centers in this dioxygenase is highly unlikely. Rather, the 2,3-HPCD enzyme can carry out the O2 activation and oxidative ring-cleavage efficiently over a large range of metal redox potentials. The structural analysis supports the proposed mechanism described above in which the ability of the enzyme to activate molecular O2 does not correlate with redox potential of the metal center. However, the current results also show that the rates of individual steps in the overall catalytic cycle can be effected by the metal present in the active site of HPCD, resulting in a earlier rate-limiting step for Co-HPCD compared to Fe-HPCD and Mn-HPCD. 3D structures of dioxygenase Dioxygenase 3D structures

3D structures of dioxygenase

Updated on 11-June-2019

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• Dioxygenase Intradiol family
• Protocatechuate 3,4-dioxygenase (PCD)
  • TET Enzymes, 3ojt, 3ojn – PpPCD α,β + Fe+3 – Pseudomonas putida
    
  • 3ojj, Dioxygenase 3D structures, 1ykm, 1yko, 3lkt, 3mfl, 3mi1, 3mv4, 3t63 – PpPCD α,β (mutant) + Fe+3
    
  • 1eo2, 1eo9, 1eoa, 2bum, 2but – AcPCD α,β + Fe+3 - Acinetobacter
    
  • 2bux – AcPCD α,β (mutant) + Fe+3
    
• PCD complex with aromatic compound
  • 3pcf, 3pch, 3pci, 4whq, 4whr, 4whs – PpPCD α,β + Fe+3 + HB derivative
    
  • 3pca, 3pcb, 3pcc – PpPCD α,β + Fe+3 + HB
    
  • 1ykl, 1ykn, 1ykp, 3lmx, 3mv6 – PpPCD α,β (mutant) + Fe+3 + DHB
    
  • 3pcj, 3pck, 3pcl, 3pcm – PpPCD α,β + Fe+3 + hydroxynicotinic acid derivative
    
  • 3pcn, 3pce, 3pcg – PpPCD α,β + Fe+3 + hydroxyphenyl acetate derivative
    
  • 1eob – AcPCD α,β + Fe+3 + DHB
    
  • 2buv, 2bv0 – AcPCD α,β (mutant) + Fe+3 + DHB
    
  • 2bur – AcPCD α,β + Fe+3 + HB
    
  • 2buw – AcPCD α,β (mutant) + Fe+3 + HB
    
  • 1eoc, 2buq – AcPCD α,β + Fe+3 + catechol derivative
    
  • 2buu, 2buy, 2buz – AcPCD α,β (mutant) + Fe+3 + catechol derivative
    
  • 3lxv, 3mi5, 3t67 – PpPCD α,β (mutant) + Fe+3 + catechol derivative
    
• Protocatechuate 4,5-dioxygenase (PCD)
  • 1b4u – SpPCD α,β + Fe+3 + DHB – Sphingomonas paucimobilis
    
  • 1bou – SpPCD α,β + Fe+3
    
• Catechol 1,2-dioxygenase (CTD)
  • 1dlm, 1dlq – AcCTD + Fe+3
    
  • 2azq – PpCTD + Fe+3
    
  • 5umh – CTD – Burkholderia multivorans
    
  • 5td3 – CTD – Burkholderia vietnamiensis
    
  • 5vxt – BaCTD + Fe+3 + catechol – Burkholderia ambifaria
    
• CTD complex with aromatic compound
  • 1dlt, 1dmh – AcCTD + Fe+3 + catechol derivative
    
  • 3hgi – RoCTD + Fe+3 + benzoic acid
    
  • 3hhy, 3hkp – RoCTD + Fe+3 + DHB
    
  • 3hj8, 3hjq, 3hjs, 3i4v, 3i4y, 3i51 – RoCTD + Fe+3 + catechol derivative
    
  • 3hhx – RoCTD + Fe+3 + pyrogallol
    
  • 2xsu – ArCTD + Fe+3 + phosphoinositol derivative – Acinetobacter radioresistens
    
