1
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Fatima S, Boggs DG, Ali N, Thompson PJ, Thielges MC, Bridwell-Rabb J, Olshansky L. Engineering a Conformationally Switchable Artificial Metalloprotein. J Am Chem Soc 2022; 144:21606-21616. [DOI: 10.1021/jacs.2c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Saman Fatima
- Department of Chemistry, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
| | - David G. Boggs
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan48109, United States
| | - Noor Ali
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Peter J. Thompson
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana47405, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan48109, United States
| | - Lisa Olshansky
- Department of Chemistry, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, 600 S. Mathews Avenue, Urbana, Illinois61801, United States
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2
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Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Angew Chem Int Ed Engl 2022; 61:e202208295. [PMID: 35793207 PMCID: PMC9545868 DOI: 10.1002/anie.202208295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 12/04/2022]
Abstract
Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012 -fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- BioTechMed-Graz8010GrazAustria
- Field of Excellence “BioHealth”University of Graz8010GrazAustria
| | - Vanessa Csitkovits
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Andrzej Łyskowski
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- Present address: Department of Biotechnology and BioinformaticsRzeszów University of Technologyal. Powstańców Warszawy 1235-959RzeszówPoland
| | - Christoph Kratky
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
- Center of Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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3
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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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4
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Park K, Mera PE, Escalante-Semerena JC, Brunold TC. Resonance Raman spectroscopic study of the interaction between Co(II)rrinoids and the ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri. J Biol Inorg Chem 2016; 21:669-81. [PMID: 27383231 PMCID: PMC5118822 DOI: 10.1007/s00775-016-1371-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022]
Abstract
The human-type ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri (LrPduO) catalyzes the adenosylation of Co(II)rrinoids to generate adenosylcobalamin (AdoCbl) or adenosylcobinamide (AdoCbi(+)). This process requires the formation of "supernucleophilic" Co(I)rrinoid intermediates in the enzyme active site which are properly positioned to abstract the adeonsyl moiety from co-substrate ATP. Previous magnetic circular dichroism (MCD) spectroscopic and X-ray crystallographic analyses revealed that LrPduO achieves the thermodynamically challenging reduction of Co(II)rrinoids by displacing the axial ligand with a non-coordinating phenylalanine residue to produce a four-coordinate species. However, relatively little is currently known about the interaction between the tetradentate equatorial ligand of Co(II)rrinoids (the corrin ring) and the enzyme active site. To address this issue, we have collected resonance Raman (rR) data of Co(II)rrinoids free in solution and bound to the LrPduO active site. The relevant resonance-enhanced vibrational features of the free Co(II)rrinoids are assigned on the basis of rR intensity calculations using density functional theory to establish a suitable framework for interpreting rR spectral changes that occur upon Co(II)rrinoid binding to the LrPduO/ATP complex in terms of structural perturbations of the corrin ring. To complement our rR data, we have also obtained MCD spectra of Co(II)rrinoids bound to LrPduO complexed with the ATP analogue UTP. Collectively, our results provide compelling evidence that in the LrPduO active site, the corrin ring of Co(II)rrinoids is firmly locked in place by several amino acid side chains so as to facilitate the dissociation of the axial ligand.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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5
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Jost M, Simpson JH, Drennan CL. The Transcription Factor CarH Safeguards Use of Adenosylcobalamin as a Light Sensor by Altering the Photolysis Products. Biochemistry 2015; 54:3231-4. [PMID: 25966286 PMCID: PMC4455981 DOI: 10.1021/acs.biochem.5b00416] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The newly discovered light-dependent
transcription factor CarH
uses adenosylcobalamin as a light sensor to regulate expression of
protective genes in bacteria upon exposure to sunlight. This use of
adenosylcobalamin is a clever adaptation of a classic enzyme cofactor,
taking advantage of its photolabile Co–C bond. However, it
is also puzzling in that photolysis of adenosylcobalamin generates
the 5′-deoxyadenosyl radical that could damage DNA. Here, using
liquid chromatography and spectroscopic techniques, we demonstrate
that CarH suppresses release of the 5′-deoxyadenosyl radical
and instead effects conversion to a nonreactive 4′,5′-anhydroadenosine.
