1
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Nguyen TQ, Nicolet Y. Structure and Catalytic Mechanism of Radical SAM Methylases. Life (Basel) 2022; 12:1732. [PMID: 36362886 PMCID: PMC9692996 DOI: 10.3390/life12111732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/14/2023] Open
Abstract
Methyl transfer is essential in myriad biological pathways found across all domains of life. Unlike conventional methyltransferases that catalyze this reaction through nucleophilic substitution, many members of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily use radical-based chemistry to methylate unreactive carbon centers. These radical SAM methylases reductively cleave SAM to generate a highly reactive 5'-deoxyadenosyl radical, which initiates a broad range of transformations. Recently, crystal structures of several radical SAM methylases have been determined, shedding light on the unprecedented catalytic mechanisms used by these enzymes to overcome the substantial activation energy barrier of weakly nucleophilic substrates. Here, we review some of the discoveries on this topic over the last decade, focusing on enzymes for which three-dimensional structures are available to identify the key players in the mechanisms, highlighting the dual function of SAM as a methyl donor and a 5'-deoxyadenosyl radical or deprotonating base source. We also describe the role of the protein matrix in orchestrating the reaction through different strategies to catalyze such challenging methylations.
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Affiliation(s)
| | - Yvain Nicolet
- Metalloproteins Unit, Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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2
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Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
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Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
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3
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Ji P, Luo YR, Xue XS, Cheng JP. Efficient estimation of bond dissociation energies of organic compounds. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2022. [DOI: 10.1016/bs.apoc.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Blue TC, Davis KM. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules 2021; 26:molecules26092590. [PMID: 33946806 PMCID: PMC8124187 DOI: 10.3390/molecules26092590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022] Open
Abstract
Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.
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5
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Suess CJ, Martins FL, Croft AK, Jäger CM. Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. J Chem Inf Model 2019; 59:5111-5125. [PMID: 31730347 DOI: 10.1021/acs.jcim.9b00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.
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Affiliation(s)
- Christian J Suess
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Floriane L Martins
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna K Croft
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
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6
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Abstract
We explored the influence of external electric fields (EEFs) on the stability of a glycine dipeptide model radical using high-level quantum chemical methods. Remotely located ions (Cl-/Na+) are used to implement EEF effects. The effects of these ions are reproduced using background point charges and oriented EEFs. Remote charges as far as 900 pm from the Cα radical center can be significantly stabilizing or destabilizing as a function of their relative orientation. The magnitude of these effects is also strongly dependent on the distance between the radical center and the charge location. After examining the strengths and weaknesses of some frequently used quantum mechanics methods in describing these effects properly, a comparison is made on the stability of dipeptide radicals bearing protonable or deprotonable side chains. In this group, the stability of the respective Cα radicals mainly depends on the preferred orientation of the charge-carrying side chain.
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Affiliation(s)
- Harish Jangra
- Department of Chemistry , LMU München , Butenandtstrasse 5-13 , 81377 München , Germany
| | - Hendrik Zipse
- Department of Chemistry , LMU München , Butenandtstrasse 5-13 , 81377 München , Germany
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7
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Ji X, Mandalapu D, Cheng J, Ding W, Zhang Q. Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xinjian Ji
- Department of ChemistryFudan University Shanghai 200433 China
| | | | - Jinduo Cheng
- Department of ChemistryFudan University Shanghai 200433 China
| | - Wei Ding
- Department of ChemistryFudan University Shanghai 200433 China
| | - Qi Zhang
- Department of ChemistryFudan University Shanghai 200433 China
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8
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Ji X, Mandalapu D, Cheng J, Ding W, Zhang Q. Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM. Angew Chem Int Ed Engl 2018; 57:6601-6604. [PMID: 29603551 DOI: 10.1002/anie.201712224] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/11/2018] [Indexed: 11/11/2022]
Abstract
The radical S-adenosylmethionine (SAM) superfamily enzymes cleave SAM reductively to generate a highly reactive 5'-deoxyadenosyl (dAdo) radical, which initiates remarkably diverse reactions. Unlike most radical SAM enzymes, the class C radical SAM methyltransferase NosN binds two SAMs in the active site, using one SAM to produce a dAdo radical and the second as a methyl donor. Here, we report a mechanistic investigation of NosN in which an allyl analogue of SAM (allyl-SAM) was used. We show that NosN cleaves allyl-SAM efficiently and the resulting dAdo radical can be captured by the olefin moieties of allyl-SAM or 5'-allylthioadenosine (ATA), the latter being a derivative of allyl-SAM. Remarkably, we found that NosN produced two distinct sets of products in the presence and absence of the methyl acceptor substrate, thus suggesting substrate-triggered production of ATA from allyl-SAM. We also show that NosN produces S-adenosylhomocysteine from 5'-thioadenosine and homoserine lactone. These results support the idea that 5'-methylthioadenosine is the direct methyl donor in NosN reactions, and demonstrate great potential to modulate radical SAM enzymes for novel catalytic activities.