  • 2xsv, 2xsr – ArCTD + Fe+3 + phosphoinositol derivative
    
• Chlorocatechol 1,2-dioxygenase (CCTD)
  • 3th1 – PpCCTD + Fe+3
    
  • 1s9a – RoCCTD + Fe+3
    
  • 3o32, 3o5u – RoCCTD + Fe+3 + dichlorocatechol derivative
    
  • 3o6j – RoCCTD + Fe+3 + hydroxyquinol
    
  • 3o6r – RoCCTD + Fe+3 + pyrogallol
    
  • 2boy – RoCCTD + Fe+3 + benzhydroxamate
    
• Hydroxyquinol 1,2-dioxygenase (HQD)
  • 1tmx – PsiHQD + Fe+3 – Pimelobacter simplex
    
  • 4zxd – PsHQD - Pseudomonas
    
  • 4zxa – PsHQD + Cd+2 + benzonitrile
    
  • 4zxc – PsHQD + Fe+3
    
  • 5m22 – SpHQD + Fe+3
    
  • 5m4o – SpHQD + Fe+3 + nitrophenol
    
  • 5m26 – SpHQD + Fe+3 + hydroquinone derivative
    
  • 5m21 – SpHQD + Fe+3 + hydroxybenzoate
    
• Nitrobenzene dioxygenase (NBDO)
  • 2bmo – CtNBDO + Fe+3 + Fe2S2
    
  • 2bmq – CtNBDO + Fe+3 + Fe2S2 + nitrobenzene
    
  • 2bmr – CtNBDO + Fe+3 + Fe2S2 + nitrotoluene
    
• α-ketoglutarate-dependent dioxygenase (Alkb)
  • 3khb – hAlkb (mutant) + Co+2 + oxoglutarate
    
  • 3i3q – hAlkb + Mn+2 + oxoglutarate
    
  • 3thp – hAlkb + Mn+2 + Zn+2 + oxoglutarate
    
  • 3tht – hAlkb (mutant) + Mn+2 + Zn+2 + oxoglutarate
    
  • 3t4h, 3t4v, 3t3y – EcAlkb + Fe+3 + inhibitor – Escherichia coli
    
  • 2fdj, 2fdg – EcAlkb + Mn+2 + succinate
    
  • 4jht – EcAlkb + Mn+2 + quinoline derivative
    
  • 4rfr – EcAlkb + Mn+2 + rhein
    
  • 2fdf – EcAlkb (mutant) + Co+2 + oxoglutarate
    
  • 4zhn – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide
    
  • 2fd8 – EcAlkb (mutant) + Fe+2 + oxoglutarate
    
• Alkb complex with DNA
  • 3rzm, 3rzl, 3rzh, 3rzg, 3btz, 4mg2, 4mgt – hAlkb (mutant) + DNA
    
  • 3h8x, 3h8r, 3h8o, 3bty – hAlkb (mutant) + DNA + inhibitor
    
  • 3btx – hAlkb (mutant) + Mg+2 + DNA
    
  • 3i49, 3i2o – hAlkb + Fe+2 + oxoglutarate + DNA
    
  • 4nid – hAlkb + Mn+2 + oxoglutarate + DNA
    
  • 4nig, 4nih, 4nii – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA
    
  • 3o1s – hAlkb + DNA
    
  • 3i3m – hAlkb + Mn+2 + oxoglutarate + DNA
    
  • 3s5a, 3s57, 3rzk, 3rzj, 3buc, 3bu0, 3bkz – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA
    
  • 3o1r, 3o1p, 3o1o, 3o1m – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor
    
