Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by 3-unsaturated 1,2-diols and thioglycerol

Journal of Biochemistry

Volumn 144, Issue 4, 2008, Pages 437-446

  Toraya, Tetsuo ^a   Tamura, Naohisa ^a   Watanabe, Takeshi ^a   Yamanishi, Mamoru ^a   Hieda, Naoki ^a   Mori, Koichi ^a  

^a OKAYAMA UNIVERSITY   (Japan)

Author keywords

Adenosylcobalamin; Coenzyme B12; Diol dehydratase; Mechanism based inactivation; Radical enzyme

Indexed keywords

1,2 BUTANEDIOL; 3 BUTENE 1,2 DIOL; 3 BUTYNE 1,2 DIOL; 5' DEOXYADENOSINE; ADENOSINE DERIVATIVE; ADENOSINE TRIPHOSPHATE; ALCOHOL DERIVATIVE; COBAMAMIDE; DIOL DEHYDRATASE; HOLOENZYME; HYDROLYASE; MAGNESIUM; PROPYLENE GLYCOL; THIOGLYCEROL; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL BOND; CHEMICAL STRUCTURE; ELECTRON SPIN RESONANCE; ENZYME ACTIVITY; ENZYME INACTIVATION; ENZYME KINETICS; ENZYME MECHANISM; ENZYME METABOLISM; ENZYME REACTIVATION; ENZYME SUBSTRATE; OXIDATION;

BUTYLENE GLYCOLS; COBAMIDES; ELECTRON SPIN RESONANCE SPECTROSCOPY; ENZYME INHIBITORS; ESCHERICHIA COLI; GLYCEROL; GLYCOLS; KINETICS; MODELS, MOLECULAR; PROPANEDIOL DEHYDRATASE;

EID: 53549085130     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvn086     Document Type: Article

References (61)

