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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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Ghosh AP, Toda MJ, Kozlowski PM. What Triggers the Cleavage of the Co–C 5′ Bond in Coenzyme B 12-Dependent Itaconyl-CoA Methylmalonyl-CoA Mutase? ACS Catal 2021. [DOI: 10.1021/acscatal.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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Kumar N, Bucher D, Kozlowski PM. Mechanistic Implications of Reductive Co–C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase. J Phys Chem B 2019; 123:2210-2216. [DOI: 10.1021/acs.jpcb.8b10820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neeraj Kumar
- Computational Biology and Bioinformatics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Denis Bucher
- Molecular Modeling & Design at leadXpro Villigen, Canton of Aargau, Switzerland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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Spataru T, Fernandez F. The Nature of the Co-C Bond Cleavage Processes in Methylcob(II)Alamin and Adenosylcob(III)Alamin. CHEMISTRY JOURNAL OF MOLDOVA 2016. [DOI: 10.19261/cjm.2016.11(1).01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Menon BRK, Menon N, Fisher K, Rigby SEJ, Leys D, Scrutton NS. Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. FEBS J 2015; 282:1242-55. [PMID: 25627283 PMCID: PMC4413051 DOI: 10.1111/febs.13215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B12 potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.
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Affiliation(s)
- Binuraj R K Menon
- Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, UK
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Pang J, Li X, Morokuma K, Scrutton NS, Sutcliffe MJ. Large-Scale Domain Conformational Change Is Coupled to the Activation of the Co–C Bond in the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A Computational Study. J Am Chem Soc 2012; 134:2367-77. [DOI: 10.1021/ja210417k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Jensen KP, Ryde U. How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study. J Am Chem Soc 2005; 127:9117-28. [PMID: 15969590 DOI: 10.1021/ja050744i] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The homolytic cleavage of the organometallic Co-C bond in vitamin B12-dependent enzymes is accelerated by a factor of approximately 10(12) in the protein compared to that of the isolated cofactor in aqueous solution. To understand this much debated effect, we have studied the Co-C bond cleavage in the enzyme glutamate mutase with combined quantum and molecular mechanics methods. We show that the calculated bond dissociation energy (BDE) of the Co-C bond in adenosyl cobalamin is reduced by 135 kJ/mol in the enzyme. This catalytic effect can be divided into four terms. First, the adenosine radical is kept within 4.2 angstroms of the Co ion in the enzyme, which decreases the BDE by 20 kJ/mol. Second, the surrounding enzyme stabilizes the dissociated state by 42 kJ/mol using electrostatic and van der Waals interactions. Third, the protein itself is stabilized by 11 kJ/mol in the dissociated state. Finally, the coenzyme is geometrically distorted by the protein, and this distortion is 61 kJ/mol larger in the Co(III) state. This deformation of the coenzyme is caused mainly by steric interactions, and it is especially the ribose moiety and the Co-C5'-C4' angle that are distorted. Without the polar ribose group, the catalytic effect is much smaller, e.g. only 42 kJ/mol for methyl cobalamin. The deformation of the coenzyme is caused mainly by the substrate, a side chain of the coenzyme itself, and a few residues around the adenosine part of the coenzyme.
