Analysis of the Cob(II)alamin-5′-deoxy-3′,4′- anhydroadenosyl radical triplet spin system in the active site of diol dehydrase

Biochemistry

Volumn 45, Issue 48, 2006, Pages 14362-14370

  Mansoorabadi, Steven O ^a,b   Magnusson, Olafur Th ^a,c   Poyner, Russell R ^a   Frey, Perry A ^a   Reed, George H ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c DECODE GENETICS   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRON SPIN RESONANCE SPECTROSCOPY; ISOTOPES; LOW TEMPERATURE EFFECTS; MAGNETIC MOMENTS; PARAMAGNETIC RESONANCE; SPECTRUM ANALYSIS; TENSORS;

DIOL DEHYDRASES; ISOTOPIC LABELING; RHOMBIC SYMMETRY;

ENZYMES;

5' DEOXY 3',4' ANHYDROADENOSYLCOBALAMIN; CARBON 13; COBALAMIN; COBALT; COBAMAMIDE; DEUTERIUM; DIOL DEHYDRASE; ENZYME; PROPYLENE GLYCOL; RADICAL;

ARTICLE; COENZYME; DIPOLE; ELECTRON SPIN RESONANCE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME SUBSTRATE; ISOTOPE LABELING; MAGNETISM; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL;

BINDING SITES; COBAMIDES; COENZYMES; ELECTRON SPIN RESONANCE SPECTROSCOPY; FREE RADICALS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OXYGEN; PROPANEDIOL DEHYDRATASE; SALMONELLA TYPHIMURIUM; VITAMIN B 12;

EID: 33845267636     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061586q     Document Type: Article

References (50)

