Dioxygenase

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<StructureSection size="" scene ="Journal:JBIC:5/Opening/2" caption="Solved Crystal Structure of Hyperactive Catechol Dioxygenase">
<StructureSection size="" scene ="Journal:JBIC:5/Opening/2" caption="Solved Crystal Structure of Hyperactive Catechol Dioxygenase">
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__TOC__
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== Function ==
'''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. <br />
'''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. <br />
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* '''Glyoxalase/bleomycin resistant protein/dioxygenase''' (GBD) catalyzes the cleavage of S-lactoyl-glutathione to methylglyoxal and glutathione.<br />
* '''Glyoxalase/bleomycin resistant protein/dioxygenase''' (GBD) catalyzes the cleavage of S-lactoyl-glutathione to methylglyoxal and glutathione.<br />
* '''Methylcytosine dioxygenase''' (TET) catalyzes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine to mediate DNA demethylation<ref>PMID:25862091</ref>. For details see [[TET Enzymes]].<br />
* '''Methylcytosine dioxygenase''' (TET) catalyzes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine to mediate DNA demethylation<ref>PMID:25862091</ref>. For details see [[TET Enzymes]].<br />
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* '''α-ketoglutarate-dependent dioxygenase Alkb''' repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation<ref>PMID:18432238</ref>.<br />
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* '''α-ketoglutarate-dependent dioxygenase Fto''' highest activity is repairing alkylated RNA containing 3-methyluracil by oxidative demethylation<ref>PMID:18775698</ref>.<br />
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=== A Hyperactive Cobalt-Substituted Extradiol-Cleaving Catechol Dioxygenase <ref>DOI 10.1007/s00775-010-0732-0</ref>===
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== A Hyperactive Cobalt-Substituted Extradiol-Cleaving Catechol Dioxygenase <ref>DOI 10.1007/s00775-010-0732-0</ref>==
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In most metalloenzyme mechanisms, O<sub>2</sub> 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 O<sub>2</sub> 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 O<sub>2</sub> complex. This hypothesis is tested here by substituting Co(II) for Fe(II) in the <scene name='Journal:JBIC:5/Cobalt_overview/1'>Homoprotocatechuate 2,3-dioxygenase</scene> (2,3-HPCD) from ''Brevibacterium fuscum''.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In most metalloenzyme mechanisms, O<sub>2</sub> 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 O<sub>2</sub> 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 O<sub>2</sub> complex. This hypothesis is tested here by substituting Co(II) for Fe(II) in the <scene name='Journal:JBIC:5/Cobalt_overview/1'>Homoprotocatechuate 2,3-dioxygenase</scene> (2,3-HPCD) from ''Brevibacterium fuscum''.
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</StructureSection>
</StructureSection>
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==References==
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==3D structures of dioxygenase==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*'''Dioxygenase Intradiol family'''
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*Protocatechuate 3,4-dioxygenase (PCD)
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**[[2pcd]], [[4who]], [[4whp]] – PpPCD α,β + Fe+3 – ''Pseudomonas putida''<br />
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**[[3pcd]], [[1ykk]], [[1ykm]], [[1yko]], [[3lkt]], [[3mfl]], [[3mi1]], [[3mv4]], [[3t63]] – PpPCD α,β (mutant) + Fe+3 <br />
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**[[1eo2]], [[1eo9]], [[1eoa]], [[2bum]], [[2but]] – AcPCD α,β + Fe+3 - ''Acinetobacter''<br />
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**[[2bux]] – AcPCD α,β (mutant) + Fe+3 <br />
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-
 