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Affiliation(s)
- Kasper P Jensen
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O. Box 124, S-221 00 Lund, Sweden
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Brown KL, Zou X, Banka RR, Perry CB, Marques HM. Solution Structure and Thermolysis of Coβ-5‘-Deoxyadenosylimidazolylcobamide, a Coenzyme B12 Analogue with an Imidazole Axial Nucleoside. Inorg Chem 2004; 43:8130-42. [PMID: 15578853 DOI: 10.1021/ic040079z] [Citation(s) in RCA: 16] [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 solution structure of Cobeta-5'-deoxyadenosylimidazolylcobamide, Ado(Im)Cbl, the coenzyme B(12) analogue in which the axial 5,6-dimethylbenzimidazole (Bzm) ligand is replaced by imidazole, has been determined by NMR-restrained molecular modeling. A two-state model, in which a conformation with the adenosyl moiety over the southern quadrant of the corrin and a conformation with the adenosyl ligand over the eastern quadrant of the corrin are both populated at room temperature, was required by the nOe data. A rotation profile and molecular dynamics simulations suggest that the eastern conformation is the more stable, in contrast to AdoCbl itself in which the southern conformation is preferred. Consensus structures of the two conformers show that the axial Co-N bond is slightly shorter and the corrin ring is less folded in Ado(Im)Cbl than in AdoCbl. A study of the thermolysis of Ado(Im)Cbl in aqueous solution (50-125 degrees C) revealed competing homolytic and heterolytic pathways as for AdoCbl but with heterolysis being 9-fold faster and homolysis being 3-fold slower at 100 degrees C than for AdoCbl. Determination of the pK(a)'s for the Ado(Im)Cbl base-on/base-off reaction and for the detached imidazole ribonucleoside as a function of temperature permitted correction of the homolysis and heterolysis rate constants for the temperature-dependent presence of the base-off species of Ado(Im)Cbl. Activation analysis of the resulting rate constants for the base-on species show that the entropy of activation for Ado(Im)Cbl homolysis (13.7 +/- 0.9 cal mol(-1) K(-1)) is identical with that of AdoCbl (13.5 +/- 0.7 cal mol(-1) K(-1)) but that the enthalpy of activation (34.8 kcal mol(-1)) is 1.0 +/- 0.4 kcal mol(-1) larger. The opposite effect is seen for heterolysis, where the enthalpies of activation are identical but the entropy of activation is 5 +/- 1 cal mol(-1) K(-1) less negative for Ado(Im)Cbl. Extrapolation to 37 degrees C provides a rate constant for Ado(Im)Cbl homolysis of 2.1 x 10(-9) s(-1), 4.3-fold smaller than for AdoCbl. Combined with earlier results for the enzyme-induced homolysis of Ado(Im)Cbl by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii, the catalytic efficiency of the enzyme for homolysis of Ado(Im)Cbl at 37 degrees C can be calculated to be 4.0 x 10(8), 3.8-fold, or 0.8 kcal mol(-1), smaller than for AdoCbl. Thus, the bulky Bzm ligand makes at best a <1 kcal mol(-1) contribution to the enzymatic activation of coenzyme B(12).
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA.
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Jensen KP, Ryde U. The axial N -base has minor influence on Co–C bond cleavage in cobalamins. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00049-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Brown KL, Marques HM. Molecular modeling of the mechanochemical triggering mechanism for catalysis of carbon-cobalt bond homolysis in coenzyme B12. J Inorg Biochem 2001; 83:121-32. [PMID: 11237251 DOI: 10.1016/s0162-0134(00)00188-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The possible contributions of the mechanochemical triggering effect to the enzymatic activation of the carbon-cobalt bond of coenzyme B12 (5'-deoxyadenosylcobalamin, AdoCbl) for homolytic cleavage have been studied by molecular modeling and semiempirical molecular orbital calculations. Classically, this effect has envisioned enzymatic compression of the axial Co-N bond in the ground state to cause upward folding of the corrin ring and subsequent sterically induced distortion of the Co-C bond leading to its destabilization. The models of this process show that in both methylcobalamin (CH3Cbl) and AdoCbl, compression of the axial Co-N bond does engender upward folding of the corrin ring, and that the extent of such upward folding is smaller in an analog in which the normal 5,6-dimethylbenzimidazole axial ligand is replaced by the