Radical mechanisms in adenosylcobalamin-dependent enzymes

Current Opinion in Chemical Biology

Volumn 8, Issue 5, 2004, Pages 477-483

  Reed, George H ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Adenosylcobalamin; AdoCbl; DDH; Dioldehydrase; EAL; Ethanolamine ammonia lyase; IE; Isotope effect; KIE; kinetic isotope effect; MCM; methylmalonyl CoA mutase; Ribonucleoside triphosphate reductase; RTPR

Indexed keywords

CARBON; COBALT; COBAMAMIDE; FREE RADICAL; HYDROGEN; ISOTOPE;

ATOM; CHEMICAL BOND; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SUBSTRATE; EPIMERIZATION; KINETICS; LACTOBACILLUS; MOLECULAR MECHANICS; MOLECULAR MODEL; MUTANT; NONHUMAN; REVIEW; STEADY STATE; STEREOCHEMISTRY; TEMPERATURE; WILD TYPE;

BINDING SITES; CARBON; COBALT; COBAMIDES; FREE RADICALS; GLUTAMIC ACID; GLUTARATES; HYDROGEN; ISOTOPE LABELING; KINETICS; MODELS, MOLECULAR; RIBONUCLEOTIDE REDUCTASES;

LACTOBACILLUS;

EID: 4644229550     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2004.08.008     Document Type: Review

References (47)