In this manner, CarH safeguards use of adenosylcobalamin in light-dependent
gene regulation.
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Affiliation(s)
- Marco Jost
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeffrey H Simpson
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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6
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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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7
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Molecular basis for the action of a dietary flavonoid revealed by the comprehensive identification of apigenin human targets. Proc Natl Acad Sci U S A 2013; 110:E2153-62. [PMID: 23697369 DOI: 10.1073/pnas.1303726110] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavonoids constitute the largest class of dietary phytochemicals, adding essential health value to our diet, and are emerging as key nutraceuticals. Cellular targets for dietary phytochemicals remain largely unknown, posing significant challenges for the regulation of dietary supplements and the understanding of how nutraceuticals provide health value. Here, we describe the identification of human cellular targets of apigenin, a flavonoid abundantly present in fruits and vegetables, using an innovative high-throughput approach that combines phage display with second generation sequencing. The 160 identified high-confidence candidate apigenin targets are significantly enriched in three main functional categories: GTPase activation, membrane transport, and mRNA metabolism/alternative splicing. This last category includes the heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2), a factor involved in splicing regulation, mRNA stability, and mRNA transport. Apigenin binds to the C-terminal glycine-rich domain of hnRNPA2, preventing hnRNPA2 from forming homodimers, and therefore, it perturbs the alternative splicing of several human hnRNPA2 targets. Our results provide a framework to understand how dietary phytochemicals exert their actions by binding to many functionally diverse cellular targets. In turn, some of them may modulate the activity of a large number of downstream genes, which is exemplified here by the effects of apigenin on the alternative splicing activity of hnRNPA2. Hence, in contrast to small-molecule pharmaceuticals designed for defined target specificity, dietary phytochemicals affect a large number of cellular targets with varied affinities that, combined, result in their recognized health benefits.
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8
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Russell HJ, Jones AR, Hay S, Greetham GM, Towrie M, Scrutton NS. Protein Motions Are Coupled to the Reaction Chemistry in Coenzyme B 12-Dependent Ethanolamine Ammonia Lyase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Russell HJ, Jones AR, Hay S, Greetham GM, Towrie M, Scrutton NS. Protein Motions Are Coupled to the Reaction Chemistry in Coenzyme B12-Dependent Ethanolamine Ammonia Lyase. Angew Chem Int Ed Engl 2012; 51:9306-10. [DOI: 10.1002/anie.201202502] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/13/2012] [Indexed: 11/12/2022]
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10
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Adenosylcobalamin enzymes: theory and experiment begin to converge. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1154-64. [PMID: 22516318 DOI: 10.1016/j.bbapap.2012.03.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/04/2012] [Accepted: 03/27/2012] [Indexed: 11/21/2022]
Abstract
Adenosylcobalamin (coenzyme B(12)) serves as the cofactor for a group of enzymes that catalyze unusual rearrangement or elimination reactions. The role of the cofactor as the initiator of reactive free radicals needed for these reactions is well established. Less clear is how these enzymes activate the coenzyme towards homolysis and control the radicals once generated. The availability of high resolution X-ray structures combined with detailed kinetic and spectroscopic analyses have allowed several adenosylcobalamin enzymes to be computationally modeled in some detail. Computer simulations have generally obtained good agreement with experimental data and provided valuable insight into the mechanisms of these unusual reactions. Importantly, atomistic modeling of the enzymes has allowed the role of specific interactions between protein, substrate and coenzyme to be explored, leading to mechanistic predictions that can now be tested experimentally. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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11