sterically smaller ligand, imidazole (CH3(lm)Cbl and Ado(lm)Cbl). Furthermore, in AdoCbl, this upward folding of the corrin is accompanied by increases in the carbon-cobalt bond length and in the Co-C-C bond angle (which are also less pronounced in Ado(Im)Cbl), and which indicate that the Co-C bond is indeed destabilized by this mechanism. However, these effects on the Co-C bond are small, and destabilization of this bond by this mechanism is unlikely to contribute more than ca. 3 kcal mol(-1) towards the enzymatic catalysis of Co-C bond homolysis, far short of the observed ca. 14 kcal mol(-1). A second version of mechanochemical triggering, in which compression of the axial Co-N bond in the transition state for Co-C bond homolysis stabilizes the transition state by increased Co-N orbital overlap, has also been investigated. Stretching the Co-C bond to simulate the approach to the transition state was found to result in an upward folding of the corrin ring, a slight decrease in the axial Co-N bond length, a slight displacement of the metal atom from the plane of the equatorial nitrogens towards the "lower" axial ligand, and a decrease in strain energy amounting to about 8 kcal mol(-1) for both AdoCbl and Ado(Im)Cbl. In such modeled transition states, compression of the axial Co-N bond to just below 2.0 A (the distance subsequently found to provide maximal stabilization of the transition state by increased orbital overlap) required about 4 kcal mol(-1) for AdoCbl, and about 2.5 kcal mol(-1) for Ado(Im)Cbl. ZINDO/1 calculations on slightly simplified structures showed that maximal electronic stabilization of the transition state by about 10 kcal mol(-1) occurred at an axial Co-N bond distance of 1.96 A for both AdoCbl and Ado(Im)Cbl. The net result is that this type of transition state mechanochemical triggering can provide 14 kcal mol(-1) of transition state stabilization for AdoCbl, and about 15.5 kcal mol(-1) for the Ado(Im)Cbl, enough to completely explain the observed enzymatic catalysis. These results are discussed in the light of current knowledge about class I AdoCbl-dependent enzymes, in which the coenzyme is bound in its "base-off" conformation, with the lower axial ligand position occupied by the imidazole moiety of an active site histidine residue, and the class II enzymes, in which AdoCbl binds to the enzyme in its "base-on" conformation, and the pendent 5,6-dimethylbenzimidazole base remains coordinated to the metal during Co-C bond activation.
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Affiliation(s)
- K L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens 45701-2979, USA.
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Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N. How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex. Structure 2000; 8:775-88. [PMID: 10903944 DOI: 10.1016/s0969-2126(00)00164-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.
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Affiliation(s)
- J Masuda
- Department of Life Science, Himeji Institute of Technology, Kamigori, Akogun, 678-1297, Japan
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Sirovatka JM, Rappé AK, Finke RG. Molecular mechanics studies of coenzyme B12 complexes with constrained CoN(axial-base) bond lengths: introduction of the universal force field (UFF) to coenzyme B12 chemistry and its use to probe the plausibility of an axial-base-induced, ground-state corrin butterfly conformational steric effect. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(00)00025-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Torrent M, Musaev DG, Morokuma K, Ke SC, Warncke K. Calculation of Nuclear Quadrupole Parameters in Imidazole Derivatives and Extrapolation to Coenzyme B12. A Theoretical Study. J Phys Chem B 1999. [DOI: 10.1021/jp991612c] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Marques HM, Brown KL. The structure of cobalt corrinoids based on molecular mechanics and NOE-restrained molecular mechanics and dynamics simulations. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00074-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Geremia S, Calligaris M, Randaccio L. A Molecular Mechanics Force Field for Alkylcobaloximes, a Model of Vitamin B12 Coenzyme – Implications of Steric and Electronic Factors in the Co–C Bond Cleavage. Eur J Inorg Chem 1999. [DOI: 10.1002/(sici)1099-0682(199906)1999:6<981::aid-ejic981>3.0.co;2-i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Luo LB, Chen Y, Chen HL, Zhang ZY, Zhou ZY, Mak TCW. Comparative Crystal Structure Studies on Distortion of iso-Butyl(aqua)cobaloxime Induced by α-Cyclodextrin and β-Cyclodextrin Hosts. Inorg Chem 1998. [DOI: 10.1021/ic980378m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Brown KL, Zou X, Marques HM. NMR-restrained molecular modeling of cobalt corrinoids: cyanocobalamin (vitamin B12) and methylcobalt corrinoids. