1
|
Deng WH, Lu Y, Liao RZ. Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. J Chem Inf Model 2021; 61:5871-5882. [PMID: 34806370 DOI: 10.1021/acs.jcim.1c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isethionate sulfite-lyase (IseG) is a recently characterized glycyl radical enzyme (GRE) that catalyzes radical-mediated C-S bond cleavage of isethionate to produce acetaldehyde and sulfite. Herein, we use quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the detailed catalytic reaction mechanism of IseG. Our calculations indicate that a previously proposed direct 1,2-elimination mechanism is disfavored. Instead, we suggest a new 1,2-migration mechanism for this enzymatic reaction: a key stepwise 1,2-SO3- radical migration occurs after the catalytically active cysteinyl radical grabs a hydrogen atom from isethionate, followed by hydrogen atom transfer from cysteine to a 1-hydroxylethane-1-sulfonate radical intermediate. Finally, the elimination of sulfite from 1-hydroxylethane-1-sulfonate to result in the final product is likely to occur outside the enzyme. Glu468 in the active site is found to help orient the substrate rather than grabbing a proton from the hydroxyl group of the substrate. Our findings help reveal the mechanisms of radical-mediated C-S bond cleavage of organosulfonates catalyzed by GREs and expand the understanding of radical-based enzymatic catalysis.
Collapse
Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - You Lu
- Scientific Computing Department, UKRI STFC Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| |
Collapse
|
2
|
Pang J, Scrutton NS, Sutcliffe MJ. Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase. Chemistry 2014; 20:11390-401. [DOI: 10.1002/chem.201402759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Indexed: 02/02/2023]
|
3
|
Chen YH, Maity AN, Frey PA, Ke SC. Mechanism-based Inhibition Reveals Transitions between Two Conformational States in the Action of Lysine 5,6-Aminomutase: A Combination of Electron Paramagnetic Resonance Spectroscopy, Electron Nuclear Double Resonance Spectroscopy, and Density Functional Theory Study. J Am Chem Soc 2012; 135:788-94. [DOI: 10.1021/ja309603a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
| |
Collapse
|
4
|
Sandala GM, Smith DM, Radom L. Modeling the reactions catalyzed by coenzyme B12-dependent enzymes. Acc Chem Res 2010; 43:642-51. [PMID: 20136160 DOI: 10.1021/ar900260c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.
Collapse
Affiliation(s)
- Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - David M. Smith
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
5
|
Wolthers KR, Rigby SEJ, Scrutton NS. Mechanism of radical-based catalysis in the reaction catalyzed by adenosylcobalamin-dependent ornithine 4,5-aminomutase. J Biol Chem 2008; 283:34615-25. [PMID: 18948256 DOI: 10.1074/jbc.m807911200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report an analysis of the reaction mechanism of ornithine 4,5-aminomutase, an adenosylcobalamin (AdoCbl)- and pyridoxal L-phosphate (PLP)-dependent enzyme that catalyzes the 1,2-rearrangement of the terminal amino group of D-ornithine to generate (2R,4S)-2,4-diaminopentanoic acid. We show by stopped-flow absorbance studies that binding of the substrate D-ornithine or the substrate analogue D-2,4-diaminobutryic acid (DAB) induces rapid homolysis of the AdoCbl Co-C bond (781 s(-1), D-ornithine; 513 s(-1), DAB). However, only DAB results in the stable formation of a cob(II)alamin species. EPR spectra of DAB and [2,4,4-(2)H(3)]DAB bound to holo-ornithine 4,5-aminomutase suggests strong electronic coupling between cob(II)alamin and a radical form of the substrate analog. Loading of substrate/analogue onto PLP (i.e. formation of an external aldimine) is also rapid (532 s(-1), D-ornithine; 488 s(-1), DAB). In AdoCbl-depleted enzyme, formation of the external aldimine occurs over long time scales (approximately 50 s) and occurs in three resolvable kinetic phases, identifying four distinct spectral intermediates (termed A-D). We infer that these represent the internal aldimine (lambda(max) 416 nm; A), two different unliganded PLP states of the enzyme (lambda(max) at 409 nm; B and C), and the external aldimine (lambda(max) 426 nm; D). An imine linkage with d-ornithine and DAB generates both tautomeric forms of the external aldimine, but with D-ornithine the equilibrium is shifted toward the ketoimine state. The influence of this equilibrium distribution of prototropic isomers in driving homolysis and stabilizing radical intermediate states is discussed. Our work provides the first detailed analysis of radical-based catalysis in this Class III AdoCbl-dependent enzyme.