1. 12-dependent isomerization (eliminating) reactions. Chem. Rev. 103, 2095-2127
2. 12-dependent mutases. Chem. Rev. 103, 2083-2094
3. 12. Chem. Rev. 105, 2075-2149
4. Lee, H.A. Jr. and Abeles, R.H. (1963) Purification and properties of dioldehydrase, an enzyme requiring a cobamide coenzyme. J. Biol. Chem. 238, 2367-2373
5. Rétey, J., Umani-Ronchi, A., Seibl, J., and Arigoni, D. (1966) On the mechanism of the propanediol dehydrase reaction. Experientia 22, 502-503
6. Zagalak, B., Frey, P.A., Karabatsos, G.L., and Abeles, R.H. (1966) The stereochemistry of the conversion of D and L 1,2-propanediols to propionaldehyde. J. Biol. Chem. 241, 3028-3035
7. Rétey, J., Umani-Ronchi, A., and Arigoni, D. (1966) On the stereochemistry of the propanediol dehydrase reaction. Experientia 22, 72-73
8. 12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A° resolution. Structure 4, 339-350
9. 12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase. Structure 7, 997-1008
10. 12-dependent enzyme provides new mechanistic insights. Structure 7, 891-902
11. Sintchak, M.D., Arjara, G., Kellogg, B.A., Stubbe, J., and Drennan, C.L. (2002) The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Nat. Struct. Biol. 9, 293-300
12. 12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur. J. Biochem. 269, 4484-4494
13. Berkovitch, F., Behshad, E., Tang, K.-H., Enns, E.A., Frey, P.A., and Drennan, C.L. (2004) A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc. Natl. Acad. Sci. USA 101, 15870-15875
14. 12: X-ray structure of a dioldehydratase-adeninylpentylcobalamin complex. Structure 8, 775-788
15. 12 dependent enzyme glutamate mutase. Angew. Chem. Int. Ed. Engl. 40, 3377-3380
16. 12 (Dolphin, D., ed.) Vol. 2, pp. 325-392, John Wiley & Sons, New York
17. Toraya, T., Watanabe, N., Ichikawa, M., Matsumoto, T., Ushio, K., and Fukui, S. (1987) Activation and cleavage of the carbon-cobalt bond of adeninylethylcobalamin by diol dehydrase. J. Biol. Chem. 262, 8544-8550
18. 12 chemistry: The crystal and molecular structure of cob(II)alamin. J. Am. Chem. Soc. 111, 8936-8938
19. 12-dependent diol dehydratase. J. Biol. Chem. 278, 22717-22725
20. 12 coenzyme-dependent ethanolamine deaminase catalysis. J. Am. Chem. Soc. 121, 10522-10528. Correction (2008) 138, 6055.
21. 13C electron nuclear double resonance studies. Biochemistry 40, 9-14
22. 12-dependent glutamate mutase from Clostridium cochlearium. Biochemistry 37, 4105-4113
23. Yamanishi, M., Ide, H., Murakami, Y., and Toraya, T. (2005) Identification of the 1,2-propanediol-1-yl radical as an intermediate in adenosylcobalamin-dependent diol dehydratase reaction. Biochemistry 44, 2113-2118
24. Mansoorabadi, S.O., Padmakumar, R., Fazliddinova, N., Vlasie, M., Banerjee, R., and Reed, G.H. (2005) Characterization of a succinyl-CoA radical-cob(II)alamin spin triplet intermediate in the reaction catalyzed by adenosylcobalamin-dependent methylmalonyl-CoA mutase. Biochemistry 44, 3153-3158
25. Wagner, O.W., Lee, H.A. Jr., Frey, P.A., and Abeles, R.H. (1966) Studies on the mechanism of action of cobamide coenzymes. Chemical properties of the enzyme-coenzyme complex. J. Biol. Chem. 241, 1751-1762
26. 12(r) in the reaction of dioldehydrase with chloroacetaldehyde. J. Biol. Chem. 247, 4197-4207
27. Abend, A., Bandarian, V., Reed, G.H., and Frey, P.A. (2000) Identification of cis-ethanesemidione as the organic radical derived from glycolaldehyde in the suicide inactivation of dioldehydrase and of ethanolamine ammonia-lyase. Biochemistry 39, 6250-6257
28. Schwartz, P., LoBrutto, R., Reed, G.H., and Frey, P.A. (2003) Suicide inactivation of dioldehydrase by 2-chloroacetaldehyde: formation of the "cis-ethanesemidione" radical, and the role of a monovalent cation. Helv. Chim. Acta 86, 3764-3775
29. Bachovchin, W.W., Eagar, R.G. Jr., Moore, K.W., and Richards, J.H. (1977) Mechanism of action of adenosylcobalamin: glycerol and other substrate analogues as substrates and inactivators for propanediol dehydratase - kinetics, stereospecificity, and mechanism. Biochemistry 16, 1082-1092
30. Tobimatsu, T., Hara, T., Sakaguchi, M., Kishimoto, Y., Wada, Y., Isoda, M., Sakai, T., and Toraya, T. (1995) Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca. J. Biol. Chem. 270, 7142-7148
31. Mori, K., Tobimatsu, T., Hara, T., and Toraya, T. (1997) Characterization, sequencing, and expression of the genes encoding a reactivating factor for glycerol-inactivated adenosylcobalamin-dependent diol dehydratase. J. Biol. Chem. 272, 32034-32041
