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Elmendorf LD, Brunold TC. Electronic structure studies of free and enzyme-bound B 12 species by magnetic circular dichroism and complementary spectroscopic techniques. Methods Enzymol 2022; 669:333-365. [PMID: 35644179 DOI: 10.1016/bs.mie.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Electronic absorption (Abs) and circular dichroism (CD) spectroscopic techniques have been used successfully for over half a century in studies of free and enzyme-bound B12 species. More recently, magnetic circular dichroism (MCD) spectroscopy and other complementary techniques have provided an increasingly detailed understanding of the electronic structure of cobalamins. While CD spectroscopy measures the difference in the absorption of left- and right-circularly polarized light, MCD spectroscopy adds the application of a magnetic field parallel to the direction of light propagation. Transitions that are formally forbidden according to the Abs and CD selection rules, such as ligand field (or d→d) transitions, can gain MCD intensity through spin-orbit coupling. As such, MCD spectroscopy provides a uniquely sensitive probe of the different binding modes, Co oxidation states, and axial ligand environments of B12 species in enzyme active sites, and thus the distinct reactivities displayed by these species. This chapter summarizes representative MCD studies of free and enzyme-bound B12 species, including those present in adenosyltransferases, isomerases, and reductive dehalogenases. Complementary spectroscopic and computational data are also presented and discussed where appropriate.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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2
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Lukinović V, Woodward JR, Marrafa TC, Shanmugam M, Heyes DJ, Hardman SJO, Scrutton NS, Hay S, Fielding AJ, Jones AR. Photochemical Spin Dynamics of the Vitamin B 12 Derivative, Methylcobalamin. J Phys Chem B 2019; 123:4663-4672. [PMID: 31081330 DOI: 10.1021/acs.jpcb.9b01969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Derivatives of vitamin B12 are six-coordinate cobalt corrinoids found in humans, other animals, and microorganisms. By acting as enzymatic cofactors and photoreceptor chromophores, they serve vital metabolic and photoprotective functions. Depending on the context, the chemical mechanisms of the biologically active derivatives of B12-methylcobalamin (MeCbl) and 5'-deoxyadenosylcobalamin (AdoCbl)-can be very different from one another. The extent to which this chemistry is tuned by the upper axial ligand, however, is not yet clear. Here, we have used a combination of time-resolved Fourier transform-electron paramagnetic resonance (FT-EPR), magnetic field effect experiments, and spin dynamic simulations to reveal that the upper axial ligand alone only results in relatively minor changes to the photochemical spin dynamics of B12. By studying the photolysis of MeCbl, we find that, similar to AdoCbl, the initial (or "geminate") radical pairs (RPs) are born predominantly in the singlet spin state and thus originate from singlet excited-state precursors. This is in contrast to the triplet RPs and precursors proposed previously. Unlike AdoCbl, the extent of geminate recombination is limited following MeCbl photolysis, resulting in significant distortions to the FT-EPR signal caused by polarization from spin-correlated methyl-methyl radical "f-pairs" formed following rapid diffusion. Despite the photophysical mechanism that precedes photolysis of MeCbl showing wavelength dependence, the subsequent spin dynamics appear to be largely independent of excitation wavelength, again similar to AdoCbl. Our data finally provide clarity to what in the literature to date has been a confused and contradictory picture. We conclude that, although the upper axial position of MeCbl and AdoCbl does impact their reactivity to some extent, the remarkable biochemical diversity of these fascinating molecules is most likely a result of tuning by their protein environment.
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Affiliation(s)
- Valentina Lukinović
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Jonathan R Woodward
- Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro-ku, Tokyo 153-8902 , Japan
| | - Teresa C Marrafa
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Sam Hay
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | | | - Alex R Jones
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
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Ghosh AP, Mamun AA, Kozlowski PM. How does the mutation in the cap domain of methylcobalamin-dependent methionine synthase influence the photoactivation of the Co–C bond? Phys Chem Chem Phys 2019; 21:20628-20640. [DOI: 10.1039/c9cp01849b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The topology of the S1 PES is modulated by introducing a mutation at the F708 position. The mutation influences the photoactivation of the Co–C bond by decreasing the rate of geminate recombination and altering the rate of radical pair formation.
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4
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Mamun AA, Toda MJ, Lodowski P, Jaworska M, Kozlowski PM. Mechanism of Light Induced Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Abdullah Al Mamun
- 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
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Food Sciences, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
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Abstract
This Perspective provides the first detailed overview of the photoresponse of vitamin B12 and its derivatives, from the early, photophysical events to the burgeoning area of B12-dependent photobiology.
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Affiliation(s)
- Alex R. Jones
- School of Chemistry
- Photon Science Institute and Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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Affiliation(s)
- Alex R. Jones
- School of Chemistry, Photon Science Institute and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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7
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The photochemical mechanism of a B12-dependent photoreceptor protein. Nat Commun 2015; 6:7907. [PMID: 26264192 PMCID: PMC4557120 DOI: 10.1038/ncomms8907] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023] Open
Abstract
The coenzyme B12-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B12 the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B12 enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B12 photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression. Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al. present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.
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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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Menon BRK, Fisher K, Rigby SEJ, Scrutton NS, Leys D. A conformational sampling model for radical catalysis in pyridoxal phosphate- and cobalamin-dependent enzymes. J Biol Chem 2014; 289:34161-74. [PMID: 25213862 PMCID: PMC4256349 DOI: 10.1074/jbc.m114.590471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cobalamin-dependent enzymes enhance the rate of C–Co bond cleavage by up to ∼1012-fold to generate cob(II)alamin and a transient adenosyl radical. In the case of the pyridoxal 5′-phosphate (PLP) and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5 aminomutase (OAM), it has been proposed that a large scale domain reorientation of the cobalamin-binding domain is linked to radical catalysis. Here, OAM variants were designed to perturb the interface between the cobalamin-binding domain and the PLP-binding TIM barrel domain. Steady-state and single turnover kinetic studies of these variants, combined with pulsed electron-electron double resonance measurements of spin-labeled OAM were used to provide direct evidence for a dynamic interface between the cobalamin and PLP-binding domains. Our data suggest that following ligand binding-induced cleavage of the Lys629-PLP covalent bond, dynamic motion of the cobalamin-binding domain leads to conformational sampling of the available space. This supports radical catalysis through transient formation of a catalytically competent active state. Crucially, it appears that the formation of the state containing both a substrate/product radical and Co(II) does not restrict cobalamin domain motion. A similar conformational sampling mechanism has been proposed to support rapid electron transfer in a number of dynamic redox systems.
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Affiliation(s)
- Binuraj R K Menon
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
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Mori K, Oiwa T, Kawaguchi S, Kondo K, Takahashi Y, Toraya T. Catalytic Roles of Substrate-Binding Residues in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. Biochemistry 2014; 53:2661-71. [DOI: 10.1021/bi500223k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Mori
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Toshihiro Oiwa
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Satoshi Kawaguchi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kyosuke Kondo
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Takahashi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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