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*''PCD complex with aromatic compound''
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**[[3pcf]], [[3pch]], [[3pci]], [[4whq]], [[4whr]], [[4whs]] – PpPCD α,β + Fe+3 + HB derivative<br />
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**[[3pca]], [[3pcb]], [[3pcc]] – PpPCD α,β + Fe+3 + HB <br />
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**[[1ykl]], [[1ykn]], [[1ykp]], [[3lmx]], [[3mv6]] – PpPCD α,β (mutant) + Fe+3 + DHB<br />
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**[[3pcj]], [[3pck]], [[3pcl]], [[3pcm]] – PpPCD α,β + Fe+3 + hydroxynicotinic acid derivative<br />
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**[[3pcn]], [[3pce]], [[3pcg]] – PpPCD α,β + Fe+3 + hydroxyphenyl acetate derivative<br />
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**[[1eob]] – AcPCD α,β + Fe+3 + DHB <br />
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**[[2buv]], [[2bv0]] – AcPCD α,β (mutant) + Fe+3 + DHB <br />
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**[[2bur]] – AcPCD α,β + Fe+3 + HB <br />
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**[[2buw]] – AcPCD α,β (mutant) + Fe+3 + HB <br />
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**[[1eoc]], [[2buq]] – AcPCD α,β + Fe+3 + catechol derivative<br />
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**[[2buu]], [[2buy]], [[2buz]] – AcPCD α,β (mutant) + Fe+3 + catechol derivative<br />
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**[[3lxv]], [[3mi5]], [[3t67]] – PpPCD α,β (mutant) + Fe+3 + catechol derivative<br />
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*Protocatechuate 4,5-dioxygenase (PCD)
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**[[1b4u]] – SpPCD α,β + Fe+3 + DHB – ''Sphingomonas paucimobilis''<br />
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**[[1bou]] – SpPCD α,β + Fe+3 <br />
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*Catechol 1,2-dioxygenase (CTD)
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**[[1dlm]], [[1dlq]] – AcCTD + Fe+3 <br />
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**[[2azq]] – PpCTD + Fe+3 <br />
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**[[5umh]] – CTD – ''Burkholderia multivorans''<br />
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**[[5td3]] – CTD – ''Burkholderia vietnamiensis''<br />
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**[[5vxt]] – BaCTD + Fe+3 + catechol – ''Burkholderia ambifaria''<br />
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*''CTD complex with aromatic compound''
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**[[1dlt]], [[1dmh]] – AcCTD + Fe+3 + catechol derivative<br />
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**[[3hgi]] – RoCTD + Fe+3 + benzoic acid <br />
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**[[3hhy]], [[3hkp]] – RoCTD + Fe+3 + DHB<br />
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**[[3hj8]], [[3hjq]], [[3hjs]], [[3i4v]], [[3i4y]], [[3i51]] – RoCTD + Fe+3 + catechol derivative<br />
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**[[3hhx]] – RoCTD + Fe+3 + pyrogallol<br />
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**[[2xsu]] – ArCTD + Fe+3 + phosphoinositol derivative – ''Acinetobacter radioresistens''<br />
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**[[2xsv]], [[2xsr]] – ArCTD + Fe+3 + phosphoinositol derivative <br />
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*Chlorocatechol 1,2-dioxygenase (CCTD)
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**[[3th1]] – PpCCTD + Fe+3 <br />
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**[[1s9a]] – RoCCTD + Fe+3 <br />
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**[[3o32]], [[3o5u]] – RoCCTD + Fe+3 + dichlorocatechol derivative<br />
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**[[3o6j]] – RoCCTD + Fe+3 + hydroxyquinol<br />
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**[[3o6r]] – RoCCTD + Fe+3 + pyrogallol<br />
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**[[2boy]] – RoCCTD + Fe+3 + benzhydroxamate<br />
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*Hydroxyquinol 1,2-dioxygenase (HQD)
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**[[1tmx]] – PsiHQD + Fe+3 – ''Pimelobacter simplex''<br />
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**[[4zxd]] – PsHQD - ''Pseudomonas''<br />
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**[[4zxa]] – PsHQD + Cd+2 + benzonitrile <br />
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**[[4zxc]] – PsHQD + Fe+3 <br />
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**[[5m22]] – SpHQD + Fe+3 <br />
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**[[5m4o]] – SpHQD + Fe+3 + nitrophenol<br />
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**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
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**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
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*Nitrobenzene dioxygenase (NBDO)
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**[[2bmo]] – CtNBDO + Fe+3 + Fe2S2 <br />
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**[[2bmq]] – CtNBDO + Fe+3 + Fe2S2 + nitrobenzene<br />
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**[[2bmr]] – CtNBDO + Fe+3 + Fe2S2 + nitrotoluene<br />
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*α-ketoglutarate-dependent dioxygenase (Alkb)
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**[[3khb]] – hAlkb (mutant) + Co+2 + oxoglutarate <br />
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**[[3i3q]] – hAlkb + Mn+2 + oxoglutarate <br />
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**[[3thp]] – hAlkb + Mn+2 + Zn+2 + oxoglutarate <br />
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**[[3tht]] – hAlkb (mutant) + Mn+2 + Zn+2 + oxoglutarate <br />
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**[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
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**[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
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**[[4jht]] – EcAlkb + Mn+2 + quinoline derivative <br />
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**[[4rfr]] – EcAlkb + Mn+2 + rhein<br />
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**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
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**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
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**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
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-
 