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00206-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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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Brown KL, Cheng S, Zou X, Zubkowski JD, Valente EJ, Knapton L, Marques HM. Cis Effects in the Cobalt Corrins. 1. Crystal Structures of 10-Chloroaquacobalamin Perchlorate, 10-Chlorocyanocobalamin, and 10-Chloromethylcobalamin. Inorg Chem 1997; 36:3666-3675. [PMID: 11670058 DOI: 10.1021/ic9615077] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structures of 10-chloroaquacobalamin perchlorate hydrate (10-Cl-H(2)OCbl.ClO(4)) (Mo Kalpha, 0.710 73 Å, monoclinic system, P2(1), a = 11.922(4) Å, b = 26.592(10) Å, c = 13.511(5) Å, beta = 93.05(3) degrees, 10 535 independent reflections, R(1) = 0.0426), 10-chlorocyanocobalamin-acetone hydrate (10-Cl-CNCbl) (Mo Kalpha, 0.710 73 Å, orthorhombic system, P2(1)2(1)2(1), a = 16.24(3) Å, b = 21.85(5) Å, c = 26.75(8) Å, 7699 independent reflections, R(1) = 0.0698), and 10-chloromethylcobalamin-acetone hydrate (10-Cl-MeCbl) (Mo Kalpha, 0.71073 Å, orthorhombic system, P2(1)2(1)2(1), a = 16.041(14) Å, b = 22.13(2) Å, c = 26.75(4) Å, 6792 independent reflections, R(1) = 0.0554), in which the C10 meso H is substituted by Cl, are reported. An unusual feature of the structures is disorder in the C ring, consistent with a two-site occupancy in which the major conformation has the C46 methyl group in the usual position, "upwardly" axial, and the C47 methyl group equatorial, while in the minor conformation both are pseudoequatorial, above and below the corrin ring. (13)C NMR chemical shifts of C46, C47, C12, and C13 suggest that the C ring disorder may persist in solution as a ring flip. Since molecular dynamics simulations fail to reveal any population of the minor conformation, the effect is likely to be electronic rather than steric. The axial bond lengths in 10-Cl-MeCbl are very similar to those in MeCbl (d(Co)(-)(C) = 1.979(7) vs 1.99(2); to 5,6-dimethylbenzimidazole, d(Co)(-)(NB3) = 2.200(7) vs 2.19(2)), but the bonds to the four equatorial N donors, d(Co)(-)(N(eq)), are on average 0.05 Å shorter. In 10-Cl-CNCbl, d(Co)(-)(C) and d(Co)(-)(NB3) are longer (by 0.10(2) and 0.03(1) Å, respectively) than the bond lengths observed in CNCbl itself, while conversely, the C-N bond length is shorter by 0.06(2) Å, but there is little difference in d(Co)(-)(N(eq)). The Co-O bond length to coordinated water in 10-Cl-H(2)OCbl(+) is very similar to that found in H(2)OCbl(+) itself, but the d(Co)(-)(NB3) bond is longer (1.967 vs1.925(2) Å), while the average d(Co)(-)(N(eq)) is very similar. The coordinated water molecule in 10-Cl-H(2)OCbl(+) is hydrogen bonded to the c side chain carbonyl oxygen, as in H(2)OCbl(+). NMR observations indicate that the H bond between coordinated H(2)O and the c side chain amide persists in solution. The equilibrium constant, K(Co), for coordination of bzm to Co(III) is smaller in 10-Cl-MeCbl and 10-Cl-CNCbl than in their C10-unsubstituted analogs (181 vs 452; 4.57 x 10(3) vs 3.35 x 10(5)), but could not be determined for 10-Cl-H(2)OCbl because hydrolysis of the phosphodiester is competitive with the establishment of the base-off equilibrium. Substitution of H by Cl at C10 causes the bands in the electronic spectrum of 10-Cl-XCbl complexes to move to lower energy, which is consistent with an increase in electron density in the corrin pi-conjugated system. This increased electron density is not due to greater electron donation from the axial ligand as bonds between these and the metal are either longer (not shorter) or unchanged, and it most probably arises from pi-donation to the corrin by Cl at C10. As the donor power of X increases (H(2)O < CN(-) < Me), the corrin ring becomes more flexible to deformation, and the number of bond lengths and bond angles that are significantly different in XCbl and 10-Cl-XCbl increases; importantly, the C10-Cl bond length, d(C10)(-)(Cl), increases as well. Thus, despite the fact that