Dioxygenase

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.

3D structures of Protocatechuate 3,4-dioxygenase

Updated on 03-July-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

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