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Affiliation(s)
- Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | | | - Jinduo Cheng
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Wei Ding
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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9
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Jäger CM, Croft AK. Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate. Chemistry 2017; 23:953-962. [PMID: 27859789 PMCID: PMC5347944 DOI: 10.1002/chem.201604719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 12/29/2022]
Abstract
Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.
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Affiliation(s)
- Christof M. Jäger
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
| | - Anna K. Croft
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
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10
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Andrea C Kneuttinger
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
| | - Gengo Kashiwazaki
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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11
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Affiliation(s)
- Davor Šakić
- University of Zagreb; Faculty of Pharmacy and Biochemistry; Ante Kovačića 1 10000 Zagreb Croatia
| | - Hendrik Zipse
- Department of Chemistry; LMU Muenchen; Butenandtstrasse 5-13 81377 Muenchen Germany
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12
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Calculated bond dissociation energies and enthalpy of formation of α-amino acid radicals. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1975-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Abstract
Radical stabilization energies (RSEs) for a wide variety of nitrogen-centered radicals and their protonated counterparts have been calculated at G3(MP2)-RAD and G3B3 level. The calculated RSE values can be rationalized through the combined effects of resonance delocalization of the unpaired spin, electron donation through adjacent alkyl groups or lone pairs, and through inductive electron donation/electron withdrawal. The influence of ring strain effects as well as the synergistic combination of individual substituent effects (captodatively stabilized N-radicals) have also been explored. In symmetric N-radicals the substituents may also affect the relative ordering of electronic states. In most cases the π-type radical (unpaired spin distribution perpendicular to the plane of the N-radical) is found to be most stable. Closed shell precursors of biological and pharmaceutical relevance, for which neither experimental nor theoretical results on radical stabilities exist, have been included.
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Affiliation(s)
- Johnny Hioe
- Department of Chemistry, LMU München, Butenandtstrasse 5-13, D-81377 München, Germany.
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14
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Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
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Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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15
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Schmerk CL, Welander PV, Hamad MA, Bain KL, Bernards MA, Summons RE, Valvano MA. Elucidation of theBurkholderia cenocepaciahopanoid biosynthesis pathway uncovers functions for conserved proteins in hopanoid-producing bacteria. Environ Microbiol 2014; 17:735-50. [DOI: 10.1111/1462-2920.12509] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/09/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Crystal L. Schmerk
- Department of Microbiology and Immunology; University of Western Ontario; London Ontario N6A 5C1 Canada
| | - Paula V. Welander
- Department of Environmental Earth System Science; Stanford University; Stanford CA USA
| | - Mohamad A. Hamad
- Department of Microbiology and Immunology; University of Western Ontario; London Ontario N6A 5C1 Canada
| | - Katie L. Bain
- Department of Microbiology and Immunology; University of Western Ontario; London Ontario N6A 5C1 Canada
| | - Mark A. Bernards
- Department of Biology; University of Western Ontario; London Ontario N6A 5C1 Canada
| | - Roger E. Summons
- Department of Earth, Atmospheric, and Planetary Sciences; Massachusetts Institute of Technology; Cambridge MA USA
| | - Miguel A. Valvano
- Department of Microbiology and Immunology; University of Western Ontario; London Ontario N6A 5C1 Canada
- Centre for Infection and Immunity; Queen's University Belfast; Belfast BT9 5AE UK
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16
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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17
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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18
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Fujimori DG. Radical SAM-mediated methylation reactions. Curr Opin Chem Biol 2013; 17:597-604. [PMID: 23835516 DOI: 10.1016/j.cbpa.2013.05.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
A subset of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily is able to catalyze methylation reactions. Substrates of these enzymes are distinct from the nucleophilic substrates that undergo methylation by a polar mechanism. Recently, activities of several radical SAM methylating enzymes have been reconstituted in vitro and their mechanisms of catalysis investigated. The RNA modifying enzymes RlmN and Cfr catalyze methylation via a methyl synthase mechanism. These enzymes use SAM in two distinct roles: as a source of a methyl group transferred to a conserved cysteine and as a source of 5'-deoxyadenosyl radical (5'-dA). Hydrogen atom abstraction by this species generates a thiomethylene radical which adds into the RNA substrate, forming an enzyme-substrate covalent adduct. In another recent study, methylation of the indole moiety of tryptophan by the radical SAM and cobalamin-binding domain enzyme TsrM has been reconstituted. Methylcobalamin serves as an intermediate methyl donor in TsrM, and is proposed to transfer the methyl group as a methyl radical. Interestingly, despite the presence of the radical SAM motif, no reductive cleavage of SAM has been observed in this methylation. These important reconstitutions set the stage for further studies on mechanisms of radical methylation.
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Affiliation(s)
- Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-2280, USA.