  • 3bie, 3bi3, 2fdh – EcAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor
    
  • 2fdi – EcAlkb + Fe+2 + oxoglutarate + DNA + inhibitor
    
  • 3khc – hAlkb (mutant) + Co+2 + oxoglutarate + DNA + inhibitor
    
  • 3o1v, 3o1u, 3o1t, 3t1s – hAlkb (mutant) + Fe+3 + succinate + DNA + inhibitor
    
• α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
  • 4nj4, 4o7x – hAlkbh5 residues 66-292 + Mn
    
  • 4o61 – hAlkbh5 residues 74-294 + citrate
    
  • 4nrm – hAlkbh5 residues 66-292 + citrate + acetate
    
  • 4nro – hAlkbh5 residues 66-292 + Mn + ketoglutarate
    
  • 4oct – hAlkbh5 residues 66-292 + Mn + oxoglutarate
    
  • 4nrp – hAlkbh5 residues 66-292 + Mn + oxalylglycine
    
  • 4nrq – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate
    
  • 4npl – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish
    
  • 4npm – zfAlkbh5 residues 38-287 + Mn + succinate
    
  • 4qkb, 4qkd – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate
    
  • 4qkf – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine
    
• α-ketoglutarate-dependent dioxygenase (Fto)
  • 4idz – hFto + Ni+2 + oxalylglycine
    
  • 4ie0, 4ie5, 4qho – hFto + Zn+2 + pyrimidine derivative
    
  • 4ie4, 4ie6 – hFto + Zn+2 + quinoline derivative
    
  • 4ie7 – hFto + Zn+2 + rhein
    
  • 4qkn – hFto + Mn+2 + meclofenamic acid
    
  • 4cxw, 4cxx, 4cxy – hFto + Ni+2 + inhibitor
    
  • 6akw – hFto + oxoglutarate + inhibitor
    
  • 5f8p, 5dab – hFto + Fe+2 + oxoglutarate + inhibitor
    
  • 4zs2, 4zs3 – hFto + Mn+2 + oxoglutarate + fluorescin
    
  • 5zmd – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine
    
  • 6eoz – EnFto + Ni+2 + cyclopeptin – Emericela nidulans
    
  • 5ybl – EnFto + Mn+2 + oxoglutarate
    
  • 5y7t, 5y7r – EnFto + Fe+3 + oxoglutarate + cyclopeptin
    
  • 5oa8, 5oa7, 5oa4 – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin
    
• α-ketoglutarate-dependent dioxygenase (ANDA)
  • 5zm2 – EvANDA – Emericella variicolor
    
  • 5zm4, 5zm3 – EvANDA + Fe+3 + oxoglutarate + preandiloid
    
• Leucoanthocyanidin dioxygenase (LACD)
  • 1gp5, 1gp6 – AtLACD + dihydroquercetin – Arabidopsis thaliana
    
  • 2brt – AtLACD + naringenin
    
• Methylcytosine dioxygenase (TET)
  • 5d9y, 5deu, 4nm6 – hTET2 + DNA
    
  • 4z3c – hTET3 + DNA
    
  • 5exh – mTET3 + DNA – mouse
    
• Dioxygenase extradiol family
• Homoprotocatechuate 2,3-dioxygenase (HPCD)
  • 1f1r, 1f1u – AgHPCD + Mn+2 – Arthrobacter globiformis
    
  • 1f1x, 1q0o – BfHPCD + Fe+3 – Brevibacterium fuscum
    
  • 2ig9, 3ojt, 5trx – BfHPCD + Fe+2
    
  • 3ecj, 4ghc, 5bwg, 5bwh, 4z6l, 4z6m, 4z6n, 4z6o, 4z6p, 4z6q – BfHPCD (mutant) + Fe+2
    
  • 4z6z – BfHPCD + Fe+2 + catechol derivative
    
  • 4z6r, 4z6s, 4z6t, 4z6u, 4z6v, 4z6w – BfHPCD (mutant) + Fe+2 + catechol derivative
    