1. 12-dependent enzymes, Biochemistry 40, 6191-6198.
2. Marsh, E. N. G., and Drennan, C. L. (2001) Adenosylcobalamin-dependent isomerases: New insights into structure and mechanism, Curr. Opin. Chem. Biol. 5, 499-505.
3. Reed, G. H. (2004) Radical mechanisms in adenosylcobalamin-dependent enzymes, Curr. Opin. Chem. Biol. 8, 477-483.
4. Finke, R. G. (1984) Thermolysis of adenosylcobalamin: A product, kinetic, and Co-C5′ bond dissociation energy study, Inorg. Chem. 23, 3041-3043.
5. Padmakumar, R., Padmakumar, R., and Banerjee, R. (1997) Evidence that cobalt-carbon bond homolysis is coupled to hydrogen atom abstraction from substrate in methylmalonyl-CoA mutase, Biochemistry 36, 3713-3718.
6. Marsh, E. N. G., and Ballou, D. P. (1998) Coupling of cobalt-carbon bond homolysis and hydrogen atom abstraction in adenosylcobalamin-dependent glutamate mutase, Biochemistry 37, 11864-11872.
7. Bandarian, V., and Reed, G. H. (2000) Isotope effects in the transient phases of the reaction catalyzed by ethanolamine ammonia-lyase: Determination of the number of exchangeable hydrogens in the enzyme-cofactor complex, Biochemistry 39, 12069-12075.
8. 12-dependent isomerization (eliminating) reactions, Chem. Rev. 103, 2095-2128.
9. 12-dependent ribonucleotide reductase: Evidence for the participation of five cysteine residues in ribonucleotide reduction, Biochemistry 33, 12676-12685.
10. Chen, D., Abend, A., Stubbe, J., and Frey, P. A. (2003) Epimerization at carbon-5′ of (5′R)-[5′-2H]adenosylcobalamin by ribonucleoside triphosphate reductase: Cysteine 408-independent cleavage of the Co-C5′ bond, Biochemistry 42, 4578-4584.
11. 12 (Banerjee, R., Ed.) pp 783-809, Wiley-Interscience, New York.
12. Walling, C., and Johnson, R. A. (1975) Fenton's reagent. Rearrangements during glycol oxidations, J. Am. Chem. Soc. 97, 2405-2407.
13. Golding, B. T., and Buckel, W. (1997) Corrin-dependent reactions, in Comprehensive Biological Catalysis (Sinnott, M. L., Ed.) pp 239-260, Academic Press, London.
14. 12-dependent diol dehydratase: A synergistic retro-push-pull proposal, J. Am. Chem. Soc. 123, 1664-1675.
15. 12-dependent diol dehyratase: Protonation state of histidine and pull effect of glutamate, J. Am. Chem. Soc. 126, 16207-16216.
16. 12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase, Struct. Folding Des., 997-1008.
17. 12-dependent diol dehydratase, J. Biochem. 126, 650-654.
18. 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.
19. 12-dependent diol dehyratase, J. Biol. Chem. 281, 18327-18334.
20. Retey, J., Umani-Ronchi, A., Seibl, J., and Arigoni, D. (1966) On the mechanism of the propanediol dehydrase reaction, Experientia 22, 502-503.
21. 12, J. Biol. Chem. 248, 1285-1290.
22. Valinsky, J. E., Abeles, R. H., and Fee, J. A. (1974) Electron spin resonance studies on diol dehydrase III. Rapid kinetic studies on the rate of formation of radicals in the reaction with propanediol, J. Am. Chem. Soc. 96, 4709-4710.
23. 12 (Dolphin, D., Ed.) pp 431-463, John Wiley & Sons, Inc., New York.
24. Valinsky, J. E., Abeles, R. H., and Mildvan, A. S. (1974) Electron spin resonance studies of diol dehydrase II. The hyperfine structure of proposed radical intermediates derived from isotopic substitution in 2- chloroacetaldehyde, J. Biol. Chem. 249, 2751-2755.
25. 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.
26. Yamanishi, M., Hirofumi, I., 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.
27. 12 analogue with unusual properties, J. Am. Chem. Soc. 122, 8807-8813.
28. 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.
29. Magnusson, O. T., Reed, G. H., and Frey, P. A. (2001) Characterization of an allylic analogue of the 5′-deoxyadenosyl radical: An intermediate in the reaction of lysine 2, 3-aminomutase, Biochemistry 40, 7773-7782.
30. 12-dependent diol dehydrase: Purification, subunit heterogeneity, and reversible association, Arch. Biochem. Biophys. 194, 379-386.
31. Kauppinen, J. K., Moffaatt, D. J., Mantsch, H. H., and Cameron, D. G. (1981) Fourier self-deconvolution: A method for resolving intrinsically overlapped bands, Appl. Spectrosc. 35, 271-276.
32. Latwesen, D. G., Poe, M., Leigh, J. S., and Reed, G. H. (1992) Electron paramagnetic resonance studies of a ras p21-MnIIGDP complex in solution, Biochemistry 31, 4946-4950.
33. Goldstein, H., Poole, C. P., Jr., and Safko, J. L. (2002) Classical Mechanics, 3rd ed., Addison Wesley, San Francisco.
34. Bandarian, V., and Reed, G. H. (1999) Hydrazine cation radical in the active site of ethanolamine ammonia-lyase: Mechanism-based inactivation by hydroxyethylhydrazine, Biochemistry 38, 12394-12402.
35. Wertz, J. E., and Bolton, J. R. (1986) Electron Spin Resonance, Chapman and Hall, New York.
36. 12 (Banerjee, R., Ed.) pp 165-195, Wiley-Interscience, New York.
37. Bencini, A., and Gatteschi, D. (1990) EPR of Exchange Coupled Systems, Springer-Verlag, New York.
38. Mukai, K., and Sogabe, A. (1980) ESR studies of radical pairs of galvinoxyl radical in corresponding phenol matrix, J. Chem. Phys. 72, 598-601.
39. Mansoorabadi, S. O., and Reed, G. H. (2003) Effects of electron spin delocalization and non-collinearity of interaction terms in EPR triplet powder patterns, in Paramagnetic resonance of metallobiomolecules (Telser, J., Ed.) pp 82-96, American Chemical Society, Washington, DC.
40. Goffe, W. L., Ferrier, G. D., and Rogers, J. (1994) Global optimization of statistical functions with simulated annealing, J. Econometrics 60, 65-100.
41. Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1989) Numerical Recipes, Cambridge University Press, New York.
42. Leach, A. R. (2001) Molecular Modeling Principles and Applications, 2nd ed., Prentice Hall, London.
43. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Jr., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Baboul, A. G., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Andres, J. L., Head-Gordon, M., Replogle, E. S., and Pople, J. A. (1998) Gaussian 98, Gaussian, Inc., Pittsburgh, PA.
44. 12: X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex, Struct. Folding Des. 8, 775-788.
45. Gerfen, G. J., Licht, S., Willems, J. P., Hoffman, B. M., and Stubbe, J. (1996) Electron paramagnetic resonance investigations of a kinetically competent intermediate formed in ribonucleotide reduction: Evidence for thiyl radical-cob(II)alamin interaction, J. Am. Chem. Soc. 118, 8192-8197.
46. 12-dependent glutamate mutase from Clostridium cochlearium, Biochemistry 37, 4105-4113.
47. Zhao, Y., Abend, A., Kunz, M., Such, P., and Retey, J. (1994) Electron paramagnetic resonance studies of the methylmalonyl-CoA mutase reaction. Evidence for radical intermediates using natural and artificial substrates as well as the competitive inhibitor 3-carboxypropyl-CoA, Eur. J. Biochem. 225, 891-896.
48. Padmakumar, R., and Banerjee, R. (1995) Evidence from electron paramagnetic resonance spectroscopy of the participation of radicalintermediates in the reaction catalyzed by methylmalonyl-coenzyme A mutase, J. Biol. Chem. 270, 9295-9300.
49. 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.
50. Eaton, G. R., and Eaton, S. S. (1989) Resolved electron-electron spin-spin splittings in EPR spectra, Biol. Magn. Reson. 8, 650.