Diols dehydratase

Towards the unification of coenzyme B12-dependent diol dehydratase stereochemical and model studies the bound radical mechanism. R. G. Finke, D. A. Schiraldi and B. J. Mayer, Coord. Chem. Rev., 1984, 54,1-22 (40). 

Schramm E, B Schink (1991) Ether-cleaving enzyme and diol dehydratase involved in anaerobic polyethylene glycol degradation by a new Acetobacterium sp. Biodegradation 2 71-79. 

The structure of the E. coli enzyme (Fig. 16-24) shows methylcobalamin bound in a base-off conformation, with histidine 759 of the protein replacing dimethylbenzimidazole in the distal coordination position on the cobalt. This histidine is part of a sequence Asp-X-His-X-X-Gly that is found not only in methionine synthase but also in methylmalonyl-CoA mutase, glutamate mutase, and 2-methyleneglutarate mutase. However, diol dehydratase lacks this sequence and binds adenosylcobalamin with the dimethylbenz-imidazole-cobalt bond intact.417... 

Toraya, T., Enzymatic radical catalysis Coenzyme B-12-dependent diol dehydratase , Chemical Record 2002, 2, 352-366. 

Fig. 19. Equilibration of substrate and intermediate between the two binding modes in the active site of diol dehydratase.

Tobimatsu, T., Sakai, T., Hashida, Y., Mizoguchi, N., Miyoshi, S., and Toraya, T., 1997, Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca, Arch. Biochem. Biophys. 347 1320140. 

Tobimatsu, T., Azuma, M., Hayashi, S., Nishimoto, K., and Toraya, T., 1998, Molecular cloning, sequencing and characterization of the genes for adenosylcobalamin-dependent diol dehydratase of Klebsiella pneumoniae. Biosci. Biotechnol. Biochem. 62(9) 1774n Mil. 

Toraya, T., Miyoshi, S., Mori, M., and Wada, K., 1994, The synthesis of a pyridyl analog of adenosylcobalamin and its coenzymic function in the diol dehydratase reaction, Biochim. Biophys. Acta. 1204 169nl74. 

Yamanishi, M., Yamada, S., Ishida, A., Yamauchi, J., and Toraya, T., 1998a, EPR spectroscopic evidence for the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydratase by coenzyme analogs, J. Biochem. (Tokyo) 124 5989601. 

About 10 coenzyme B -dependent enzymes are now known (reviewed in References 13,14, and 76 see Table 1) four carbon skeleton mutases (methylmalonyl-CoA mutase (MMCM), glutamate mutase (GM), methylene glu-tarate mutase (MGM), isobutyryl-CoA mutase (ICM) ), diol dehydratase (DD), glycerol dehydratase, ethanol-amine anunonia lyase (EAL), two amino mutases, and Bi2-dependent ribonucleotide reductase. The coenzyme Bi2-dependent enzymes are unevenly distributed in the living world, and MMCM is the only enzyme that is also indispensable in human metabolism. ... 

This property of alkylcobaloximes and alkylcobalamins has been used to model the conversion of 1,2-diols to aldehydes catalyzed by the adenosyl-cobalamin-dependent enzyme diol dehydratase. For example, both organo-cobalamins (726, 126a) and alkylcobaloximes 126a, b) were shown to convert 1,2-diols to aldehydes under photolytic conditions. Lappert et al. 

Kamachi T, Toraya T, Yoshizawa K. Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B 12-dependent diol dehydratase. Chem. Eur. J. 2007 13 7864-7873. 

The enzyme-coenzyme partnership involving diol dehydratase catalyzes the dehydration of both ethane-1,2-diol and propane-1,2-diol. 

The first common step in AdoCbl-dependent readions is homolytic cleavage of the cobalt-carbon bond to generate a radical pair, cob(ii)alamin and the carbon-centered dAdo radical (Scheme 19.3). This reaction experiences a 10 -fold rate enhancement in B12 enzymes [14, 15] in the presence of substrate, and the mechanism for this rate acceleration has been the subject of extensive scrutiny. Thus, in methylmalonyl-CoA mutase and in glutamate mutase, little if any destabilization of the cobalt-carbon bond is observed in the reactant state, as revealed by resonance Raman spectroscopy [16, 17], and the intrinsic substrate binding is utilized to labilize the bond. In contrast, approximately half of the destabilization of the cobalt-carbon bond in diol dehydratase is expressed in the reactant state. This re-... 

Diol dehydratase and ethanolamine ammonia lyase exhibit the largest overall tritium isotope effects that have been measured in Bi2-dependent enzymes [44, 45], the overall deuterium kinetic isotope effect is also substantial [10, 34, 45]. The observation of a deuterium isotope effect on the pre-steady-state formation of cob(ii)alamin in diol dehyratase [10] and in ethanolamine ammonia lyase [25] is consistent with kinetic coupling between the homolysis and H-transfer steps. 

Toraya et al. [60-63] used B3LYP (with the 6-311G(d) basis set) for calculations on the H-atom transfer steps in diol dehydratase reaction. Both H-atom transfers, i.e., from the substrate and re-abstraction of a hydrogen atom from 5 -deoxyadenosine, were considered. The models used in these studies included the substrate, 1,2-propanediol, a potassium cation found in the active site, and an ethyl radical as a mimic of the dAdo radical (Fig. 19.1). The activation barrier for the abstraction of the pro-S hydrogen atom of substrate by dAdo was calculated to be 9.0 kcal mol while the activation barrier for the reverse reaction between product radical and 5 -deoxyadenosine was 15.7 kcal moUk In the absence of the potassium cation the forward activation barrier is 9.6 kcal moU indicating that coordination of the substrate by the potassium cation has a minimal energetic effect on the H-atom transfer step, but seems to hold the substrate and intermediates in... 

Figure 19.1. Model [61-63] of hydrogen atom transfer steps in diol dehydratase reaction.

Shibata, N., Masuda, J., Tobimatsu, T., Toraya, T., Suto, K., Morimoto, Y., Yasuoka, N. (1999) A new mode of Bi2 binding and the direct participation of a potassium ion in enzyme catalysis X-ray structure of diol dehydratase, Structure Fold Des. 7, 997-1008. 

Mori, K., Toraya, T. (1999) Mechanism of reactivation of coenzyme B12-dependent diol dehydratase by a molecular chaperone-like reactivating factor. Biochemistry 38, 13170-13178. 

Radom, L. (2001) Understanding the mechanism of Bi2-dependent diol dehydratase a synergistic retro-push-pull proposal,/. Am. Chem. Soc. 123, 1664-1675. 

Toraya, T., Yoshizawa, K., Eda, M., Yamabe, K. (1999) Direct participation of potassium ion in the catalysis of coenzyme Bi2-dependent diol dehydratase,/. Biochem. Tokyo) 126, 650-654. 

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