  • 3bza, 3ojn – BfHPCD + Mn+2
    
  • 3ojj – BfHPCD + MCo+2
    
• HPCD complex with aromatic compound
  • 1f1v – AgHPCD + Mn+2 + dihydroxyphenyl acetate
    
  • 1q0c, 4ghg – BfHPCD + Fe+2 + dihydroxyphenyl acetate
    
  • 4ghd – BfHPCD (mutant) + Fe+2 + dihydroxyphenyl acetate
    
  • 2iga – BfHPCD + Fe+2 + O2 + reaction intermediates
    
  • 3eck – BfHPCD (mutant) + Fe+2 + reaction intermediates
    
  • 3ojk – BfHPCD + Co+2 + catechol derivative
    
  • 4ghe, 4ghf – BfHPCD (mutant) + Fe+2 + catechol derivative
    
  • 4ghh – BfHPCD + Fe+2 + catechol derivative
    
• Catechol 2,3-dioxygenase (MPC)
  • 1mpy – PpMPC + Fe+2
    
  • 3hpv – PsMPC + Fe+2
    
  • 3hpy – PsMPC + Fe+2 + catechol derivative
    
  • 3hq0 – PsMPC + Fe+3 + product
    
  • 2wl3, 2wl9 - RoMPC + Fe+3 - Rhodococcus opacus
    
  • 3lm4 – RoMPC + Fe+3 + H2O2
    
  • 5zsz – DiMPC + Fe+3 - Diaphorobacter
    
  • 5znh – DiMPC + Fe+3 + catechol derivative
    
• Naphthalene 1,2-dioxygenase (NDO)
  • 1ndo, 1o7h, 1o7w – PpNDO + Fe+3 + Fe2S2
    
  • 2hmj – PpNDO (mutant) + Fe+3 + Fe2S2
    
  • 2b1x – RoNDO + Fe+3 + Fe2S2
    
• NDO complex with aromatic compound
  • 1eg9 – PpNDO + Fe+3 + Fe2S2 + indole
    
  • 1o7g – PpNDO + Fe+3 + Fe2S2 + naphthalene
    
  • 1o7m – PpNDO + Fe+3 + Fe2S2 + O2
    
  • 1o7n – PpNDO + Fe+3 + Fe2S2 + O2 + indole
    
  • 1o7p – PpNDO + Fe+3 + Fe2S2 + dihydronaphthalene
    
  • 1uuv, 1uuw – PpNDO + Fe+3 + Fe2S2 + NO3
    
  • 2hmk, 2hml – PpNDO (mutant) + Fe+3 + Fe2S2 + phenanthrene
    
  • 2hmm, 2hmn – PpNDO (mutant) + Fe+3 + Fe2S2 + anthracene
    
  • 2hmo – PpNDO + Fe+3 + Fe2S2 + nitrotoluene
    
  • 2b24 – RoNDO + Fe+3 + Fe2S2 + indole
    
  • 4hm0, 4hm1, 4hm4, 4hm5 – PsNDO + Fe+3 + Fe2S2 + indole derivative
    
  • 4hm2, 4hm3, 4hm6, 4hm7, 4hm8 – PsNDO + Fe+3 + Fe2S2 + phenyl derivative
    
  • 4hjl – PsNDO + Fe+3 + Fe2S2 + chloronaphthalene
    
  • 4hkv – PsNDO + Fe+3 + Fe2S2 + benzamide
    
• Dihydronaphthalene 1,2-dioxygenase (HNDO)
  • 2ehz, 2ei2 – PsHNDO + Fe+2
    
  • 2ei0, 2ei1, 2ei3 – PsHNDO + Fe+2 + dihydroxybephenyl
    
• 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBP)
  • 1dhy, 1eil, 1eiq, 1eir – PsDHBP + Fe+3
    
  • 1kw3 – PsDHBP + Fe+2
    
  • 1kw8 – PsDHBP + Fe+2 + NO
    
  • 1kwb – PsDHBP (mutant)
    
