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Last modified: 1 February 1999

Extradiol aromatic­ring­cleavage dioxygenases (EARCD)
Mononuclear iron centre Iron ligands Formal iron
oxidation/spin
states
Fe centre

Fe(NepsilonHis)2OepsilonGlu·2H2O
2×NepsilonHis;

eta1­OepsilonGlu;

2×H2O

FeII (S=2)
Fe centre+substrate

Fe(NepsilonHis)2OepsilonGlu·Substrate
2 × NepsilonHis;

eta1­OepsilonGlu;

eta2­OCatechol

FeII (S=2);

FeIII (S=5/2)

The aromatic­ring­cleavage dioxygenases open the aromatic ring by incorporating two atoms of dioxygen (O2) in their substrates, typically carrying two or more hydroxyl groups on the aromatic ring [1, 2]. If two of the hydroxyl groups of a substrate are in the ortho position, the ring fission by the extradiol aromatic­ring­cleavage dioxygenases (EARCD) occurs at a bond proximal to one of the two two hydroxyl groups (1) (cf. intradiol aromatic­ring­cleavage dioxygenases):

EARCD enzymes are highly diversified in terms of substrate specificity [1, 3]. The single FeII (or, in a few cases, MnII) serves as a prosthetic group. The sequence data [4-7] attest that there are at least two evolutionary unrelated classes of EARCD, termed type I and type II [7]. Type I EARCD contain the PROSITE EXTRADIOL_DIOXYGENAS signature and were defined as a superfamily consisting of five families and several subfamilies. The type II EARCD superfamily includes the large (ß) subunit of Pseudomonas paucimobilis protocatechuate 4,5­dioxygenase (4,5­PCD), Alcaligenes eutrophus catechol 2,3­dioxygenase I, Escherichia coli 3,4­dihydroxyphenylacetate 2,3­dioxygenase and E. coli 2,3­dihydroxyphenylpropionate 1,2­dioxygenase [5, 7].

The 3­D structures of the ligand­free form and two substrate complexes of 2,3­dihydroxybiphenyl 1,2­dioxygenase (BhpC; EC 1.13.11.39) from Pseudomonas have been reported [8, 9]. The enzyme consists of two domains which share the same fold; each domain contains two ßalphaßßß repeats (see Figure 1HAN a). The three iron ligand residues are provided by the C­terminal domain. The coordination geometry of the iron can be described as square pyramidal with His­146 serving as an axial ligand and His­210, Glu­260 and two solvent­derived ligands (presumably water) serving as equatorial ligands (Figure 1HAN b). In the BphC­substrate complexes, two hydroxyl groups of the substrate and three amino acid ligands are roughly arranged around the active site iron in a trigonal bipyramidal configuration; one catecholate hydroxyl occupies the vacant axial position, whereas the other hydroxyl displaces a solvent­derived ligand [9].

A substrate activation mechanism for EARCD has been proposed [2].

The native enzyme contains a high­spin, pentacoordinate FeII centre (I). Upon substrate binding, the solvent­derived ligands are displaced by the bidentate catecholate monoanion (II) (cf. bidentate catecholate dianion in intradiol aromatic­ring­cleavage reaction). The attack of O2 yields a superoxide­like ferric (III) or ferrous (IV) intermediate. The bound O2 attacks the meta carbon to form a peroxy intermediate (V) which decomposes by a Crigee­type rearrangement (VI) to yield the product and free enzyme (I) [2].