chlorine is an inductively electron withdrawing substituent, its resonance electron donation is the more important effect on electron distribution in the corrin ring. Mulliken charges obtained from semiempirical RHF-SCF MO calculations using the ZINDO/1 model on XCbl and their 10-Cl analogs at the crystal structure geometry are shown to correlate reasonably well with (13)C NMR shifts and may be used to determine the pattern of electron distribution in these complexes. Substitution by Cl at C10 causes an increase in charge density at Co when X = H(2)O and CN(-), while the charge density on the four equatorial N donors remains virtually unchanged, but a decrease when X = Me, while the charge density on the equatorial N donors also decreases. In response, d(Co)(-)(NB3) increases in the first two complexes but the equatorial bond lengths remain virtually unchanged, while d(Co)(-)(NB3) remains unchanged and the average d(Co)(-)(N(eq)) decreases in 10-Cl-MeCbl. Furthermore, the partial charge on chlorine increases as the donor power of X increases. The small decrease in the pK(a) of coordinated H(2)O in 10-Cl-H(2)OCbl(+) compared to H(2)OCbl(+) itself (7.65 vs 8.09) is due to a decreased charge density on oxygen in 10-Cl-OHCbl compared to OHCbl. The picture that emerges, therefore, is of competitive electron donation by X and Cl toward the corrin system. In 10-Cl-CNCbl, the decrease in the C&tbd1;N bond length as Co-C increases compared to CNCbl suggests that dpi-ppi bonding between cobalt and cyanide is important. (13)C and (15)N NMR observations on 10-Cl-(13)C(15)NCbl are consistent with these effects.
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Affiliation(s)
- Kenneth L. Brown
- Department of Chemistry, Ohio University, Athens, Ohio 45701, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, Department of Chemistry, Mississippi College, Clinton, Mississippi 39058, and Centre for Molecular Design, Department of Chemistry, University of the Witwatersrand, PO Wits, 2050 Johannesburg, South Africa
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Chapter 45 Vitamin B12. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s1569-2582(97)80106-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
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Garr CD, Sirovatka JM, Finke RG. Adocobinamide, the Base-off Analog of Coenzyme B12 (Adocobalamin). 2.1 Probing the “Base-on” Effect in Coenzyme B12 via Cobalt−Carbon Bond Thermolysis Product and Kinetic Studies as a Function of Exogenous Pyridine Bases. J Am Chem Soc 1996. [DOI: 10.1021/ja954110v] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cheryl D. Garr
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Jeanne M. Sirovatka
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Richard G. Finke
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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Brown KL, Evans DR, Cheng S, Jacobsen DW. Thermolysis of Neopentylcobalamin Analogs Complexed to Haptocorrin: Side Chain Entropy and Activation of Organocobalamins for Carbon-Cobalt Bond Homolysis. Inorg Chem 1996; 35:217-222. [PMID: 11666187 DOI: 10.1021/ic9506466] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of the thermal Co-C bond homolysis of the complexes of a vitamin B(12) binding protein (haptocorrin) with a series of analogs of neopentylcobalamin modified in side chain structure have been studied. The analogs include the C13 epimer in which the e propionamide side chain adopts an "upwardly" axial conformation and a series of c side chain-modified analogs, including the c-monocarboxylate, the c-N-methylamide, the c-N,N-dimethylamide, and the c-N-isopropylamide. Activation parameters for the thermal homolysis of these complexes show that the previously observed stabilization of alkylcobalamins by haptocorrin is due to both enthalpic and entropic factors. With the exception of that for the analog having the bulkiest c side chain substituent, neopentylcobalamin-c-N-isopropylamide, the enthalpies of activation are independent of analog structure, but the entropies of activation increase with the steric bulk of the c side chain and with the number of "upwardly" projecting side chains, as previously observed for protein-free neopentylcobalamin and its analogs. The results are discussed in terms of the solvent cage effect on Co-C bond homolysis and the importance of corrin ring side chain thermal motions to the entropy of activation for this reaction.