  • 1han, 1kmy – BxDHBP (mutant) + Fe+3 – Burkholderia xenovorans
    
• DHBP complex with aromatic compound
  • 1knd, 1knf – BxDHBP + Fe+3 + catechol derivative
    
  • 1lgt, 1lkd – BxDHBP + Fe+2 + dihydroxybephenyl
    
  • 1kw6, 1kw9 – PsDHBP + Fe+2 + dihydroxybephenyl
    
  • 1kwc – PsDHBP (mutant) + dihydroxybephenyl
    
• Salicylate 1,2-dioxygenase (SDO)
  • 2phd – PssSDO + Fe+3 – Pseudaminobacter salicylatoxidans
    
  • 4fah, 4fbf – PssSDO (mutant) + Fe+3
    
  • 3nst – PssSDO (mutant) + Fe+2
    
  • 3njz – PssSDO + Fe+2 +salicylate
    
  • 3nvc – PssSDO (mutant) + Fe+2 +salicylate
    
  • 3nkt – PssSDO + Fe+2 +naphthoate
    
  • 3nl1 – PssSDO + Fe+2 +gentisate
    
  • 3nw4, 4fag – PssSDO (mutant) + Fe+2 +gentisate
    
• Biphenyl 1,2-dioxygenase (BDO)
  • 3gzy – CtBDO + Fe+2 + Fe2S2 – Comamonas testosteroni
    
  • 2xr8 – BxBDO + Fe+2 + Fe2S2
    
  • 2xso, 2yfi, 5aeu – BxBDO (mutant) + Fe+2 + Fe2S2
    
  • 1uli - RoBDO + Fe+2 + Fe2S2
    
  • 2gbw - SyBDO + Fe+2 + Fe2S2 + O2 – Sphingobium yanoikuyae
    
• BDO complex with aromatic compound
  • 3gzx – CtBDO + Fe+2 + Fe2S2 + biphenyl
    
  • 2xrx – BxBDO + Fe+2 + Fe2S2 + biphenyl
    
  • 2xsh, 5aew – BxBDO (mutant) + Fe+2 + Fe2S2 + biphenyl
    
  • 2yfj, 2yfl – BxBDO (mutant) + Fe+2 + Fe2S2 + dibenzofuran
    
  • 1ulj - RoBDO + Fe+2 + Fe2S2 + biphenyl
    
  • 2gbx - SyBDO + Fe+2 + Fe2S2 + biphenyl
    
• Tryptophan 2,3-dioxygenase (TDO)
  • 4pw8 - hTDO + Co+2
    
  • 5tia, 5ti9 – hTDO + heme + tryptophan
    
  • 6a4i – hTDO + heme + tryptophan + inhibitor
    
  • 1yw0 – XcTDO + Mg – Xanthomonas campestris
    
  • 2nw7 – XcTDO + heme
    
  • 4hka – TDO + heme – Drosophila melanogaster
    
  • 3bk9, 3e08 – XcTDO (mutant) + heme + tryptophan
    
  • 2nw8, 2nw9 – XcTDO + heme + Mn + tryptophan derivative
    
  • 2nox – CmTDO + heme – Cupriavidus metallidurans
    
• Cysteine dioxygenase type I (CysDO)
  • 6bgm, 6bgf, 6e87 – hCysDO + Fe+2
    
  • 2ic1, 6n42 – hCysDO + Fe+2 + cysteine
    
  • 6cdh, 6bpw, 6bpu, 6bpt – hCysDO + Fe+2 + Tyr derivative
    
  • 6cdn, 6bpx, 6bpv, 6bps – hCysDO + Fe+2 + cysteine + Tyr derivative
    
  • 6bpr – hCysDO + Fe+3 + cysteine + Tyr derivative + NO
    
  • 6n43 – hCysDO + Fe+3 + cysteine + NO
    
  • 2gh2, 4ieo, 4iep, 4ieq, 4ier, 4ies, 4iet, 4ieu, 4iev, 4iew, 4iex, 4iey, 4iez, 4jtn, 4jto, 4kwj, 4kwk, 4kwl, 2b5h – rCysDO + Fe+2 – rat
    
