101
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Smith DM, Golding BT, Radom L. Understanding the Mechanism of B12-Dependent Methylmalonyl-CoA Mutase: Partial Proton Transfer in Action. J Am Chem Soc 1999. [DOI: 10.1021/ja991649a] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Smith
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | - Bernard T. Golding
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
| | - Leo Radom
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and Department of Chemistry, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K
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102
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Dong S, Padmakumar R, Banerjee R, Spiro TG. Co−C Bond Activation in B12-Dependent Enzymes: Cryogenic Resonance Raman Studies of Methylmalonyl-Coenzyme A Mutase. J Am Chem Soc 1999. [DOI: 10.1021/ja982753f] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shoulian Dong
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Biochemistry Department, University of Nebraska, Lincoln Nebraska 68588
| | - Raghavakaimal Padmakumar
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Biochemistry Department, University of Nebraska, Lincoln Nebraska 68588
| | - Ruma Banerjee
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Biochemistry Department, University of Nebraska, Lincoln Nebraska 68588
| | - Thomas G. Spiro
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and Biochemistry Department, University of Nebraska, Lincoln Nebraska 68588
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103
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Roymoulik I, Chen HP, Marsh EN. The reaction of the substrate analog 2-ketoglutarate with adenosylcobalamin-dependent glutamate mutase. J Biol Chem 1999; 274:11619-22. [PMID: 10206971 DOI: 10.1074/jbc.274.17.11619] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutamate mutase is one of several adenosylcobalamin-dependent enzymes that catalyze unusual rearrangements that proceed through a mechanism involving free radical intermediates. The enzyme exhibits remarkable specificity, and so far no molecules other than L-glutamate and L-threo-3-methylaspartate have been found to be substrates. Here we describe the reaction of glutamate mutase with the substrate analog, 2-ketoglutarate. Binding of 2-ketoglutarate (or its hydrate) to the holoenzyme elicits a change in the UV-visible spectrum consistent with the formation of cob(II)alamin on the enzyme. 2-ketoglutarate undergoes rapid exchange of tritium between the 5'-position of the coenzyme and C-4 of 2-ketoglutarate, consistent with the formation of a 2-ketoglutaryl radical analogous to that formed with glutamate. Under aerobic conditions this leads to the slow inactivation of the enzyme, presumably through reaction of free radical species with oxygen. Despite the formation of a substrate-like radical, no rearrangement of 2-ketoglutarate to 3-methyloxalacetate could be detected. The results indicate that formation of the C-4 radical of 2-ketoglutarate is a facile process but that it does not undergo further reactions, suggesting that this may be a useful substrate analog with which to investigate the mechanism of coenzyme homolysis.
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Affiliation(s)
- I Roymoulik
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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104
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Sirovatka JM, Finke RG. Coenzyme B(12) Axial-Base Chemical Precedent Studies. Adenosylcobinamide Plus Sterically Hindered Axial-Base Co-C Bond Cleavage Product and Kinetic Studies: Evidence for the Dominance of Axial-Base Transition-State Effects and for Co-N(Axial-Base) Distance-Dependent, Competing sigma and pi Effects. Inorg Chem 1999; 38:1697-1707. [PMID: 11670936 DOI: 10.1021/ic980608x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosylcobinamide (AdoCbi(+)) plus the sterically hindered bases 1,2-dimethylimidazole, 2-methylpyridine, and 2,6-dimethylpyridine, as well as control experiments with imidazolate and 4-methylimidazolate, have been investigated to provide chemical precedent for the benzimidazole base-off, protein histidine imidazole base-on form of adenosylcobalamin (AdoCbl, also coenzyme B(12)). This imidazole base-on form of AdoCbl was observed in the recent X-ray crystallographic structural study of methylmalonyl-CoA (MMCoA) mutase; of interest to the present work is the fact that MMCoA mutase contains a long, ca. 2.5 Å, Co-N(imidazole) axial bond, at least in the enzyme's crystallographically characterized Co(II)/Co(III) state and conformation. In the present studies, upper limits for the axial-base binding K(assoc) parameters to form [AdoCbi.bulky base](+) BF(4)(-) have been obtained; these thermodynamic studies reveal that sterically hindered bases do not bind detectably to AdoCbi(+) in the ground state, which results in negligible ground-state free-energy stabilization via the formation of [AdoCbi.bulky base](+). The sterically hindered bases do, however, bind to Co(II)Cbi(+), a good energetic model of the [Ado. - - -.CoCbi](+) homolysis transition state. Kinetic studies demonstrate that the sterically hindered bases are involved in the rate-determining step of Co-C bond homolysis, accelerating it by 200-fold; hence, Co-C cleavage does occur via the low-level and otherwise nondetectable amount of [AdoCbi.bulky base](+) formed in solution. Product studies reveal (i) that both Co-C heterolysis and homolysis occur, and (ii) that there is no simple correlation between the ratio of Co-C heterolysis to homolysis and the Co-N(axial-base) bond length. Overall, the results provide strong evidence for the dominance of axial-base transition-state effects on Co-C bond cleavage, and reveal a subtle interplay of sigma and pi effects as a function of the Co-N(axial-base) bond length.