Collapse
Affiliation(s)
- Kirsten R Wolthers
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess St., Manchester M1 7DN, United Kingdom.
| | | | | |
Collapse
|
6
|
Buckel W, Kratky C, Golding BT. Stabilisation of methylene radicals by cob(II)alamin in coenzyme B12 dependent mutases. Chemistry 2007; 12:352-62. [PMID: 16304645 DOI: 10.1002/chem.200501074] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Coenzyme B12 initiates radical chemistry in two types of enzymatic reactions, the irreversible eliminases (e.g., diol dehydratases) and the reversible mutases (e.g., methylmalonyl-CoA mutase). Whereas eliminases that use radical generators other than coenzyme B12 are known, no alternative coenzyme B12 independent mutases have been detected for substrates in which a methyl group is reversibly converted to a methylene radical. We predict that such mutases do not exist. However, coenzyme B12 independent pathways have been detected that circumvent the need for glutamate, beta-lysine or methylmalonyl-CoA mutases by proceeding via different intermediates. In humans the methylcitrate cycle, which is ostensibly an alternative to the coenzyme B12 dependent methylmalonyl-CoA pathway for propionate oxidation, is not used because it would interfere with the Krebs cycle and thereby compromise the high-energy requirement of the nervous system. In the diol dehydratases the 5'-deoxyadenosyl radical generated by homolysis of the carbon-cobalt bond of coenzyme B12 moves about 10 A away from the cobalt atom in cob(II)alamin. The substrate and product radicals are generated at a similar distance from cob(II)alamin, which acts solely as spectator of the catalysis. In glutamate and methylmalonyl-CoA mutases the 5'-deoxyadenosyl radical remains within 3-4 A of the cobalt atom, with the substrate and product radicals approximately 3 A further away. It is suggested that cob(II)alamin acts as a conductor by stabilising both the 5'-deoxyadenosyl radical and the product-related methylene radicals.
Collapse
Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie, Philipps-Universität, 35032 Marburg, Germany.
| | | | | |
Collapse
|
7
|
Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
| | | | | |
Collapse
|
8
|
Affiliation(s)
- Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden
| | | |
Collapse
|
9
|
Khoroshun DV, Warncke K, Ke SC, Musaev DG, Morokuma K. Internal degrees of freedom, structural motifs, and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study. J Am Chem Soc 2003; 125:570-9. [PMID: 12517173 DOI: 10.1021/ja028393k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order Møller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.