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*''Alkb complex with DNA''
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**[[3rzm]], [[3rzl]], [[3rzh]], [[3rzg]], [[3btz]], [[4mg2]], [[4mgt]] – hAlkb (mutant) + DNA<br />
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**[[3h8x]], [[3h8r]], [[3h8o]], [[3bty]] – hAlkb (mutant) + DNA + inhibitor<br />
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**[[3btx]] – hAlkb (mutant) + Mg+2 + DNA <br />
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**[[3i49]], [[3i2o]] – hAlkb + Fe+2 + oxoglutarate + DNA <br />
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**[[4nid]] – hAlkb + Mn+2 + oxoglutarate + DNA <br />
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**[[4nig]], [[4nih]], [[4nii]] – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA <br />
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**[[3o1s]] – hAlkb + DNA <br />
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**[[3i3m]] – hAlkb + Mn+2 + oxoglutarate + DNA<br />
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**[[3s5a]], [[3s57]], [[3rzk]], [[3rzj]], [[3buc]], [[3bu0]], [[3bkz]] – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA<br />
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**[[3o1r]], [[3o1p]], [[3o1o]], [[3o1m]] – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor<br />
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**[[3bie]], [[3bi3]], [[2fdh]] – EcAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor<br />
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**[[2fdi]] – EcAlkb + Fe+2 + oxoglutarate + DNA + inhibitor<br />
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**[[3khc]] – hAlkb (mutant) + Co+2 + oxoglutarate + DNA + inhibitor<br />
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**[[3o1v]], [[3o1u]], [[3o1t]], [[3t1s]] – hAlkb (mutant) + Fe+3 + succinate + DNA + inhibitor<br />
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*α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
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**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
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**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
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**[[4nrm]] – hAlkbh5 residues 66-292 + citrate + acetate<br />
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**[[4nro]] – hAlkbh5 residues 66-292 + Mn + ketoglutarate <br />
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**[[4oct]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate <br />
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**[[4nrp]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine <br />
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**[[4nrq]] – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate <br />
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**[[4npl]] – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish<br />
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**[[4npm]] – zfAlkbh5 residues 38-287 + Mn + succinate <br />
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**[[4qkb]], [[4qkd]] – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate <br />
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**[[4qkf]] – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine <br />
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* α-ketoglutarate-dependent dioxygenase (Fto)
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**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
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**[[4ie0]], [[4ie5]], [[4qho]] – hFto + Zn+2 + pyrimidine derivative<br />
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**[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
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**[[4ie7]] – hFto + Zn+2 + rhein<br />
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**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
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**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
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**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
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**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
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**[[4zs2]], [[4zs3]] – hFto + Mn+2 + oxoglutarate + fluorescin<br />
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**[[5zmd]] – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine<br />
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**[[6eoz]] – EnFto + Ni+2 + cyclopeptin – Emericela nidulans<br />
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**[[5ybl]] – EnFto + Mn+2 + oxoglutarate <br />
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**[[5y7t]], [[5y7r]] – EnFto + Fe+3 + oxoglutarate + cyclopeptin<br />
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**[[5oa8]], [[5oa7]], [[5oa4]] – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin<br />
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* α-ketoglutarate-dependent dioxygenase (ANDA)
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**[[5zm2]] – EvANDA – ''Emericella variicolor''<br />
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**[[5zm4]], [[5zm3]] – EvANDA + Fe+3 + oxoglutarate + preandiloid<br />
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*Leucoanthocyanidin dioxygenase (LACD)
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**[[1gp5]], [[1gp6]] – AtLACD + dihydroquercetin – ''Arabidopsis thaliana'' <br />
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**[[2brt]] – AtLACD + naringenin <br />
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*Methylcytosine dioxygenase (TET)
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**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + DNA <br />
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**[[4z3c]] – hTET3 + DNA <br />
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**[[5exh]] – mTET3 + DNA – mouse <br />
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*'''Dioxygenase extradiol family'''
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*Homoprotocatechuate 2,3-dioxygenase (HPCD)
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**[[1f1r]], [[1f1u]] – AgHPCD + Mn+2 – ''Arthrobacter globiformis''<br />
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**[[1f1x]], [[1q0o]] – BfHPCD + Fe+3 – ''Brevibacterium fuscum''<br />
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**[[2ig9]], [[3ojt]], [[5trx]] – BfHPCD + Fe+2<br />
+
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**[[3ecj]], [[4ghc]], [[5bwg]], [[5bwh]], [[4z6l]], [[4z6m]], [[4z6n]], [[4z6o]], [[4z6p]], [[4z6q]] – BfHPCD (mutant) + Fe+2<br />
+
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**[[4z6z]] – BfHPCD + Fe+2 + catechol derivative<br />
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**[[4z6r]], [[4z6s]], [[4z6t]], [[4z6u]], [[4z6v]], [[4z6w]] – BfHPCD (mutant) + Fe+2 + catechol derivative<br />
+
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**[[3bza]], [[3ojn]] – BfHPCD + Mn+2<br />
+
-
**[[3ojj]] – BfHPCD + MCo+2<br />
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-
 
