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.
Contents
- 1 3D structures of Protocatechuate 3,4-dioxygenase
- 1.1 Dioxygenase Intradiol family
- 1.2 Protocatechuate 4,5-dioxygenase (PCD)
- 1.3 Catechol 1,2-dioxygenase (CTD)
- 1.4 Chlorocatechol 1,2-dioxygenase (CCTD)
- 1.5 Catechol 2,3-dioxygenase (CTD)
- 1.6 Hydroxyquinol 1,2-dioxygenase (HQD)
- 1.7 Nitrobenzene dioxygenase (NBDO)
- 1.8 α-ketoglutarate-dependent dioxygenase (Alkb)
- 1.9 Dioxygenase extradiol family
- 1.10 Homoprotocatechuate 2,3-dioxygenase (HPCD)
- 1.11 Catechol 2,3-dioxygenase (MPC)
- 1.12 Naphthalene 1,2-dioxygenase (NDO)
- 1.13 Dihydronaphthalene 1,2-dioxygenase (HNDO)
- 1.14 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBP)
- 1.15 Salicylate 1,2-dioxygenase (SDO)
- 1.16 Biphenyl 1,2-dioxygenase (BDO)
- 1.17 Tryptophan 2,3-dioxygenase (TDO)
- 1.18 Cysteine dioxygenase type I (CysDO)
- 1.19 4-hydroxyphenylpyruvate dioxygenase (HPPD)
- 1.20 Quercetin 2,3-dioxygenase (QDO)
- 1.21 Taurine/α-ketoglutarate dioxygenase (TauD)
- 1.22 3-hydroxyanthranilate 3,4-dioxygenase (HAD)
- 1.23 Carbazole 1,9a-dioxygenase (CDO)
- 1.24 Homogentisate 1,2-dioxygenase (HGDO)
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3D structures of Protocatechuate 3,4-dioxygenase
Updated on 17-August-2014
Dioxygenase Intradiol family
2pcd – PpPCD α,β + Fe+3 – Pseudomonas putida
3pcd, 1ykk, 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 – 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
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
Catechol 2,3-dioxygenase (CTD)
2wl3, 2wl9 - RoCTD + Fe+3 - Rhodococcus opacus
3lm4 – RoCTD + Fe+3 + H2O2
Hydroxyquinol 1,2-dioxygenase (HQD)
1tmx – PpHQD + Fe+3 – Pimelobacter simplex
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)
3t4h, 3t4v, 3t3y – EcAlkb + Fe+3 + inhibitor – Escherichia coli
2fdj, 2fdg – EcAlkb + Mn+2 + succinate
4jht – EcAlkb + Mn+2 + qinoline derivative
2fdf – EcAlkb (mutant) + Co+2 + oxoglutarate
2fd8 – EcAlkb (mutant) + Fe+2 + oxoglutarate
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
4idz – hFto + Ni+2 + oxalylglycine
4ie0, 4ie5 – hFto + Zn+2 + pyrimidine derivative
4ie4, 4ie6 – hFto + Zn+2 + quinoline derivative
4ie7 – hFto + Zn+2 + rhein
Alkb complex with DNA
3rzm, 3rzl, 3rzh, 3rzg, 3btz – hAlkb (mutant) + DNA
3h8x, 3h8r, 3h8o, 3bty – hAlkb (mutant) + DNA + inhibitor
3btx – hAlkb (mutant) + Mg+2 + DNA
3i49, 3i2o – hAlkb + Fe+2 + oxoglutarate + 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
Dioxygenase extradiol family
Homoprotocatechuate 2,3-dioxygenase (HPCD)
1f1r, 1f1u – AgHPCD + Mn+2 – Arthrobacter globiformis
1f1x, 1q0o – BfHPCD + Fe+3 – Brevibacterium fuscum
2ig9, 3ojt – BfHPCD + Fe+2
3ecj, 4ghc – BfHPCD (mutant) + Fe+2
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 - Pseudomonas
3hpy – PsMPC + Fe+2 + catechol derivative
3hq0 – PsMPC + Fe+3 + product
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 – 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 – 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)
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)
2gh2, 4ieo, 4iep, 4ieq, 4ier, 4ies, 4iet, 4ieu, 4iev, 4iew, 4iex, 4iey, 4iez, 4jtn, 4jto, 4kwj, 4kwk, 4kwl – rCysDO + Fe+2 – rat
3eln – rCysDO + Fe+2 + cysteine derivative
2q4s – mCysDO + Ni+2
2ic1 – hCysDO + Fe+2 + cysteine
4-hydroxyphenylpyruvate dioxygenase (HPPD)
1cjx – HPPD + Fe+2 – Pseudomonas fluorescens
1t47 – HPPD + Fe+2 – Streptomyces avermitilis
1sqd, 1sp9 – AtHPPD + Fe+3 – Arabidopsis thaliana
1sqi – HPPD + Fe+3 + inhibitor - rat
1tfz, 1tg5 – AtHPPD + Fe+3 + inhibitor
3isq – hHPPD + Co+2 - human
1sp8 – HPPD + Fe+2 – corn
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
3-hydroxyanthranilate 3,4-dioxygenase (HAD)
1yfu – CmHAD + Fe+3
1yfw – CmHAD + Fe+3 + O2 + hydroxyanthranilate
1yfx – CmHAD + Fe+3 + NO + hydroxyanthranilate
1yfy – CmHAD + Fe+3 + hydroxyanthranilate
1zvf – HAD + Ni+2 - yeast
2qnk – hHAD + Ni+2
3fe5 – HAD + Fe+3 - bovine
Carbazole 1,9a-dioxygenase (CDO)
1vck – HAD ferredoxin component + Fe+3 + Fe2S2 – Pseudomonas resinovorans
2de5, 2de6 – JaHAD ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 – Janthinobacterium
2de7, 3vmg – JaHAD ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole
3vmh – JaHAD ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + O2
3vmi – JaHAD ferredoxin and terminal oxygenase components + Fe+3 + Fe2S2 + carbazole + O2
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