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Gruber K, Puffer B, Kräutler B. Vitamin B12-derivatives-enzyme cofactors and ligands of proteins and nucleic acids. Chem Soc Rev 2011; 40:4346-63. [PMID: 21687905 DOI: 10.1039/c1cs15118e] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
B(12)-cofactors play important roles in the metabolism of microorganisms, animals and humans. Microorganisms are the only natural sources of B(12)-derivatives, and the latter are "vitamins" for other B(12)-requiring organisms. Some B(12)-dependent enzymes catalyze complex isomerisation reactions, such as methylmalonyl-CoA mutase. They need coenzyme B(12), an organometallic B(12)-derivative, to induce enzymatic radical reactions. Another group of widely relevant enzymes catalyzes the transfer of methyl groups, such as methionine synthase, which uses methylcobalamin as cofactor. This tutorial review covers structure and reactivity of B(12)-derivatives and structural aspects of their interactions with proteins and nucleotides, which are crucial for the efficient catalysis by the important B(12)-dependent enzymes, and for achieving and regulating uptake and transport of B(12)-derivatives.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50/3, Graz, A-8010, Austria
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12
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Robertson WD, Wang M, Warncke K. Characterization of protein contributions to cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase by using photolysis in the ternary complex. J Am Chem Soc 2011; 133:6968-77. [PMID: 21491908 PMCID: PMC3092035 DOI: 10.1021/ja107052p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein contributions to the substrate-triggered cleavage of the cobalt-carbon (Co-C) bond and formation of the cob(II)alamin-5'-deoxyadenosyl radical pair in the adenosylcobalamin (AdoCbl)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been studied by using pulsed-laser photolysis of AdoCbl in the EAL-AdoCbl-substrate ternary complex, and time-resolved probing of the photoproduct dynamics by using ultraviolet-visible absorption spectroscopy on the 10(-7)-10(-1) s time scale. Experiments were performed in a fluid dimethylsulfoxide/water cryosolvent system at 240 K, under conditions of kinetic competence for thermal cleavage of the Co-C bond in the ternary complex. The static ultraviolet-visible absorption spectra of holo-EAL and ternary complex are comparable, indicating that the binding of substrate does not labilize the cofactor cobalt-carbon (Co-C) bond by significantly distorting the equilibrium AdoCbl structure. Photolysis of AdoCbl in EAL at 240 K leads to cob(II)alamin-5'-deoxyadenosyl radical pair quantum yields of <0.01 at 10(-6) s in both holo-EAL and ternary complex. Three photoproduct states are populated following a saturating laser pulse, and labeled, P(f), P(s), and P(c). The relative amplitudes and first-order recombination rate constants of P(f) (0.4-0.6; 40-50 s(-1)), P(s) (0.3-0.4; 4 s(-1)), and P(c) (0.1-0.2; 0) are comparable in holo-EAL and in the ternary complex. Time-resolved, full-spectrum electron paramagnetic resonance (EPR) spectroscopy shows that visible irradiation alters neither the kinetics of thermal cob(II)alamin-substrate radical pair formation, nor the equilibrium between ternary complex and cob(II)alamin-substrate radical pair, at 246 K. The results indicate that substrate binding to holo-EAL does not "switch" the protein to a new structural state, which promptly stabilizes the cob(II)alamin-5'-deoxyadenosyl radical pair photoproduct, either through an increased barrier to recombination, a decreased barrier to further radical pair separation, or lowering of the radical pair state free energy, or a combination of these effects. Therefore, we conclude that such a change in protein structure, which is independent of changes in the AdoCbl structure, and specifically the Co-C bond length, is not a basis of Co-C bond cleavage catalysis. The results suggest that, following the substrate trigger, the protein interacts with the cofactor to contiguously guide the cleavage of the Co-C bond, at every step along the cleavage coordinate, starting from the equilibrium configuration of the ternary complex. The cleavage is thus represented by a diagonal trajectory across a free energy surface, that is defined by chemical (Co-C separation) and protein configuration coordinates.