+
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*''HPCD complex with aromatic compound''
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-
 
+
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**[[1f1v]] – AgHPCD + Mn+2 + dihydroxyphenyl acetate <br />
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-
**[[1q0c]], [[4ghg]] – BfHPCD + Fe+2 + dihydroxyphenyl acetate <br />
+
-
**[[4ghd]] – BfHPCD (mutant) + Fe+2 + dihydroxyphenyl acetate <br />
+
-
**[[2iga]] – BfHPCD + Fe+2 + O2 + reaction intermediates<br />
+
-
**[[3eck]] – BfHPCD (mutant) + Fe+2 + reaction intermediates<br />
+
-
**[[3ojk]] – BfHPCD + Co+2 + catechol derivative<br />
+
-
**[[4ghe]], [[4ghf]] – BfHPCD (mutant) + Fe+2 + catechol derivative<br />
+
-
**[[4ghh]] – BfHPCD + Fe+2 + catechol derivative<br />
+
-
 
+
-
*Catechol 2,3-dioxygenase (MPC)
+
-
 
+
-
**[[1mpy]] – PpMPC + Fe+2 <br />
+
-
**[[3hpv]] – PsMPC + Fe+2 <br />
+
-
**[[3hpy]] – PsMPC + Fe+2 + catechol derivative<br />
+
-
**[[3hq0]] – PsMPC + Fe+3 + product<br />
+
-
**[[2wl3]], [[2wl9]] - RoMPC + Fe+3 - ''Rhodococcus opacus'' <br />
+
-
**[[3lm4]] – RoMPC + Fe+3 + H2O2<br />
+
-
**[[5zsz]] – DiMPC + Fe+3 - ''Diaphorobacter''<br />
+
-
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
+
-
 
+
-
*Naphthalene 1,2-dioxygenase (NDO)
+
-
 
+
-
**[[1ndo]], [[1o7h]], [[1o7w]] – PpNDO + Fe+3 + Fe2S2<br />
+
-
**[[2hmj]] – PpNDO (mutant) + Fe+3 + Fe2S2 <br />
+
-
**[[2b1x]] – RoNDO + Fe+3 + Fe2S2<br />
+
-
 
+
-
*''NDO complex with aromatic compound''
+
-
 
+
-
**[[1eg9]] – PpNDO + Fe+3 + Fe2S2 + indole<br />
+
-
**[[1o7g]] – PpNDO + Fe+3 + Fe2S2 + naphthalene<br />
+
-
**[[1o7m]] – PpNDO + Fe+3 + Fe2S2 + O2<br />
+
-
**[[1o7n]] – PpNDO + Fe+3 + Fe2S2 + O2 + indole<br />
+
-
**[[1o7p]] – PpNDO + Fe+3 + Fe2S2 + dihydronaphthalene<br />
+
-
**[[1uuv]], [[1uuw]] – PpNDO + Fe+3 + Fe2S2 + NO3<br />
+
-
**[[2hmk]], [[2hml]] – PpNDO (mutant) + Fe+3 + Fe2S2 + phenanthrene<br />
+
-
**[[2hmm]], [[2hmn]] – PpNDO (mutant) + Fe+3 + Fe2S2 + anthracene<br />
+
-
**[[2hmo]] – PpNDO + Fe+3 + Fe2S2 + nitrotoluene<br />
+
-
**[[2b24]] – RoNDO + Fe+3 + Fe2S2 + indole<br />
+
-
**[[4hm0]], [[4hm1]], [[4hm4]], [[4hm5]] – PsNDO + Fe+3 + Fe2S2 + indole derivative<br />
+
-
**[[4hm2]], [[4hm3]], [[4hm6]], [[4hm7]], [[4hm8]] – PsNDO + Fe+3 + Fe2S2 + phenyl derivative<br />
+
-
**[[4hjl]] – PsNDO + Fe+3 + Fe2S2 + chloronaphthalene<br />
+
-
**[[4hkv]] – PsNDO + Fe+3 + Fe2S2 + benzamide<br />
+
-
 
+
-
*Dihydronaphthalene 1,2-dioxygenase (HNDO)
+
-
 
+
-
**[[2ehz]], [[2ei2]] – PsHNDO + Fe+2 <br />
+
-
**[[2ei0]], [[2ei1]], [[2ei3]] – PsHNDO + Fe+2 + dihydroxybephenyl<br />
+
-
 