32. 12-dependent diol dehydratase. J. Biol. Chem. 274, 3372-3377
33. 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. Biphys. 347, 132-140
34. Toraya, T., Ushio, K., Fukui, S., and Hogenkamp, H.P.C. (1977) Studies on the mechanism of the adenosylcobalamin-dependent diol dehydrase reaction by the use of analogs of the coenzyme. J. Biol. Chem. 252, 963-970
35. Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319-326
36. Beinert, H. (1983) Semi-micro methods for analysis of labile sulfide and of labile sulfide plus sulfane sulfur in unusually stable iron-sulfur proteins. Anal. Biochem. 131, 373-378
37. Barker, H.A., Smyth, R.D., Weissbach, H., Munch-Petersen, A., Toohey, J.I., Ladd, J.N., Volcani, B.E., and Wilson, R.M. (1960) Assay, purification, and properties of the adenylcobamide coenzyme. J. Biol. Chem. 235, 181-190
38. Yamanishi, M., Yamada, S., Muguruma, H., Murakani, Y., Tobimatsu, T., Ishida, A., Yamauchi, J., and Toraya, T. (1998) Evidence for axial coordination of 5,6-dimethylbenzimidazole to the cobalt atom of adenosylcobalamin bound to diol dehydratase. Biochemistry 37, 4799-4803
39. 12-dependent diol dehydratase by a molecular chaperone-like reactivating factor. Biochemistry 38, 13170-13178
40. 12-dependent diol dehydrase: glycerol as both a good substrate and a potent inactivator. Biochem. Biophys. Res. Commun. 69, 475-480
41. 12 (Banerjee, R., ed.) pp. 783-809, John Wiley & Sons, New York
42. Toraya, T., Watanabe, N., Ushio, K., Matsumoto, T., and Fukui, S. (1983) Ligand exchange reactions of diol dehydrase-bound cobalamins and the effect of the nucleoside binding. J. Biol. Chem. 258, 9296-9301
43. 12 coenzymes in the reaction catalyzed by dioldehydrase. Biochemistry 18, 417-426
44. 12-dependent propanediol dehydratase systems. Ternary complex between apoenzyme, coenzyme, and substrate analog. Biochim. Biophys. Acta 284, 536-548
45. 12. Biochim. Biophys. Acta 397, 510-518
46. 12-enzyme reaction. Biochim. Biophys. Acta 480, 495-505
47. 12-dependent enzyme reactions. J. Chem. Soc. Faraday II 74, 417-431
48. Sandala, G.M., Smith, D.M., Coote, M.L., Golding, B.T., and Radom, L. (2006) Insights into the hydrogen-abstraction reactions of diol dehydratase: relevance to the catalytic mechanism and suicide inactivation. J. Am. Chem. Soc. 128, 3433-3444
49. Bandarian, V., Poyner, R.R., and Reed, G.H. (1999) Hydrogen atom exchange between 5′-deoxyadenosine and hydroxyethylhydrazine during the single turnover inactivation of ethanolamine ammonia-lyase. Biochemistry 38, 12403-12407
50. Yoon, M., Patwardhan, A., Qiao, C., Mansoorabadi, S.O., Menefee, A.L., Reed, G.H., and Marsh, E.N.G. (2006) Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thioglutarate. Biochemistry 45, 11650-11657
51. Tang,, K.-H, Chang, C.H., and Frey, P.A. (2001) Electron transfer in the substrate-dependent suicide inactivation of lysine 5,6-aminomutase. Biochemistry 40, 5190-5199
52. Magnusson, O.T. and Frey, P.A. (2002) Interactions of diol dehydrase and 3′,4′-anhydroadenosylcobalamin: suicide inactivation by electron transfer. Biochemistry 41, 1695-1702
53. 12-dependent methylmalonyl-CoA mutase. Biochemistry 45, 2951-2959
54. Vlasie, M.D. and Banerjee, R. (2004) When a spectator turns killer: suicidal electron transfer from cobalamin in methyl-malonyl-CoA mutase. Biochemistry 43, 8410-8417
55. Huhta, M.S., Ciceri, D., Golding, B.T., and Marsh, E.N.G. (2002) A novel reaction between adenosylcobalamin and 2-methyleneglutarate catalyzed by glutamate mutase. Biochemistry 41, 3200-3206
56. 12 analog. Arch. Biochem. Biophys. 203, 174-180
57. Toraya, T. and Ishida, A. (1991) Roles of the D-ribose and 5,6-dimethylbenzimidazole moieties of the nucleotide loop of adenosylcobalamin in manifestation of coenzymic function in the diol dehydrase reaction. J. Biol. Chem. 266, 5430-5437
58. Ishida, A. and Toraya, T. (1993) Adenosylcobinamide methyl phosphate as a pseudocoenzyme for diol dehydrase. Biochemistry 32, 1535-1540
59. Mori, K., Bando, R., Hieda, N., and Toraya, T. (2004) Identification of a reactivating factor for adenosylcobalamin-dependent ethanolamine ammonia lyase. J. Bacteriol. 186, 6845-6854
60. Kajiura, H., Mori, K., Tobimatsu, T., and Toraya, T. (2001) Characterization and mechanism of action of a reactivating factor for adenosylcobalamin-dependent glycerol dehydratase. J. Biol. Chem. 276, 36514-36519
61. 12- dependent glycerol dehydratase of Citrobacter freundii. Eur. J. Biochem. 268, 2369-2378