  • 4ubg, 4ubh, 5ezw, 5efu, 4ysf, 4yyo – rCysDO (mutant) + Fe+2
    
  • 5fdb – rCysDO (mutant)
    
  • 4yni – rCysDO
    
  • 5i0r, 4xet, 4xfb, 4xfc, 4pix – rCysDO (mutant) + Fe+3
    
  • 3eln – rCysDO + Fe+2 + cysteine derivative
    
  • 4z82 – rCysDO (mutant) + Fe+2 + cysteine derivative
    
  • 5i0u, 5i0t, 5i0s, 4xf4, 4xf9, 4xfa, 4piz – rCysDO + Fe+3 + cysteine derivative
    
  • 4xf0, 4xf1, 4xfg, 4xfh, 4xfi, 4piy – rCysDO (mutant) + Fe+3 + cysteine derivative
    
  • 4xez, 4xff – rCysDO (mutant) + Fe+3 + inhibitor
    
  • 4xf3 – rCysDO (mutant) + Fe+3 + inhibitor + cysteine
    
  • 2q4s, 2atf – mCysDO + Ni+2
    
• 4-hydroxyphenylpyruvate dioxygenase (HPPD)
  • 3isq, 5ec3 – hHPPD + Co+2
    
  • 1sqi – rHPPD + Fe+3 + inhibitor - rat
    
  • 1cjx – HPPD + Fe+2 – Pseudomonas fluorescens
    
  • 1t47 – HPPD + Fe+2 – Streptomyces avermitilis
    
  • 3zgj – HPPD + Co+2 + mandelic acid – Streptomyces coelicolor
    
  • 1sqd, 1sp9 – AtHPPD + Fe+3
    
  • 1tfz, 1tg5, 6j63, 5ywh, 5ywg - AtHPPD + Fe+3 + inhibitor
    
  • 5xgk – AtHPPD + Fe+3 + hydroxyphenylpyruvate
    
  • 6isd – AtHPPD + Fe+3 + sulcotrione
    
  • 5yy7, 5yy6, 5ywk – AtHPPD + Co+2 + benquitrione
    
  • 5ywi – AtHPPD (mutant) + Co+2 + NTBC
    
  • 1sp8 – HPPD + Fe+2 – corn
    
  • 5hmq – PpHPPD + Mg+2
    
• Quercetin 2,3-dioxygenase (QDO)
  • 1juh – AjQDO + Cu+2 – Aspergillus japonicus
    
  • 2h0v – QDO + Fe+3 – Bacillus subtilis
    
  • 1gqg, 1gqh – AjQDO + Cu+2 + inhibitor
    
  • 1h1i – AjQDO + Cu+2 + quercetin
    
  • 1h1m – AjQDO + Cu+2 + kaempferol
    
• Taurine/α-ketoglutarate dioxygenase (TauD)
  • 1gqw, 1gy9, 1os7 – EcTauD + Fe+2 + taurine + oxoglutarate
    