+
-
*2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBP)
+
-
 
+
-
**[[1dhy]], [[1eil]], [[1eiq]], [[1eir]] – PsDHBP + Fe+3 <br />
+
-
**[[1kw3]] – PsDHBP + Fe+2 <br />
+
-
**[[1kw8]] – PsDHBP + Fe+2 + NO<br />
+
-
**[[1kwb]] – PsDHBP (mutant) <br />
+
-
**[[1han]], [[1kmy]] – BxDHBP (mutant) + Fe+3 – ''Burkholderia xenovorans''<br />
+
-
 
+
-
*''DHBP complex with aromatic compound''
+
-
 
+
-
**[[1knd]], [[1knf]] – BxDHBP + Fe+3 + catechol derivative<br />
+
-
**[[1lgt]], [[1lkd]] – BxDHBP + Fe+2 + dihydroxybephenyl<br />
+
-
**[[1kw6]], [[1kw9]] – PsDHBP + Fe+2 + dihydroxybephenyl<br />
+
-
**[[1kwc]] – PsDHBP (mutant) + dihydroxybephenyl<br />
+
-
 
+
-
*Salicylate 1,2-dioxygenase (SDO)
+
-
 
+
-
**[[2phd]] – PssSDO + Fe+3 – ''Pseudaminobacter salicylatoxidans''<br />
+
-
**[[4fah]], [[4fbf]] – PssSDO (mutant) + Fe+3<br />
+
-
**[[3nst]] – PssSDO (mutant) + Fe+2 <br />
+
-
**[[3njz]] – PssSDO + Fe+2 +salicylate<br />
+
-
**[[3nvc]] – PssSDO (mutant) + Fe+2 +salicylate<br />
+
-
**[[3nkt ]] – PssSDO + Fe+2 +naphthoate<br />
+
-
**[[3nl1]] – PssSDO + Fe+2 +gentisate<br />
+
-
**[[3nw4]], [[4fag]] – PssSDO (mutant) + Fe+2 +gentisate<br />
+
-
 
+
-
*Biphenyl 1,2-dioxygenase (BDO)
+
-
 
+
-
**[[3gzy]] – CtBDO + Fe+2 + Fe2S2 – ''Comamonas testosteroni''<br />
+
-
**[[2xr8]] – BxBDO + Fe+2 + Fe2S2 <br />
+
-
**[[2xso]], [[2yfi]], [[5aeu]] – BxBDO (mutant) + Fe+2 + Fe2S2 <br />
+
-
**[[1uli]] - RoBDO + Fe+2 + Fe2S2 <br />
+
-
**[[2gbw]] - SyBDO + Fe+2 + Fe2S2 + O2 – ''Sphingobium yanoikuyae''<br />
+
-
 
+
-
*''BDO complex with aromatic compound''
+
-
 
+
-
**[[3gzx]] – CtBDO + Fe+2 + Fe2S2 + biphenyl <br />
+
-
**[[2xrx]] – BxBDO + Fe+2 + Fe2S2 + biphenyl <br />
+
-
**[[2xsh]], [[5aew]] – BxBDO (mutant) + Fe+2 + Fe2S2 + biphenyl <br />
+
-
**[[2yfj]], [[2yfl]] – BxBDO (mutant) + Fe+2 + Fe2S2 + dibenzofuran <br />
+
-
**[[1ulj]] - RoBDO + Fe+2 + Fe2S2 + biphenyl <br />
+
-
**[[2gbx]] - SyBDO + Fe+2 + Fe2S2 + biphenyl <br />
+
-
 
+
-
*Tryptophan 2,3-dioxygenase (TDO)
+
-
 
+
-
**[[4pw8]] - hTDO + Co+2 <br />
+
-
**[[5tia]], [[5ti9]] – hTDO + heme + tryptophan <br />
+
-
**[[6a4i]] – hTDO + heme + tryptophan + inhibitor<br />
+
-
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
+
-
**[[2nw7]] – XcTDO + heme <br />
+
-
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
+
-
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + tryptophan <br />
+
-
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + tryptophan derivative<br />
+
-
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
+
-
 
