Dioxygenase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
<StructureSection load='1eob' size='350' side='right' caption='Structure of protocatechuate 3,4-dioxygenase with Fe+3 complex with dihydroxybenzoate (PDB entry [[1eob]])' scene=''>
<StructureSection load='1eob' size='350' side='right' caption='Structure of protocatechuate 3,4-dioxygenase with Fe+3 complex with dihydroxybenzoate (PDB entry [[1eob]])' scene=''>
-
'''Protocatechuate 3,4-dioxygenase''' (PCD) 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.
+
'''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==
==3D structures of Protocatechuate 3,4-dioxygenase==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
 +
 +
'''Dioxygenase Intradiol family'''
[[2pcd]] – PpPCD α,β + Fe+3 – ''Pseudomonas putida''<br />
[[2pcd]] – PpPCD α,β + Fe+3 – ''Pseudomonas putida''<br />
Line 26: Line 28:
[[2buu]], [[2buy]], [[2buz]] – AcPCD α,β (mutant) + Fe+3 + catechol derivative<br />
[[2buu]], [[2buy]], [[2buz]] – AcPCD α,β (mutant) + Fe+3 + catechol derivative<br />
[[3lxv]], [[3mi5]], [[3t67]] – PpPCD α,β (mutant) + Fe+3 + catechol derivative<br />
[[3lxv]], [[3mi5]], [[3t67]] – PpPCD α,β (mutant) + Fe+3 + catechol derivative<br />
 +
 +
'''Protocatechuate 4,5-dioxygenase (PCD)'''
 +
 +
[[1b4u]] – SpPCD α,β + Fe+3 + DHB – ''Sphingomonas paucimobilis''<br />
 +
[[1bou]] – SpPCD α,β + Fe+3 <br />
'''Catechol 1,2-dioxygenase (CTD''')
'''Catechol 1,2-dioxygenase (CTD''')
[[1dlm]], [[1dlq]] – AcCTD + Fe+3 <br />
[[1dlm]], [[1dlq]] – AcCTD + Fe+3 <br />
 +
[[2azq]] – PpCTD + Fe+3 <br />
 +
[[2wl3]], [[2wl9]] - RoCTD + Fe+3 - ''Rhodococcus opacus'' <br />
''CTD complex with aromatic compound''
''CTD complex with aromatic compound''
[[1dlt]], [[1dmh]] – AcCTD + Fe+3 + catechol derivative<br />
[[1dlt]], [[1dmh]] – AcCTD + Fe+3 + catechol derivative<br />
-
[[3hgi]] – RoCTD + Fe+3 + benzoic acid – ''Rhodocoddus opacus''<br />
+
[[3hgi]] – RoCTD + Fe+3 + benzoic acid <br />
[[3hhy]], [[3hkp]] – RoCTD + Fe+3 + DHB<br />
[[3hhy]], [[3hkp]] – RoCTD + Fe+3 + DHB<br />
[[3hj8]], [[3hjq]], [[3hjs]], [[3i4v]], [[3i4y]], [[3i51]] – RoCTD + Fe+3 + catechol derivative<br />
[[3hj8]], [[3hjq]], [[3hjs]], [[3i4v]], [[3i4y]], [[3i51]] – RoCTD + Fe+3 + catechol derivative<br />
Line 48: Line 57:
[[3o6j]] – RoCCTD + Fe+3 + hydroxyquinol<br />
[[3o6j]] – RoCCTD + Fe+3 + hydroxyquinol<br />
[[3o6r]] – RoCCTD + Fe+3 + pyrogallol<br />
[[3o6r]] – RoCCTD + Fe+3 + pyrogallol<br />
 +
[[2boy]] – RoCCTD + Fe+3 + benzhydroxamate<br />
 +
 +
'''Catechol 2,3-dioxygenase (CTD)'''
 +
 +
[[3lm4]] – RoCTD + Fe+3 + H2O2<br />
 +
 +
'''Hydroxyquinol 1,2-dioxygenase (HQD)'''
 +
 +
[[1tmx]] – PpHQD + Fe+3 – ''Pimelobacter simplex''<br />
 +
 +
'''Nitrobenzene dioxygenase (NBDO)'''
 +
 +
[[2bmo]] – CtNBDO + Fe+3 + Fe2S2 <br />
 +
[[2bmq]] – CtNBDO + Fe+3 + Fe2S2 + nitrobenzene<br />
 +
[[2bmr]] – CtNBDO + Fe+3 + Fe2S2 + nitrotoluene<br />
 +
 +
'''α-ketoglutarate-dependent dioxygenase'''
 +
 +
[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
 +
[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
 +
[[4jht]] – EcAlkb + Mn+2 + qinoline derivative <br />
 +
[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
 +
[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
 +
[[3khb]] – hAlkb (mutant) + Co+2 + oxoglutarate <br />
 +
[[3i3q]] – hAlkb + Mn+2 + oxoglutarate <br />
 +
[[3thp]] – hAlkb + Mn+2 + Zn+2 + oxoglutarate <br />
 +
[[3tht]] – hAlkb (mutant) + Mn+2 + Zn+2 + oxoglutarate <br />
 +
[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
 +
[[4ie0]], [[4ie5]] – hFto + Zn+2 + pyrimidine derivative<br />
 +
[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
 +
[[4ie7]] – hFto + Zn+2 + rhein<br />
 +
 +
'''Alkb complex with DNA'''
 +
 +
[[3rzm]], [[3rzl]], [[3rzh]], [[3rzg]], [[3btz]] – hAlkb (mutant) + DNA<br />
 +
[[3h8x]], [[3h8r]], [[3h8o]], [[3bty]] – hAlkb (mutant) + DNA + inhibitor<br />
 +
[[3btx]] – hAlkb (mutant) + Mg+2 + DNA <br />