  • 1otj – EcTauD + taurine
    
  • 3pvj, 3v15 – PpTauD
    
  • 3v17 – PpTauD + oxoglutarate
    
  • 3r1j – HAD + Fe+3 – Mycobacterium avium
    
  • 4j5i – HAD + Fe+3 – Mycobacterium smegmatis
    
  • 3swt – HAD + Fe+3 – Mycobacterium marinum
    
  • 5keu – BxHAD + Mg+2
    
  • 5vn6 – BaHAD + Mg+2
    
• 3-hydroxyanthranilate 3,4-dioxygenase (HAD)
  • 2qnk – hHAD + Ni+2
    
  • 5tkq – hHAD + Zn+2
    
  • 5tk5 – hHAD + Fe+3
    
  • 3fe5 – HAD + Fe+3 - bovine
    
  • 1zvf – HAD + Ni+2 - yeast
    
  • 5v28, 4r52 – CmHAD + Fe+2 – Cupriavidus metallidurans
    
  • 5v27, 5v26, 6d60, 6bvr, 6bvp – CmHAD (mutant) + Fe+2
    
  • 1yfu, 4hvq, 4hvr, 4i3p, 4l2n – CmHAD + Fe+3
    
  • 4hvo – CmHAD + Fe+3 + Cu+2
    
  • 1yfw – CmHAD + Fe+3 + O2 + hydroxyanthranilate
    
  • 1yfx – CmHAD + Fe+3 + NO + hydroxyanthranilate
    
  • 1yfy – CmHAD + Fe+3 + hydroxyanthranilate
    
  • 6d62, 6d61, 6cd3, 6bvs, 6bvq – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative
    
  • 4wzc – HAD + Fe+2 + enedioate derivative – Ralstonia metallidurans
    
• Carbazole 1,9a-dioxygenase (CDO)
  • 1vck – CDO ferredoxin component + Fe+3 + Fe2S2 – Pseudomonas resinovorans
    
  • 2de5, 2de6 – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 – Janthinobacterium
    
  • 2de7, 3vmg – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole
    
  • 3vmh – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + O2
    
  • 4nb8, 4nb9, 4nba, 4nbb, 4nbc, 4nbd, 4nbe, 4nbf, 4nbg, 4nbh – JaCDO ferredoxin and terminal oxygenase components (mutant) + Fe+2 + Fe2S2
    
  • 3vmi – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole + O2
    
  • 3gcf – CDO terminal oxygenase component + Fe+2 + Fe2S2 – Nocardioides aromaticivorans
    
  • 3gkq – SpCDO terminal oxygenase component + Fe+2 + Fe2S2
    
• Homogentisate 1,2-dioxygenase (HGDO)
  • 1ey2 – hHGDO + Fe+2
    
  • 1eyb – hHGDO
    
  • 4aq2 – PpHGDO + Fe+3
    
  • 4aq6 – PpHGDO + Fe+3 + substrate
    
  • 3zds – PpHGDO + Fe+3 + O2
    
• Hydroxyethylphosphonate dioxygenase (PHPD)
  • 4yar, 3g7d – SvPHPD + Cd+2 – Streptomyces viridochromogenes
    
  • 3rzz – SvPHPD (mutant) + Cd+2
    
  • 3gbf – SvPHPD + Cd+2 + hydroxyethylphosphonate
    
  • 6b9r – PHPD + Fe+3 + hydroxyethylphosphonate - Streptomyces albus
    
• Gallate dioxygenase (GD)
  • 3wrc – SpGD + Fe+2 + dehydroxybenzoate
    
  • 3wku, 3wpm, 3wr4 – SpGD + Fe+3 + gallate
    
  • 3wr3, 3wr9 – SpGD + Fe+2 + gallate
    
  • 3wrb – SpGD (mutant) + Fe+2 + gallate
    
  • 3wr8, 3wra – SpGD + Fe+2
    
• Glyoxalase/bleomycin resistant protein/dioxygenase (GBD)
  • 2rbb – GBD – Burkholderia phytofirmans
    
  • 2rk9 – GBD – Vibrio splendidus
    
  • 3b59 – GBD – Novosphingobium aromaticivorans
    
  • 3kol – GBD – Nostoc punctiforme
    
  • 3rri – GBD – Alicyclobacillus acidocaldarius
    
  • 3vb0 – GBD – Sphingomonas wittichii
    
  • 3vcx – GBD – Pseudomonas palustris
    
  • 4g6x – CaGBD – Catenulispora acidiphila
    
  • 4n04 – CaGBD (mutant)
    