+
-
*Cysteine dioxygenase type I (CysDO)
+
-
 
+
-
**[[6bgm]], [[6bgf]], [[6e87]] – hCysDO + Fe+2 <br />
+
-
**[[2ic1]], [[6n42]] – hCysDO + Fe+2 + cysteine<br />
+
-
**[[6cdh]], [[6bpw]], [[6bpu]], [[6bpt]] – hCysDO + Fe+2 + Tyr derivative<br />
+
-
**[[6cdn]], [[6bpx]], [[6bpv]], [[6bps]] – hCysDO + Fe+2 + cysteine + Tyr derivative<br />
+
-
**[[6bpr]] – hCysDO + Fe+3 + cysteine + Tyr derivative + NO<br />
+
-
**[[6n43]] – hCysDO + 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 />
+
-
**[[4ubg]], [[4ubh]], [[5ezw]], [[5efu]], [[4ysf]], [[4yyo]] – rCysDO (mutant) + Fe+2 <br />
+
-
**[[5fdb]] – rCysDO (mutant) <br />
+
-
**[[4yni]] – rCysDO <br />
+
-
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]] – rCysDO (mutant) + Fe+3 <br />
+
-
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
+
-
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
+
-
**[[5i0u]], [[5i0t]], [[5i0s]], [[4xf4]], [[4xf9]], [[4xfa]], [[4piz]] – rCysDO + Fe+3 + cysteine derivative<br />
+
-
**[[4xf0]], [[4xf1]], [[4xfg]], [[4xfh]], [[4xfi]], [[4piy]] – rCysDO (mutant) + Fe+3 + cysteine derivative<br />
+
-
**[[4xez]], [[4xff]] – rCysDO (mutant) + Fe+3 + inhibitor <br />
+
-
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
+
-
**[[2q4s]], [[2atf]] – mCysDO + Ni+2 <br />
+
-
 
+
-
*4-hydroxyphenylpyruvate dioxygenase (HPPD)
+
-
 
+
-
**[[3isq]], [[5ec3]] – hHPPD + Co+2 <br />
+
-
**[[1sqi]] – rHPPD + Fe+3 + inhibitor - rat<br />
+
-
**[[1cjx]] – HPPD + Fe+2 – ''Pseudomonas fluorescens''<br />
+
-
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
+
-
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
+
-
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
+
-
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
+
-
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
+
-
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
+
-
**[[5yy7]], [[5yy6]], [[5ywk]] – AtHPPD + Co+2 + benquitrione <br />
+
-
**[[5ywi]] – AtHPPD (mutant) + Co+2 + NTBC <br />
+
-
**[[1sp8]] – HPPD + Fe+2 – corn<br />
+
-
**[[5hmq]] – PpHPPD + Mg+2 <br />
+
-
 
+
-
*Quercetin 2,3-dioxygenase (QDO)
+
-
 
+
-
**[[1juh]] – AjQDO + Cu+2 – ''Aspergillus japonicus''<br />
+
-
**[[2h0v]] – QDO + Fe+3 – ''Bacillus subtilis''<br />
+
-
**[[1gqg]], [[1gqh]] – AjQDO + Cu+2 + inhibitor<br />
+
-
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
+
-
**[[1h1m]] – AjQDO + Cu+2 + kaempferol<br />
+
-
 
+
-
*Taurine/α-ketoglutarate dioxygenase (TauD)
+
-
 
+
-
**[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
+
-
**[[1otj]] – EcTauD + taurine <br />
+
-
**[[3pvj]], [[3v15]] – PpTauD <br />
+
-
**[[3v17]] – PpTauD + oxoglutarate <br />
+
-
**[[3r1j]] – HAD + Fe+3 – ''Mycobacterium avium''<br />
+
-
**[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
+
-
**[[3swt]] – HAD + Fe+3 – ''Mycobacterium marinum''<br />
+
-
**[[5keu]] – BxHAD + Mg+2<br />
+
-
**[[5vn6]] – BaHAD + Mg+2<br />
+
-
 
+
-
*3-hydroxyanthranilate 3,4-dioxygenase (HAD)
+
-
 
+
-
**[[2qnk]] – hHAD + Ni+2 <br />
+
-
**[[5tkq]] – hHAD + Zn+2 <br />
+
-
**[[5tk5]] – hHAD + Fe+3 <br />
+
-
**[[3fe5]] – HAD + Fe+3 - bovine<br />
+
-
**[[1zvf]] – HAD + Ni+2 - yeast<br />
+
-
**[[5v28]], [[4r52]] – CmHAD + Fe+2 – ''Cupriavidus metallidurans''<br />
+
-
**[[5v27]], [[5v26]], [[6d60]], [[6bvr]], [[6bvp]] – CmHAD (mutant) + Fe+2 <br />
+
-
**[[1yfu]], [[4hvq]], [[4hvr]], [[4i3p]], [[4l2n]] – CmHAD + Fe+3<br />
+
-
**[[4hvo]] – CmHAD + Fe+3 + Cu+2<br />
+
-
**[[1yfw]] – CmHAD + Fe+3 + O2 + hydroxyanthranilate<br />
+
-
**[[1yfx]] – CmHAD + Fe+3 + NO + hydroxyanthranilate<br />
+
-
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
+
-
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
+
-
**[[4wzc]] – HAD + Fe+2 + enedioate derivative – ''Ralstonia metallidurans''<br />
+
-
 