Collapse
Affiliation(s)
- Dmitry V Khoroshun
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | | | | | | | | |
Collapse
|
10
|
Pierik AJ, Ciceri D, Bröker G, Edwards CH, McFarlane W, Winter J, Buckel W, Golding BT. Rotation of the exo-methylene group of (R)-3-methylitaconate catalyzed by coenzyme B(12)-dependent 2-methyleneglutarate mutase from Eubacterium barkeri. J Am Chem Soc 2002; 124:14039-48. [PMID: 12440902 DOI: 10.1021/ja020340f] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2-Methyleneglutarate mutase from the anaerobe Eubacterium (Clostridium) barkeri is an adenosylcobalamin (coenzyme B(12))-dependent enzyme that catalyzes the equilibration of 2-methyleneglutarate with (R)-3-methylitaconate. Two possibilities for the mechanism of the carbon skeleton rearrangement of the substrate-derived radical to the product-related radical are considered. In both mechanisms an acrylate group migrates from C-3 of 2-methyleneglutarate to C-4. In the "addition-elimination" mechanism this 1,2-shift occurs via an intermediate, a 1-methylenecyclopropane-1,2-dicarboxylate radical, in which the migrating acrylate is simultaneously attached to both C-3 and C-4. In the "fragmentation-recombination" mechanism the migrating group, a 2-acrylyl radical, becomes detached from C-3 before it starts bonding to C-4. In an attempt to distinguish between these two possibilities we have investigated the action of 2-methyleneglutarate mutase on the stereospecifically deuterated substrates (Z)-3-methyl[2'-(2)H(1)]itaconate and (Z)-3-[2'-(2)H(1),methyl-(2)H(3)]methylitaconate. The enzyme catalyzes the equilibration of both compounds with their corresponding E-isomers and with a 1:1 mixture of the corresponding (E)- and (Z)-2-methylene[2'-(2)H(1)]glutarates, as shown by monitoring of the reactions with (1)H and (2)H NMR. In the initial phase of the enzyme-catalyzed equilibration a significant excess (8-11%) of (E)-3-methyl[2'-(2)H(1)]itaconate over its equilibrium value was observed ("E-overshoot"). The E-overshoot was only 3-4% with (Z)-3-[2'-(2)H(1),methyl-(2)H(3)]methylitaconate because the presence of the deuterated methyl group raises the energy barrier from 3-methylitaconate to the corresponding radical. The overshoot is explained by postulating that the migrating acrylate group has to overcome an additional energy barrier from the state leading back to the substrate-derived radical to the state leading forward to the product-related radical. It is concluded that the fragmentation-recombination mechanism can provide an explanation for the results in terms of an additional energy barrier, despite the higher calculated activation energy for this pathway.
Collapse
Affiliation(s)
- Antonio J Pierik
- Department of Chemistry, Bedson Building, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
The crystal structure of glutamate mutase with bound coenzyme B(12) suggests a radical shuttling mechanism within the active site of the enzyme. Quantum chemical calculations of the rearrangement in combination with kinetic and mutational studies suggest the catalytic mechanism of this enzyme to proceed via a fragmentation/recombination sequence with intermediates stabilized by partial protonation/deprotonation. Crucial residues in the active site have been identified. Solution structure studies indicate the mechanism of B(12) binding to the apoenzyme.
Collapse
Affiliation(s)
- Karl Gruber
- Institut für Chemie, Universität Graz, Heinrichstrasse 28, Austria.
| | | |
Collapse
|
12
|
Semialjac M, Schwarz H. Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation. J Am Chem Soc 2002; 124:8974-83. [PMID: 12137553 DOI: 10.1021/ja020101s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.
Collapse
Affiliation(s)
- Marija Semialjac
- Institut für Chemie der Technischen Universität Berlin, D-10623 Berlin, Germany.
| | | |
Collapse
|
13
|
Eda M, Kamachi T, Yoshizawa K, Toraya T. Theoretical Study on the Mechanism of Catalysis of Coenzyme B12-Dependent Diol Dehydratase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1469] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
14
|
Abstract
Recent progress in computational modeling of the catalytic activation of cobalt-carbon bond cleavage shows that quantum chemical calculations could be an important part of coenzyme B(12) research. Particular emphasis has been placed on density functional theory, which is now emerging as a powerful tool to elucidate the electronic structure and spectroscopic properties of the active sites of metalloenzymes.