1. J. Stubbe, and W. van der Donk Protein radicals in enzyme catalysis Chem Rev 98 1998 705 762
2. P.A. Frey Radical mechanisms in enzymatic catalysis Annu Rev Biochem 70 2001 121 148
3. H.J. Sofia, G. Chen, B.G. Hetzler, J.F. Reyes-Spindola, and N.E. Miller Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods Nucleic Acids Res 29 2001 1097 1106
4. L. Ouyang, P. Rulis, W.Y. Ching, G. Nardin, and L. Randaccio Accurate redetermination of the x-ray structure and electronic bonding in adenosylcobalamin Inorg Chem 43 2004 1235 1241
5. 12-dependent enzymes Biochemistry 40 2001 6191 6198
6. R. Banerjee, and S.W. Ragsdale The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes Annu Rev Biochem 72 2003 209 247
7. T. Toraya Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions Chem Rev 103 2003 2095 2128
8. E.N.G. Marsh, and C.L. Drennan Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism Curr Opin Chem Biol 5 2001 499 505
9. R. Banerjee Radical carbon skeleton rearrangements: catalysis by coenzyme B12-dependent mutases Chem Rev 103 2003 2083 2094
10. R. Banerjee, and M. Vlasie Controlling the reactivity of radical intermediates by coenzyme B12-dependent methylmalonyl-CoA mutase Biochem Soc Trans 30 2002 621 624
11. D. Chen, A. Abend, J. Stubbe, and P.A. Frey 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 2003 4578 4584 Stereochemical evidence that Co-C5′ bond cleavage occurs in the absence of H atom abstraction and hence of the existence of the 5′-deoxyadenosyl radical.
12. M. Fontecave, and E. Mulliez Ribonucleotide reductases R. Banerjee Chemistry and Biochemistry of B12 1999 Wiley Interscience New York 731 756
13. S.S. Licht, S. Booker, and J. Stubbe Studies on the catalysis of carbon-cobalt bond homolysis by ribonucleoside triphosphate reductase: evidence for concerted carbon-cobalt bond homolysis and thiyl radical formation Biochemistry 38 1999 1221 1233
14. R.H. Abeles, and W.S. Beck The mechanism of action of cobamide coenzyme in the ribonucleotide reductase reaction J Biol Chem 242 1967 3589 3593
15. A. Gaudemer, J. Zylber, N. Zylber, M. Baran-Marszac, W.E. Hull, M. Fountoulakis, A. Konig, K. Wolfle, and J. Retey Reversible cleavage of the cobalt-carbon bond to coenzyme B12 catalysed by methylmalonyl-CoA mutase from Propionibacterium shermanii. The use of coenzyme B12 stereospecifically deuterated position 5′ Eur J Biochem 119 1981 279 285
16. M.D. Sintchak, G. Arjara, B.A. Kellogg, J. Stubbe, and C.L. Drennan The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer Nat Struct Biol 9 2002 293 300
17. G.J. Gerfen, S. Licht, J.P. Willems, B.M. Hoffman, and J. Stubbe 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 1996 8192 8197
18. V. Bandarian, and G.H. Reed Analysis of the electron paramagnetic resonance spectrum of a radical intermediate in the coenzyme B12 dependent ethanolamine ammonia-lyase catalyzed reaction with S-2-aminopropanol Biochemistry 41 2002 8580 8599
19. R. LoBrutto, V. Bandarian, O.T. Magnusson, X. Chen, V.L. Schramm, and G.H. Reed 5′-Deoxyadenosine contacts the substrate radical intermediate in the active site of ethanolamine ammonia lyase Biochemistry 40 2001 9 14
20. K. Warncke, and A.S. Utada Interaction of the substrate radical and the 5′-deoxyadenosine methyl group in vitamin B12 coenzyme-dependent ethanolamine deaminase J Am Chem Soc 123 2001 8564 8572
21. M.K. Essenberg, P.A. Frey, and R.H. Abeles Studies on the mechanism of hydrogen transfer in the coenzyme B12 dependent dioldehydrase reaction II J Am Chem Soc 93 1971 1242 1251
22. 12-dependent enzyme J Biol Chem 246 1971 6064 6071
23. E.N.G. Marsh, and D.P. Ballou Coupling of cobalt-carbon bond homolysis and hydrogen atom abstraction in adenosylcobalamin-dependent glutamate mutase Biochemistry 37 1998 11864 11872
24. R. Padmakumar, R. Padmakumar, and R. Banerjee Evidence that cobalt-carbon bond homolysis is coupled to hydrogen atom abstraction from substrate in methylmalonyl-CoA mutase Biochemistry 36 1997 3713 3718
25. S. Chowdhury, and R. Banerjee Evidence for quantum mechanical tunneling in the coupled cobalt-carbon bond homolysis-sustrate radical generation reaction catalyzed by methylmalonyl-CoA mutase J Am Chem Soc 122 2000 5417 5418
26. V. Bandarian, and G.H. Reed 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 2000 12069 12075
27. P. Madhavapeddi, D.P. Ballou, and E.N.G. Marsh Pre-steady state kinetic studies on the Glu171Gln active site mutant of adenosylcobalamin-dependent glutamate mutase Biochemistry 41 2002 15803 15809 Study showing that substrate binding energy is probably used to promote Co-C5′ bond cleavage in glutamate mutase.
28. L. Xia, D.P. Ballou, and E.N.G. Marsh Role of Arg100 in the active site of adensylcobalamin-dependent glutamate mutase Biochemistry 43 2004 3238 3245 Study showing that substrate binding energy is probably used to promote Co-C5′ bond cleavage in glutamate mutase.
29. M. Vlasie, and R. Banerjee Tyrosine 89 accelerates Co-carbon bond homolysis in methylmalonyl-CoA mutase J Am Chem Soc 125 2003 5431 5435 A paper showing that Tyr89 influences the rate of Co-C5′ bond cleavage.
30. F. Mancia, and P.R. Evans Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism Structure 6 1998 711 720
31. N.H. Thoma, T.W. Meier, P.R. Evans, and P.F. Leadlay Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase Biochemistry 37 1998 14386 14393
32. K.M. Doll, B.R. Bender, and R.G. Finke The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling J Am Chem Soc 125 2003 10877 10884 A study of tunneling in H atom abstraction by adenosyl radicals in non-enzymatic reactions.
33. K.M. Doll, and R.G. Finke A compelling experimental test of the hypothesis that enzymes have evolved to enhance quantum mechanical tunneling in hydrogen transfer reactions: the β-neopentylcobalamin system combined with prior adocobalamin data Inorg Chem 42 2003 4849 4856 A study that permits analysis of tunneling contributions in non-enzymatic H atom abstractions mimicking those in AdoCbl-dependent enzymes.
34. 3H IEs in glutamate mutase.
35. P.A. Frey, and C.H. Chang Aminomutases R. Banerjee Chemistry and Biochemistry of B12 1999 Wiley-Interscience New York 835 857
36. 2H KIEs are used to determine the rate-limiting step of the reaction.
37. Semialjac M, Schwartz H: Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia-lyase. J Am Chem Soc 2002, 124:8974-8989-8983. A computational study of the radical reaction pathway of EAL.
38. S.D. Wetmore, D.M. Smith, J.T. Bennett, and L. Radom Understanding the mechanism of action of B12-dependent ethanolamine ammonia-lyase: synergistic interactions at play J Am Chem Soc 124 2002 14054 14065 A computational study of the lowest energy pathways of the EAL reaction.
39. J. Retey, C.J. Suckling, D. Arigoni, and M. Babior The stereochemistry of the reaction catalyzed by ethanolamine ammonia-lyase, an adenosylcobalamin- dependent enzyme. An example of racemization accompanying substitution J Biol Chem 249 1974 6359 6360
40. J. Rétey Enzymic stereospecificity as a probe for the occurrence of radical intermediates P.A. Frey Mechanisms of Enzymatic Reactions: Stereochemistry 1986 Elsevier New York 217 232
41. J. Retey, A. Umani-Ronchi, J. Seibl, and D. Arigoni On the mechanism of the propanediol dehydrase reaction Experientia 22 1966 502 503
42. K. Warncke, and J.M. Canfield Direct determination of product radical structure reveals the radical rearrangement pathway in a coenzyme B12-dependent enzyme J Am Chem Soc 126 2004 5930 5931
43. M. Freindorf, and P.M. Kozlowski A combined density functional theory and molecular mechanics study of the relationship between the structure of coenzyme B12 and its binding to methylmalonyl-CoA mutase J Am Chem Soc 126 2004 1928 1929
44. U. Weigl, M. Heimberger, A.J. Pierick, and J. Retey Synthesis of enantiomerically-pure [13C]aristeromycylcobalamin and its reactivity in dioldehyratase, glyceroldehydratase, ethanolamine ammonia-lyase and methylmalonyl-CoA mutase reactions Chem Eur J 9 2003 652 660 Description of the synthesis and activity of a carbocyclic analog of AdoCbl.
45. M.S. Huhta, D. Ciceri, B.T. Golding, and E.N.G. Marsh A novel reaction between adenosylcobalamin and 2-methyleneglutarate catalyzed by glutamate mutase Biochemistry 41 2002 3200 3206 A study describing the suicide inactivation of glutamate mutase by a radical addition mechanism.
46. A. Abend, V. Bandarian, G.H. Reed, and P.A. Frey Identification of cis-ethanesemidione as the organic radical derived from glycolaldehyde in the suicide inactivation of dioldehydrase and of ethanolamine ammonia-lyase Biochemistry 39 2000 6250 6257
47. P. Schwartz, R. LoBrutto, G.H. Reed, and P.A. Frey Suicide inactivation of dioldehydraase by 2-chloroacetaldehyde: formation of the cis-ethanesemidione radical, and the role of a monovalent cation Helv Chim Acta 86 2003 3764 3775 A study showing a second suicide substrate that gives a cis-ethanesemidione radical product.