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19
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Challand MR, Salvadori E, Driesener RC, Kay CWM, Roach PL, Spencer J. Cysteine methylation controls radical generation in the Cfr radical AdoMet rRNA methyltransferase. PLoS One 2013; 8:e67979. [PMID: 23861844 PMCID: PMC3702613 DOI: 10.1371/journal.pone.0067979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
The 'radical S-adenosyl-L-methionine (AdoMet)' enzyme Cfr methylates adenosine 2503 of the 23S rRNA in the peptidyltransferase centre (P-site) of the bacterial ribosome. This modification protects host bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), from numerous antibiotics, including agents (e.g. linezolid, retapamulin) that were developed to treat such organisms. Cfr contains a single [4Fe-4S] cluster that binds two separate molecules of AdoMet during the reaction cycle. These are used sequentially to first methylate a cysteine residue, Cys338; and subsequently generate an oxidative radical intermediate that facilitates methyl transfer to the unreactive C8 (and/or C2) carbon centres of adenosine 2503. How the Cfr active site, with its single [4Fe-4S] cluster, catalyses these two distinct activities that each utilise AdoMet as a substrate remains to be established. Here, we use absorbance and electron paramagnetic resonance (EPR) spectroscopy to investigate the interactions of AdoMet with the [4Fe-4S] clusters of wild-type Cfr and a Cys338 Ala mutant, which is unable to accept a methyl group. Cfr binds AdoMet with high (∼ 10 µM) affinity notwithstanding the absence of the RNA cosubstrate. In wild-type Cfr, where Cys338 is methylated, AdoMet binding leads to rapid oxidation of the [4Fe-4S] cluster and production of 5'-deoxyadenosine (DOA). In contrast, while Cys338 Ala Cfr binds AdoMet with equivalent affinity, oxidation of the [4Fe-4S] cluster is not observed. Our results indicate that the presence of a methyl group on Cfr Cys338 is a key determinant of the activity of the enzyme towards AdoMet, thus enabling a single active site to support two distinct modes of AdoMet cleavage.
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Affiliation(s)
- Martin R. Challand
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | | | - Christopher W. M. Kay
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - Peter L. Roach
- Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
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Kneuttinger AC, Heil K, Kashiwazaki G, Carell T. The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair. Chem Commun (Camb) 2013; 49:722-4. [PMID: 23228940 DOI: 10.1039/c2cc37735g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spore photoproduct lyase is a radical SAM enzyme, which repairs 5-(α-thyminyl)-5,6-dihydrothymidine. Here we show that the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrative Protein Science at the Department for Chemistry, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 Munich, Germany
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Lin G, Li L. Oxidation and reduction of the 5-(2'-deoxyuridinyl)methyl radical. Angew Chem Int Ed Engl 2013; 52:5594-8. [PMID: 23589226 PMCID: PMC3689432 DOI: 10.1002/anie.201209454] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/25/2013] [Indexed: 11/09/2022]
Abstract
Sleeping beauty: The 5-(2’-Deoxyuridinyl) methyl radical 1 is a key intermediate in the thymine oxidative reaction mediated by reactive oxygen species. Evidence is presented that 1 is prone to both oxidation and reduction reactions at the absence of O2. These results question the current paradigm and suggest that the redox chemistry of 1 , which has been largely overlooked in the past, may play a major role in determining the fate of 1 .
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Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA)
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA)
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Yang L, Nelson RS, Benjdia A, Lin G, Telser J, Stoll S, Schlichting I, Li L. A radical transfer pathway in spore photoproduct lyase. Biochemistry 2013; 52:3041-50. [PMID: 23607538 DOI: 10.1021/bi3016247] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a covalent UV-induced thymine dimer, spore photoproduct (SP), in germinating endospores and is responsible for the strong UV resistance of endospores. SPL is a radical S-adenosyl-l-methionine (SAM) enzyme, which uses a [4Fe-4S](+) cluster to reduce SAM, generating a catalytic 5'-deoxyadenosyl radical (5'-dA(•)). This in turn abstracts a H atom from SP, generating an SP radical that undergoes β scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. Recent biochemical and structural data suggest that a conserved cysteine donates a H atom to the thymine radical, resulting in a putative thiyl radical. Here we present structural and biochemical data that suggest that two conserved tyrosines are also critical in enzyme catalysis. One [Y99(Bs) in Bacillus subtilis SPL] is downstream of the cysteine, suggesting that SPL uses a novel hydrogen atom transfer (HAT) pathway with a pair of cysteine and tyrosine residues to regenerate SAM. The other tyrosine [Y97(Bs)] has a structural role to facilitate SAM binding; it may also contribute to the SAM regeneration process by interacting with the putative (•)Y99(Bs) and/or 5'-dA(•) intermediates to lower the energy barrier for the second H abstraction step. Our results indicate that SPL is the first member of the radical SAM superfamily (comprising more than 44000 members) to bear a catalytically operating HAT chain.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
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23
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Lin G, Li L. Oxidation and Reduction of the 5-(2′-Deoxyuridinyl)methyl Radical. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hioe J, Mosch M, Smith DM, Zipse H. Dissociation energies of Cα–H bonds in amino acids – a re-examination. RSC Adv 2013. [DOI: 10.1039/c3ra42115e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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