Collapse
Affiliation(s)
- P M Kozlowski
- Department of Chemistry, University of Louisville, Kentucky 40292, USA.
| |
Collapse
|
15
|
Wetmore SD, Smith DM, Golding BT, Radom L. Interconversion of (S)-glutamate and (2S,3S)-3-methylaspartate: a distinctive B(12)-dependent carbon-skeleton rearrangement. J Am Chem Soc 2001; 123:7963-72. [PMID: 11506551 DOI: 10.1021/ja004246f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interconversion of (S)-glutamate and (2S,3S)-3-methylaspartate catalyzed by B(12)-dependent glutamate mutase is discussed using results from high-level ab initio molecular orbital calculations. Evidence is presented regarding the possible role of coenzyme-B(12) in substrate activation and product formation via radical generation. Calculated electron paramagnetic resonance parameters support experimental evidence for the involvement of substrate-derived radicals and will hopefully aid the future detection of other important radical intermediates. The height of the rearrangement barrier for a fragmentation-recombination pathway, calculated with a model that includes neutral amino and carboxylic acid substituents in the migrating glycyl group, supports recent experimental evidence for the interconversion of (S)-glutamate and (2S,3S)-3-methylaspartate through such a pathway. Our calculations suggest that the enzyme may facilitate the rearrangement of (S)-glutamate through (partial) proton-transfer processes that control the protonation state of substituents in the migrating group.
Collapse
Affiliation(s)
- S D Wetmore
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | | | | | | |
Collapse
|
16
|
Dölker N, Maseras F, Lledós A. A Density Functional Study on the Effect of the Trans Axial Ligand of Cobalamin on the Homolytic Cleavage of the Co−C Bond. J Phys Chem B 2001. [DOI: 10.1021/jp010144f] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nicole Dölker
- Unitat de Química Física, Edifici C.n, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Feliu Maseras
- Unitat de Química Física, Edifici C.n, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Agustí Lledós
- Unitat de Química Física, Edifici C.n, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
| |
Collapse
|
17
|
Theoretical studies of coenzyme B12-dependent carbon-skeleton rearrangements. THEORETICAL AND COMPUTATIONAL CHEMISTRY 2001. [DOI: 10.1016/s1380-7323(01)80006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
18
|
Kunz M, Rétey J. Evidence for a 1,2 Shift of a Hydrogen Atom in a Radical Intermediate of the Methylmalonyl-CoA Mutase Reaction. Bioorg Chem 2000; 28:134-139. [PMID: 10915551 DOI: 10.1006/bioo.2000.1165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An excellent substrate of methylmalonyl-CoA mutase, methylmalonyl-carba-(dethia) coenzyme A (methylmalonyl-CH(2)-CoA), was synthesized by a chemoenzymatic method and its alpha-proton was exchanged with deuterium by long-term incubation in deuterium oxide at pH 6.9. After addition of highly purified epimerase-free methylmalonyl-CoA mutase the enzymatic rearrangement was monitored by 1H NMR spectroscopy. Already in the initial phases of the reaction only 72% of the produced succinyl-CH(2)-CoA was monodeuterated, while unlabeled and geminally dideuterated species, 14% of each, were also formed. After the addition of more enzyme the equilibrium (methylmalonyl-CoA:succinyl-CoA = 1:20) was quickly established, while the proportion of unlabeled succinyl-CH(2)-CoA rose to 30% and the geminally dideuterated species were slowly transformed to vicinally dideuterated ones. After 19 h of incubation the ratio of the unlabeled, monodeuterated, and dideuterated species was roughly 1:1:1 while no appreciable deuterium incorporation from the solvent occurred. The unexpected disproportionation of deuterium can be best explained by a 1,2 shift of a hydrogen atom in the succinyl-CH(2)-CoA radical intermediate competing with the hydrogen transfer from 5'-deoxyadenosine. A precedence for such a hydrogen shift in a radical was previously observed only in the mass spectrometer and was supported by ab initio calculations. Copyright 2000 Academic Press.
Collapse
Affiliation(s)
- M Kunz
- Institute of Organic Chemistry, University of Karlsruhe, Karlsruhe, D-76128, Germany
| | | |
Collapse
|
19
|
Buckel W, Golding BT. Radical species in the catalytic pathways of enzymes from anaerobes. FEMS Microbiol Rev 1998. [DOI: 10.1111/j.1574-6976.1998.tb00385.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|