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Affiliation(s)
- Jeanne M. Sirovatka
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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105
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Dong S, Padmakumar R, Maiti N, Banerjee R, Spiro TG. Resonance Raman Spectra Show That Coenzyme B12 Binding to Methylmalonyl-Coenzyme A Mutase Changes the Corrin Ring Conformation but Leaves the Co−C Bond Essentially Unaffected. J Am Chem Soc 1998. [DOI: 10.1021/ja981584w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shoulian Dong
- Department of Chemistry, Princeton University Princeton, New Jersey 08544 Biochemistry Department, University of Nebraska Lincoln, Nebraska 68588
| | - Raghavakaimal Padmakumar
- Department of Chemistry, Princeton University Princeton, New Jersey 08544 Biochemistry Department, University of Nebraska Lincoln, Nebraska 68588
| | - Nilesh Maiti
- Department of Chemistry, Princeton University Princeton, New Jersey 08544 Biochemistry Department, University of Nebraska Lincoln, Nebraska 68588
| | - Ruma Banerjee
- Department of Chemistry, Princeton University Princeton, New Jersey 08544 Biochemistry Department, University of Nebraska Lincoln, Nebraska 68588
| | - Thomas G. Spiro
- Department of Chemistry, Princeton University Princeton, New Jersey 08544 Biochemistry Department, University of Nebraska Lincoln, Nebraska 68588
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106
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Brown KL, Li J. Activation Parameters for the Carbon−Cobalt Bond Homolysis of Coenzyme B12 Induced by the B12-Dependent Ribonucleotide Reductase from Lactobacillus leichmannii. J Am Chem Soc 1998. [DOI: 10.1021/ja981729z] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kenneth L. Brown
- Contribution from the Department of Chemistry, Ohio University, Athens, Ohio 45701
| | - Jing Li
- Contribution from the Department of Chemistry, Ohio University, Athens, Ohio 45701
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107
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Mancia F, Evans PR. Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism. Structure 1998; 6:711-20. [PMID: 9655823 DOI: 10.1016/s0969-2126(98)00073-2] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Methylmalonyl CoA mutase catalyses the interconversion of succinyl CoA and methylmalonyl CoA via a free radical mechanism. The enzyme belongs to a family of enzymes that catalyse intramolecular rearrangement reactions in which a group and a hydrogen atom on adjacent carbons are exchanged. These enzymes use the cofactor adenosylcobalamin (coenzyme B12) which breaks to form an adenosyl radical, thus initiating the reaction. Determination of the structure of substrate-free methylmalonyl CoA mutase was initiated to provide further insight into the mechanism of radical formation. RESULTS We report here two structures of methylmalonyl CoA mutase from Propionibacterium shermanii. The first structure is of the enzyme in a nonproductive complex with CoA at 2.5 A resolution. This structure serves as a model for the substrate-free conformation of the enzyme, as it is very similar to the second much poorer 2.7 A resolution structure derived from a truly substrate-free crystal. The true substrate-free structure also shows the adenosyl group bound to the cobalt atom. Comparison of this structure with that of the previously reported complex of the enzyme with a substrate analogue shows that major conformational changes occur upon substrate binding. The substrate-binding site of the enzyme is located within a (beta alpha)8 TIM-barrel domain. In the absence of substrate, this TIM-barrel domain is split apart and the active site is accessible to solvent. When substrate binds, the barrel closes up with the substrate along its axis and the active site becomes completely buried. CONCLUSIONS The closure of the active-site cavity upon substrate binding displaces the adenosyl group of the cofactor from the central cobalt atom into the active-site cavity. This triggers the formation of the free radical that initiates the rearrangement reaction. The TIM-barrel domain is substantially different from all others yet reported: in its unliganded form it is broken open, exposing the small hydrophilic sidechains which fill the centre. The typical barrel structure is only formed when substrate is bound.
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Affiliation(s)
- F Mancia
- MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 2QH, UK
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108
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Dong S, Padmakumar R, Banerjee R, Spiro TG. Co-C force constants from resonance Raman spectra of alkylcobalamins: insensitivity to dimethylbenzylimidazole coordination. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)05994-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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109
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Scheuring E, Padmakumar R, Banerjee R, Chance MR. Extended X-ray Absorption Fine Structure Analysis of Coenzyme B12 Bound to Methylmalonyl-Coenzyme A Mutase Using Global Mapping Techniques. J Am Chem Soc 1997. [DOI: 10.1021/ja9635239] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eva Scheuring
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Rugmini Padmakumar
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Ruma Banerjee
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
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110
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Abstract
Spectroscopic and kinetic evidence for substrate-based radicals in the reactions of lysine 2,3-aminomutase and methane monooxygenase has recently been gathered. Evidence for a protein-based thiyl radical in the mechanism of the action of ribonucleotide reductase has been correlated with the proposed mechanism involving substrate-based radicals. Controversies have arisen about the mechanisms of ribonucleotide reductase and methane monooxygenase reactions.
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Affiliation(s)
- P A Frey
- Institute for Enzyme Research, University of Wisconsin-Madison, 1710 University Avenue, Madison, WI 53705, USA.
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111
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Abstract
The cobalamins are B12 cofactors with a reactive cobalt-carbon bond at their core and support the activity of two mammalian enzymes that are both medically important. The reactive organometallic bond of the cofactor can be cleaved either homolytically or heterolytically, but what determines how the enzymes control the fate of this bond?
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Affiliation(s)
- R Banerjee
- Biochemistry Department University of Nebraska Lincoln, NE 68588-0664, USA
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112
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Yoshimura A, Zimmers T, Neumann D, Longmore G, Yoshimura Y, Lodish H. Mutations in the Trp-Ser-X-Trp-Ser motif of the erythropoietin receptor abolish processing, ligand binding, and activation of the receptor. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49956-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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