+
-
*Carbazole 1,9a-dioxygenase (CDO)
+
-
 
+
-
**[[1vck]] – CDO ferredoxin component + Fe+3 + Fe2S2 – ''Pseudomonas resinovorans''<br />
+
-
**[[2de5]], [[2de6]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 – ''Janthinobacterium''<br />
+
-
**[[2de7]], [[3vmg]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole<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 />
+
-
**[[3vmi]] – JaCDO ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole + O2<br />
+
-
**[[3gcf]] – CDO terminal oxygenase component + Fe+2 + Fe2S2 – ''Nocardioides aromaticivorans''<br />
+
-
**[[3gkq]] – SpCDO terminal oxygenase component + Fe+2 + Fe2S2 <br />
+
-
 
+
-
*Homogentisate 1,2-dioxygenase (HGDO)
+
-
 
+
-
**[[1ey2]] – hHGDO + Fe+2 <br />
+
-
**[[1eyb]] – hHGDO <br />
+
-
**[[4aq2]] – PpHGDO + Fe+3 <br />
+
-
**[[4aq6]] – PpHGDO + Fe+3 + substrate<br />
+
-
**[[3zds]] – PpHGDO + Fe+3 + O2<br />
+
-
 
+
-
*Hydroxyethylphosphonate dioxygenase (PHPD)
+
-
 
+
-
**[[4yar]], [[3g7d]] – SvPHPD + Cd+2 – ''Streptomyces viridochromogenes''<br />
+
-
**[[3rzz]] – SvPHPD (mutant) + Cd+2 <br />
+
-
**[[3gbf]] – SvPHPD + Cd+2 + hydroxyethylphosphonate <br />
+
-
**[[6b9r]] – PHPD + Fe+3 + hydroxyethylphosphonate - ''Streptomyces albus''<br />
+
-
 
+
-
*Gallate dioxygenase (GD)
+
-
 
+
-
**[[3wrc]] – SpGD + Fe+2 + dehydroxybenzoate<br />
+
-
**[[3wku]], [[3wpm]], [[3wr4]] – SpGD + Fe+3 + gallate<br />
+
-
**[[3wr3]], [[3wr9]] – SpGD + Fe+2 + gallate<br />
+
-
**[[3wrb]] – SpGD (mutant) + Fe+2 + gallate<br />
+
-
**[[3wr8]], [[3wra]] – SpGD + Fe+2<br />
+
-
 
+
-
* Glyoxalase/bleomycin resistant protein/dioxygenase (GBD)
+
-
 
+
-
**[[2rbb]] – GBD – ''Burkholderia phytofirmans''<br />
+
-
**[[2rk9]] – GBD – ''Vibrio splendidus''<br />
+
-
**[[3b59]] – GBD – ''Novosphingobium aromaticivorans''<br />
+
-
**[[3kol]] – GBD – ''Nostoc punctiforme''<br />
+
-
**[[3rri]] – GBD – ''Alicyclobacillus acidocaldarius''<br />
+
-
**[[3vb0]] – GBD – ''Sphingomonas wittichii''<br />
+
-
**[[3vcx]] – GBD – ''Pseudomonas palustris''<br />
+
-
**[[4g6x]] – CaGBD – ''Catenulispora acidiphila''<br />
+
-
**[[4n04]] – CaGBD (mutant)<br />
+
-
**[[4gym]] – GBD – ''Conexibacter woesei''<br />
+
-
**[[4hc5]] – GBD – ''Sphaerobacter thermophilus''<br />
+
-
**[[4mym]] – GBD – ''Nocardioides''<br />
+
-
**[[4qb5]] – GBD – ''Albidiferax ferrireducens''<br />
+
-
**[[4rt5]] – GBD – ''Planctomyces limnophilus''<br />
+
-
**[[5uhj]], [[5ujp]] – GBD + Ni+2 – ''Streptomyces''<br />
+
-
**[[5c4p]], [[5c68]], [[5cb9]] – TcGBD + Ni+2 – ''Thermomonospora curvata''<br />
+
-
**[[5c6x]] – TcGBD + Co+2 <br />
+
-
**[[4z04]] – GBD + Zn+2 + glutathione – ''Brucella abortu''s <br />
+
-
 