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Affiliation(s)
| | - Miao Wang
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA 30322
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13
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Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
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Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
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14
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Robertson WD, Warncke K. Photolysis of adenosylcobalamin and radical pair recombination in ethanolamine ammonia-lyase probed on the micro- to millisecond time scale by using time-resolved optical absorption spectroscopy. Biochemistry 2009; 48:140-7. [PMID: 19072291 DOI: 10.1021/bi801659e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The quantum yield and kinetics of decay of cob(II)alamin formed by pulsed-laser photolysis of adenosylcobalamin (AdoCbl; coenzyme B(12)) in AdoCbl-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been studied on the 10(-7)-10(-1) s time scale at 295 K by using transient ultraviolet-visible absorption spectroscopy. The aim is to probe the mechanism of formation and stabilization of the cob(II)alamin-5'-deoxyadenosyl radical pair, which is a key intermediate in EAL catalysis, and the influence of substrate binding on this process. Substrate binding is required for cobalt-carbon bond cleavage in the native system. Photolysis of AdoCbl in EAL leads to a quantum yield at 10(-7) s for cob(II)alamin of 0.08 +/- 0.01, which is 3-fold smaller than for AdoCbl in aqueous solution (0.23 +/- 0.01). The protein binding site therefore suppresses photoproduct radical pair formation. Three photoproduct states, P(f), P(s), and P(c), are identified in holo-EAL by the different cob(II)alamin decay kinetics (subscripts denote fast, slow, and constant, respectively). These states have the following first-order decay rate constants and quantum yields: 2.2 x 10(3) s(-1) and 0.02 for P(f), 4.2 x 10(2) s(-1) and 0.01 for P(s), and constant amplitude, with no recombination, and 0.05 for P(c), respectively. Binding of the substrate analogue (S)-1-amino-2-propanol to EAL eliminates the P(f) state and lowers the quantum yield of P(c) (0.03) relative to that of P(s) (0.01) but does not significantly change the quantum yield or decay rate constant of P(s), relative to those of holo-EAL. The substrate analogue thus influences the quantum yield at 10(-7) s by changing the cage escape rate from the geminate cob(II)alamin-5'-deoxyadenosyl radical pair state. However, the predicted substrate analogue binding-induced increase in the quantum yield is not observed. It is proposed that the substrate analogue does not induce the radical pair stabilizing changes in the protein that are characteristic of true substrates.
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15
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Kozlowski PM, Andruniow T, Jarzecki AA, Zgierski MZ, Spiro TG. DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors. Inorg Chem 2007; 45:5585-90. [PMID: 16813422 PMCID: PMC2773831 DOI: 10.1021/ic052069j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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16
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Patwardhan A, Marsh ENG. Changes in the free energy profile of glutamate mutase imparted by the mutation of an active site arginine residue to lysine. Arch Biochem Biophys 2007; 461:194-9. [PMID: 17306212 PMCID: PMC1995565 DOI: 10.1016/j.abb.2007.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 01/04/2007] [Indexed: 11/23/2022]
Abstract
Arginine 100 plays an important role in substrate recognition in adenosylcobalamin-dependent glutamate mutase. We have examined how the mutation of this residue to lysine affects the partitioning of tritium, incorporated at the exchangeable position of the coenzyme, between substrate and product. We find that partitioning of tritium back to the substrate predominates in the mutant enzyme, regardless of whether the reaction is run in the forward or reverse direction. This contrasts with the behavior of the wild-type enzyme in which tritium partitions equally between substrate and product, independent of the direction of the reaction. From this we conclude that the mutation significantly impairs the ability of the enzyme to catalyze the rearrangement of substrate radical to product radical. The results illustrate the importance of electrostatic interactions in stabilizing free radical intermediates in this class of enzymes.
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17
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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.
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Affiliation(s)
- Karl Gruber
- Institut für Chemie, Universität Graz, Heinrichstrasse 28, Austria.
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Marsh EN, Drennan CL. Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism. Curr Opin Chem Biol 2001; 5:499-505. [PMID: 11578922 DOI: 10.1016/s1367-5931(00)00238-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Adenosylcobalamin-dependent isomerases catalyze a variety of chemically difficult 1,2-rearrangements that proceed through a mechanism involving free radical intermediates. These radicals are initially generated by homolysis of the cobalt-carbon bond of the coenzyme. Recently, the crystal structures of several of these enzymes have been solved, revealing two modes of coenzyme binding and highlighting the role of the protein in controlling the rearrangement of reactive substrate radical intermediates. Complementary data from kinetic, spectroscopic and theoretical studies have produced insights into the mechanism by which substrate radicals are generated at the active site, and the pathways by which they rearrange.
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Affiliation(s)
- E N Marsh
- Department of Chemistry and Division of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
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