Catechol dioxygenases structure

Figure 13.21 Mononuclear non-haem iron enzymes from each of the five families in structures which are poised for attack by 02. (a) The extradiol-cleaving catechol dioxygenase, 2,3-dihydroxy-biphenyl 1,2-dioxygenase (b) the Rieske dioxygenase, naphthalene 1,2-dioxygenase (c) isopenicillin N-synthase (d) the ot-ketoglutarate dependent enzyme clavaminate synthase and (e) the pterin-dependent phenylalanine hydroxylase. (From Koehntop et al., 2005. With kind permission of Springer Science and Business Media.)...

Figure 2.3 Molecular structure of [Fe(Me3TACN)(DBC)CI], a model complex for a catechol dioxygenase coordinated to its substrate molecule [28]. Hydrogen atoms have been omitted for clarity. The l,4,7-trimethyl-l,4,7-triazacyclononane (Me3TACN) ligand coordinates facially to the iron center. The remaining three coordination sites are occupied by 3,5-di-tert-butylcatecholate (DBC) and a chlorido ligand.

Dioxygenase enzymes are known that contain heme iron, nonheme iron, copper, or manganese.The substrates whose oxygenations are catalyzed by these enzymes are very diverse, as are the metal-binding sites so probably several, possibly unrelated, mechanisms operate in these different systems. For many of these enzymes, there is not yet much detailed mechanistic information. However, some of the intradiol catechol dioxygenases isolated from bacterial sources have been studied in great detail, and both structural and mechanistic information is available. These are the systems that will be described here. 

A large family of these enzymes is now known, and their enzymology and structures have been reviewed. A number of crystal structures have been obtained for enzymes in this family, and in each case the mononuclear iron(II) center is coordinated by a His,His,Glu motif, also observed in the extradiol catechol dioxygenases, and in other nonheme iron-dependent enzymes. Structural studies on clavaminic acid synthase have indicated the structural basis for the separate hydroxylation and oxidative cyclization/ desaturation reactions catalyzed by this enzyme. ... 

The asymmetric bonding motif of the catecholate to the ferric ion in these complexes duplicates the binding motif in the enzyme-substrate structures that have been characterized. While the original belief that this asymmetry in Fe—O bond lengths was critical to the reactivity of the systems has since proven incorrect,the complexes remain as functional models for the catechol dioxygenases due to both their structural and reactivity features. All complexes have been characterized as high-spin ferric catecholate complexes by UV-visible, EPR and NMR spectroscopy, and an examination of C—O bond length in these complexes shows all of the complexes to bind in the catecholate form with no semiquinonate character. ... 

Coordination of the active site metal by water molecules and substrates is obviously much more variable and the X-ray structure may be of little assistance. In order to determine experimentally the orientation of the substrate, a crystal would need to be grown with the substrate bound. Notwithstanding the problems of obtaining X-ray quality crystals in the first place, by its very nature, the enzyme will attempt to convert the substrate to product and capturing a bound state may not be possible. However, many reactions require an additional reactant—say a molecule of O2—and thus the substrate-bound form may remain stable under anaerobic conditions. The structure of catechol dioxygenase with substrate bound has been determined in this way [36]. 

The other important contribution of the model systems to the progress in enzymatic studies is to obtain information about structures and reactivities of substrate-metal intermediates. One of the characteristic examples is the isolation of mono- and bi-dentate catecholatoiron(III) complexes in relevance to catechol dioxygenases. Reactivities of these... 

This result indicates that modification of ligands provides good functional models for catechol dioxygenases. Recently, both functional and structural model studies for Fe -enzymes have started. This is a challenge to the model studies for the V 102 systems which seem to have the higher barrier to be overcome than the Fe /02 system. It is expected that catalytic systems for selective extradiol oxygenation of catechols by iron complexes will be developed in future. 

Structural models for substrateAron binary intermediates of intradioTcleaving catechol dioxygenases... 

As described in Chapter 2, the intermediate formation of binary (ES) and ternary species (ESO2) has been proposed in the oxygenation by catechol dioxygenase (E) as shown in eq. (10) [68, 69]. It is assumed that ES exhibits a peak around 700 nm, and ESO2 at 540 nm [69]. Many reports have appeared for the formation and structures of ES from both enzymes and model studies, but until now there has been no direct evidence for the formation of ESO2 species. 

Structural models for substrate-iron binary intermediates of extradiol-cleaving catechol dioxygenases... 

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