+
-
* Procollagen-proline dioxygenase (PPD)
+
-
 
+
-
**[[5iat]] – BaPDD – ''Bacillus anthracis''<br />
+
-
**[[5iax]] – BaPDD + Co+2 + oxoglutarate <br />
+
-
**[[5iav]] – BaPDD + Co+2 + malonate<br />
+
-
 
+
-
* 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
+
-
 
+
-
**[[5i8s]] – mKMTPD + Ni+2 + pentanoate + valerate<br />
+
-
**[[5i8t]] – mKMTPD + Ni+2 + lactate <br />
+
-
**[[5i8y]] – mKMTPD + Co+2 + keto-methylthio-butyrate<br />
+
-
**[[5i91]] – mKMTPD + Ni+2 + keto-methylthio-butyrate<br />
+
-
**[[5i93]] – mKMTPD + Ni+2 + keto-pentanoate<br />
+
-
**[[4qgn]] – hKMTPD + Fe+3<br />
+
-
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
+
-
 
+
-
* Indoleamine 2,3-dioxygenase 1 (IAD)
+
-
 
+
-
**[[6azu]] – hIAD + heme <br />
+
-
**[[6e45]], [[6e44]] – hIAD 1 (mutant) + heme <br />
+
-
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]] – hIAD + heme + imidazole derivative<br />
+
-
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
+
-
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
+
-
**[[6azw]], [[6azv]] – hIAD + inhibitor<br />
+
-
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]] – hIAD + heme + inhibitor<br />
+
-
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
+
-
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
+
-
**[[5wmv]] – hIAD + heme + CN + indole derivative + Trp<br />
+
-
**[[5wmx]] – hIAD (mutant) + heme + CN + indole derivative + Trp<br />
+
-
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
+
-
**[[6e46]] – hIAD 1 + heme + Trp<br />
+
-
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
+
-
 
+
-
* Thymine dioxygenase (TD)
+
-
 
+
-
**[[5c3o]] – NcTD – ''Neurospora crassa''<br />
+
-
**[[5c3p]] – NcTD + oxoglutarate + Ni+2 <br />
+
-
**[[5c3q]] – NcTD + oxoglutarate + Ni+2 + thymine<br />
+
-
**[[5c3s]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative <br />
+
-
**[[5c3r]] – NcTD + oxoglutarate + Ni+2 + pyrimidine derivative + uracil derivative<br />
+
-
 
+
-
* 2,4’-dihydroxyacetophenone dioxygenase (APD)
+
-
 
+
-
**[[5bpx]], [[4p9g]] – APD + Fe+3 – ''Alcaligenes''<br />
+
-
 
+
-
*Thiol dioxygenase (ThD)
+
-
 
+
-
**[[4tlf]] – PaThD + Fe+2 – ''Pseudomonas aeruginosa''<br />
+
-
**[[4wvz]] – PaThD (mutant) + Fe+2 <br />
+
-
 
+
-
*FT_T dioxygenase (FTTD)
+
-
 
+
-
**[[6d3j]] – ShFTTD + Co+2 + oxoglutarate – ''Sphingobium herbicidovorans''<br />
+
-
**[[6d3m]] – ShFTTD + Co+2 + oxoglutarate + quinoxalin<br />
+
-
**[[6d3i]], [[6d3h]] – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative<br />
+
-
}}
+
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Solved Crystal Structure of Hyperactive Catechol Dioxygenase

Drag the structure with the mouse to rotate

References

  1. ↑ Ichiyama K, Chen T, Wang X, Yan X, Kim BS, Tanaka S, Ndiaye-Lobry D, Deng Y, Zou Y, Zheng P, Tian Q, Aifantis I, Wei L, Dong C. The methylcytosine dioxygenase Tet2 promotes DNA demethylation and activation of cytokine gene expression in T cells. Immunity. 2015 Apr 21;42(4):613-26. doi: 10.1016/j.immuni.2015.03.005. Epub 2015 , Apr 7. PMID:25862091 doi:http://dx.doi.org/10.1016/j.immuni.2015.03.005
  2. ↑ Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238 doi:http://dx.doi.org/10.1038/nature06889
  3. ↑ Jia G, Yang CG, Yang S, Jian X, Yi C, Zhou Z, He C. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 2008 Oct 15;582(23-24):3313-9. doi: 10.1016/j.febslet.2008.08.019., Epub 2008 Sep 5. PMID:18775698 doi:10.1016/j.febslet.2008.08.019
  4. ↑ Fielding AJ, Kovaleva EG, Farquhar ER, Lipscomb JD, Que L Jr. A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase. J Biol Inorg Chem. 2010 Dec 14. PMID:21153851 doi:10.1007/s00775-010-0732-0

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

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