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Affiliation(s)
- Kenneth L. Brown
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, and Departments of Cell Biology and Clinical Pathology, The Research Institute of the Cleveland Clinic Foundation, Cleveland, Ohio 44195
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Brown KL, Evans DR. Heteronuclear NMR studies of cobalt corrinoids—17. characterization of neopentylcobinamide and neopentyl-13-epicobinamide by 1H and 13C NMR spectroscopy: Inferred corrin ring conformations from chemical shift differentials. Polyhedron 1995. [DOI: 10.1016/0277-5387(95)00123-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tobimatsu T, Hara T, Sakaguchi M, Kishimoto Y, Wada Y, Isoda M, Sakai T, Toraya T. Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca. J Biol Chem 1995; 270:7142-8. [PMID: 7706251 DOI: 10.1074/jbc.270.13.7142] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The pdd genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca were cloned by using a synthetic oligodeoxyribonucleotide as a hybridization probe followed by measuring the enzyme activity of each clone. Five clones of Escherichia coli exhibited diol dehydrase activity. At least one of them was shown to express diol dehydrase genes under control of their own promoter. Sequence analysis of the DNA fragments found in common in the inserts of these five clones and the flanking regions revealed four open reading frames separated by 10-18 base pairs. The sequential three open reading frames from the second to the fourth (pddA, pddB, and pddC genes) encoded polypeptides of 554, 224, and 173 amino acid residues with predicted molecular weights of 60,348 (alpha), 24,113 (beta), and 19,173 (gamma), respectively. Overexpression of these three genes in E. coli produced more than 50-fold higher level of functional apodiol dehydrase than that in K. oxytoca. The recombinant enzyme was indistinguishable from the wild-type one of K. oxytoca by the criteria of polyacrylamide gel electrophoretic and immunochemical properties. It was thus concluded that these three gene products are the subunits of functional diol dehydrase. Comparisons of the deduced amino acid sequences of the three subunits with other proteins failed to reveal any apparent homology.
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Affiliation(s)
- T Tobimatsu
- Department of Biotechnology, Faculty of Engineering, Okayama University, Japan
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Affiliation(s)
- J P Glusker
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
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Toraya T, Miyoshi S, Mori M, Wada K. The synthesis of a pyridyl analog of adenosylcobalamin and its coenzymic function in the diol dehydratase reaction. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1204:169-74. [PMID: 8142456 DOI: 10.1016/0167-4838(94)90005-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A novel analog of adenosylcobalamin in which 5,6-dimethylbenzimidazole and D-ribose moieties of the nucleotide loop are replaced by pyridine and the trimethylene group, respectively, was synthesized and examined for coenzymic function. The coordination of pyridine to the cobalt atom in this analog was stronger than that of 5,6-dimethylbenzimidazole in the corresponding homolog. The adenosyl form of pyridyl analog served as partially active coenzyme for diol dehydratase. The kcat/Km values calculated from the initial velocity indicate that this analog is a better coenzyme than the 5,6-dimethylbenzimidazolyl or imidazolyl counterpart. However, the reaction with the pyridyl analog as coenzyme was accompanied with a concomitant inactivation during catalysis, with a kcat/Kinact value 50-100 times lower than that for adenosylcobalamin or the 5,6-dimethylbenzimidazolyl analog. Therefore, it can be concluded that the 5,6-dimethylbenzimidazole moiety of adenosylcobalamin is important for continuous progress of a catalytic cycle by protecting the reactive intermediates from side reactions.
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Affiliation(s)
- T Toraya
- Department of Biotechnology, Faculty of Engineering, Okayama University, Japan
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Brown KL, Brooks HB, Behnke D, Jacobsen DW. Stabilization of thermally labile alkylcobalamins by a haptocorrin from chicken serum. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89561-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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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 1991. [DOI: 10.1016/s0021-9258(19)67613-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Chen E, Chance MR. Nanosecond transient absorption spectroscopy of coenzyme B12. Quantum yields and spectral dynamics. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38257-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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