EARCD in enzyme databases

ENZYME LIGAND BRENDA UMBBD Official name Alternative names
1.13.11.2 1.13.11.2 1.13.11.2 e0156 Catechol 2,3­dioxygenase Metapyrocatechase
1.13.11.8 1.13.11.8 1.13.11.8 e0115 Protocatechuate 4,5­dioxygenase Protocatechuate 4,5­oxygenase
1.13.11.15 1.13.11.15 1.13.11.15 e0125 3,4­Dihydroxyphenylacetate 2,3­dioxygenase Homoprotocatechuate 2,3­dioxygenase; HPC dioxygenase
1.13.11.16 1.13.11.16 1.13.11.16
-
 3­Carboxyethylcatechol 2,3­dioxygenase 2,3­Dihydroxy­ß­phenylpropionate oxygenase
1.13.11.39 1.13.11.39 1.13.11.39 e0127 Biphenyl­2,3­diol 1,2­dioxygenase 2,3­Dihydroxybiphenyl 1,2­dioxygenase
1.13.11.- 1.13.11.- 1.13.11.- e0032 2,2',3­Trihydroxybiphenyl dioxygenase

EARCD in motif databases

PRINTS ID PRINTS AC PROSITE/BLOCKS ID PROSITE AC BLOCKS AC
-
-
 EXTRADIOL_DIOXYGENAS PS00082 BL00082

EARCD in alignment databases

Protein Superfamily Pfam LPFC 3­D alignment
00180; catechol 2,3­dioxygenase II
00184; biphenyl­2,3­diol 1,2­dioxygenase
00184; Rhodococcus biphenyl­2,3­diol 1,2­dioxygenase
-
-

EARCD in 3­D databases

EARCD contain a single iron atom in the active site; * binds an extra iron atom (see Figure 1HAN).

PDB scop BSMRELI
Base		 Header MMS Abstract ¹
1dhy 1dhy 1dhy 1dhy 2,3­Dihydroxybiphenyl 1,2­dioxygenase (BhpC enzyme); Pseudomonas sp. strain KKS102
-
1han* 1han* 1han* 1han* 2,3­Dihydroxybiphenyl 1,2­dioxygenase (BhpC enzyme) (complex with tertiary­butyl alcohol); Pseudomonas cepacia strain LB400 MS6TG1

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

  1. Harayama, S., Kok, M. and Neidle, E.L. (1992) Functional and evolutionary relationships among diverse oxygenases. Annu. Rev. Microbiol. 46, 565-601.
  2. Que, L., Jr. and Ho, R.Y.N. (1996) Dioxygen activation by enzymes with mononuclear non­heme iron active sites. Chem. Rev. 96, 2607-2624.
  3. Hirose, J., Kimura, N., Suyama, A., Kobayashi, A., Hayashida, S. and Furukawa, K. (1994) Functional and structural relationship of various extradiol aromatic ring­cleavage dioxygenases of Pseudomonas origin. FEMS Microbiol. Lett. 118, 273-277.
  4. Boldt, Y.R., Sadowsky, M.J., Ellis, L.B., Que, L., Jr. and Wackett, L.P. (1995) A manganese­dependent dioxygenase from Arthrobacter globiformis CM­2 belongs to the major extradiol dioxygenase family. J. Bacteriol. 177, 1225-1232.
  5. Spence, E.L., Kawamukai, M., Sanvoisin, J., Braven, H. and Bugg, T.D. (1996) Catechol dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (MpcI): sequence analysis and biochemical properties of a third family of extradiol dioxygenases. J. Bacteriol. 178, 5249-5256.
  6. Takami, H., Kudo, T. and Horikoshi, K. (1997) Isolation of extradiol dioxygenase genes that are phylogenetically distant from other meta­cleavage dioxygenase genes. Biosci. Biotechnol. Biochem. 61, 530-532.
  7. Eltis, L.D. and Bolin, J.T. (1996) Evolutionary relationships among extradiol dioxygenases. J. Bacteriol. 178, 5930-5937.
  8. Han, S., Eltis, L.D., Timmis, K.N., Muchmore, S.W. and Bolin, J.T. (1995) Crystal structure of the biphenyl­cleaving extradiol dioxygenase from a PCB­degrading pseudomonad. Science 270, 976-980.
  9. Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., Sato, M., Yano, K. and Mitsui, Y. (1996) Three­dimensional structures of free form and two substrate complexes of an extradiol ring­cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J. Mol. Biol. 255, 735-752.
Bibliography on structural studies of extradiol aromatic­ring­cleavage dioxygenases
Reviews on aromatic­ring­cleavage dioxygenases