  • 4gym – GBD – Conexibacter woesei
    
  • 4hc5 – GBD – Sphaerobacter thermophilus
    
  • 4mym – GBD – Nocardioides
    
  • 4qb5 – GBD – Albidiferax ferrireducens
    
  • 4rt5 – GBD – Planctomyces limnophilus
    
  • 5uhj, 5ujp – GBD + Ni+2 – Streptomyces
    
  • 5c4p, 5c68, 5cb9 – TcGBD + Ni+2 – Thermomonospora curvata
    
  • 5c6x – TcGBD + Co+2
    
  • 4z04 – GBD + Zn+2 + glutathione – Brucella abortus
    
• Procollagen-proline dioxygenase (PPD)
  • 5iat – BaPDD – Bacillus anthracis
    
  • 5iax – BaPDD + Co+2 + oxoglutarate
    
  • 5iav – BaPDD + Co+2 + malonate
    
• 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
  • 5i8s – mKMTPD + Ni+2 + pentanoate + valerate
    
  • 5i8t – mKMTPD + Ni+2 + lactate
    
  • 5i8y – mKMTPD + Co+2 + keto-methylthio-butyrate
    
  • 5i91 – mKMTPD + Ni+2 + keto-methylthio-butyrate
    
  • 5i93 – mKMTPD + Ni+2 + keto-pentanoate
    
  • 4qgn – hKMTPD + Fe+3
    
  • 4qgl, 4qgm – BaKMTPD + Cd+2
    
• Indoleamine 2,3-dioxygenase 1 (IAD)
  • 6azu – hIAD + heme
    
  • 6e45, 6e44 – hIAD 1 (mutant) + heme
    
  • 5ek2, 5ek3, 5ek4, 4pk5, 5xe1, 5wn8 – hIAD + heme + imidazole derivative
    
  • 4u72, 4u74, 6e42, 6e41, 6e40 – hIAD (mutant) + heme + imidazole derivative
    
  • 6f0a – hIAD + heme + imidazole derivative + Ala
    
  • 6azw, 6azv – hIAD + inhibitor
    
  • 5etw, 6mq6, 6dpr, 6dpq – hIAD + heme + inhibitor
    
  • 5wmu, 6e35 – hIAD + heme + CN + Trp
    
  • 5wmw, 6cxv, 6cxu – hIAD (mutant) + heme + CN + Trp
    
  • 5wmv – hIAD + heme + CN + indole derivative + Trp
    
  • 5wmx – hIAD (mutant) + heme + CN + indole derivative + Trp
    
  • 5whr – hIAD + heme + pyrrolydine derivative
    
  • 6e46 – hIAD 1 + heme + Trp
    
  • 6e43 – hIAD 1 (mutant) + inhibitor
    
• Thymine dioxygenase (TD)
  • 5c3o – NcTD – Neurospora crassa
    
  • 5c3p – NcTD + oxoglutarate + Ni+2
    
  • 5c3q – NcTD + oxoglutarate + Ni+2 + thymine
    
  • 5c3s – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative
    
  • 5c3r – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative + uracil derivative
    
• 2,4’-dihydroxyacetophenone dioxygenase (APD)
  • 5bpx, 4p9g – APD + Fe+3 – Alcaligenes
    
• Thiol dioxygenase (ThD)
  • 4tlf – PaThD + Fe+2 – Pseudomonas aeruginosa
    
  • 4wvz – PaThD (mutant) + Fe+2
    
• FT_T dioxygenase (FTTD)
  • 6d3j – ShFTTD + Co+2 + oxoglutarate – Sphingobium herbicidovorans
    
  • 6d3m – ShFTTD + Co+2 + oxoglutarate + quinoxalin
    
  • 6d3i, 6d3h – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative
    

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel, Joel L. Sussman, Jaime Prilusky