 +
[[3i49]], [[3i2o]] – hAlkb + Fe+2 + oxoglutarate + DNA <br />
 +
[[3i3m]] – hAlkb + Mn+2 + oxoglutarate + DNA<br />
 +
[[3s5a]], [[3s57]], [[3rzk]], [[3rzj]], [[3buc]], [[3bu0]], [[3bkz]] – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA<br />
 +
[[3o1r]], [[3o1p]], [[3o1o]], [[3o1m]] – hAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor<br />
 +
[[3bie]], [[3bi3]], [[2fdh]] – EcAlkb (mutant) + Mn+2 + oxoglutarate + DNA + inhibitor<br />
 +
[[2fdi]] – EcAlkb + Fe+2 + oxoglutarate + DNA + inhibitor<br />
 +
[[3khc]] – hAlkb (mutant) + Co+2 + oxoglutarate + DNA + inhibitor<br />
 +
[[3o1v]], [[3o1u]], [[3o1t]], [[3t1s]] – hAlkb (mutant) + Fe+3 + succinate + DNA + inhibitor<br />
'''Dioxygenase extradiol family'''
'''Dioxygenase extradiol family'''
Line 82: Line 136:
[[1ndo]], [[1o7h]], [[1o7w]] – PpNDO + Fe+3 + Fe2S2<br />
[[1ndo]], [[1o7h]], [[1o7w]] – PpNDO + Fe+3 + Fe2S2<br />
[[2hmj]] – PpNDO (mutant) + Fe+3 + Fe2S2 <br />
[[2hmj]] – PpNDO (mutant) + Fe+3 + Fe2S2 <br />
 +
[[2b1x]] – RoNDO + Fe+3 + Fe2S2<br />
''NDO complex with aromatic compound''
''NDO complex with aromatic compound''
Line 94: Line 149:
[[2hmm]], [[2hmn]] – PpNDO (mutant) + Fe+3 + Fe2S2 + anthracene<br />
[[2hmm]], [[2hmn]] – PpNDO (mutant) + Fe+3 + Fe2S2 + anthracene<br />
[[2hmo]] – PpNDO + Fe+3 + Fe2S2 + nitrotoluene<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)'''
'''Dihydronaphthalene 1,2-dioxygenase (HNDO)'''
Line 131: Line 191:
[[2xr8]] – BxBDO + Fe+2 + Fe2S2 <br />
[[2xr8]] – BxBDO + Fe+2 + Fe2S2 <br />
[[2xso]], [[2yfi]] – BxBDO (mutant) + Fe+2 + Fe2S2 <br />
[[2xso]], [[2yfi]] – 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''
''BDO complex with aromatic compound''
Line 138: Line 200:
[[2xsh]] – BxBDO (mutant) + Fe+2 + Fe2S2 + biphenyl <br />
[[2xsh]] – BxBDO (mutant) + Fe+2 + Fe2S2 + biphenyl <br />
[[2yfj]], [[2yfl]] – BxBDO (mutant) + Fe+2 + Fe2S2 + dibenzofuran <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)'''
'''Tryptophan 2,3-dioxygenase (TDO)'''
Line 147: Line 211:
[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + tryptophan derivative<br />
[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + tryptophan derivative<br />
[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
 +
 +
'''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 <br />
 +
[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
 +
[[2q4s]] – mCysDO + Ni+2 <br />
 +
[[2ic1]] – hCysDO + Fe+2 + cysteine<br />
'''4-hydroxyphenylpyruvate dioxygenase (HPPD)'''
'''4-hydroxyphenylpyruvate dioxygenase (HPPD)'''
Line 156: Line 227:
[[1tfz]], [[1tg5]] – AtHPPD + Fe+3 + inhibitor <br />
[[1tfz]], [[1tg5]] – AtHPPD + Fe+3 + inhibitor <br />
[[3isq]] – hHPPD + Co+2 - human<br />
[[3isq]] – hHPPD + Co+2 - human<br />
 +
[[1sp8]] – HPPD + Fe+2 – corn<br />
'''Quercetin 2,3-dioxygenase (QDO)'''
'''Quercetin 2,3-dioxygenase (QDO)'''
Line 167: Line 239:
'''Taurine/α-ketoglutarate dioxygenase (TauD)'''
'''Taurine/α-ketoglutarate dioxygenase (TauD)'''
-
[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate – ''Escherichia coli''<br />
+
[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
[[1otj]] – EcTauD + taurine <br />
[[1otj]] – EcTauD + taurine <br />
[[3pvj]], [[3v15]] – PpTauD <br />
[[3pvj]], [[3v15]] – PpTauD <br />
[[3v17]] – PpTauD + oxoglutarate <br />
[[3v17]] – PpTauD + oxoglutarate <br />
 +
[[3r1j]] – HAD + Fe+3 – ''Mycobacterium avium''<br />
 +
[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
'''3-hydroxyanthranilate 3,4-dioxygenase (HAD)'''
'''3-hydroxyanthranilate 3,4-dioxygenase (HAD)'''

Revision as of 10:09, 26 February 2014

Structure of protocatechuate 3,4-dioxygenase with Fe+3 complex with dihydroxybenzoate (PDB entry 1eob)

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

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

Retrieved from "http://52.214.119.220/wiki/index.php/Dioxygenase"
Personal tools