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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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2
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Ngiam L, Schembri MA, Weynberg K, Guo J. Bacteriophage isolated from non-target bacteria demonstrates broad host range infectivity against multidrug-resistant bacteria. Environ Microbiol 2021; 23:5569-5586. [PMID: 34390602 DOI: 10.1111/1462-2920.15714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance represents a global health challenge. The emergence of multidrug-resistant (MDR) bacteria such as uropathogenic Escherichia coli (UPEC) has attracted significant attention due to increased MDR properties, even against the last line of antibiotics. Bacteriophage, or simply phage, represents an alternative treatment to antibiotics. However, phage applications still face some challenges, such as host range specificity and development of phage resistant mutants. In this study, using both UPEC and non-UPEC hosts, five different phages were isolated from wastewater. We found that the inclusion of commensal Escherichia coli as target hosts during screening improved the capacity to select phage with desirable characteristics for phage therapy. Whole-genome sequencing revealed that four out of five phages adopt strictly lytic lifestyles and are taxonomically related to different phage families belonging to the Myoviridae and Podoviridae. In comparison to single phage treatment, the application of phage cocktails targeting different cell surface receptors significantly enhanced the suppression of UPEC hosts. The emergence of phage-resistant mutants after single phage treatment was attributed to mutational changes in outer membrane protein components, suggesting the potential receptors recognized by these phages. The findings highlight the use of commensal E. coli as target hosts to isolate broad host range phage with infectivity against MDR bacteria.
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Affiliation(s)
- Lyman Ngiam
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld, Australia
| | - Karen Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, University of Queensland, Brisbane, Qld, Australia
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3
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Schneiker A, Góbi S, Joshi PR, Bazsó G, Lee YP, Tarczay G. Non-energetic, Low-Temperature Formation of C α-Glycyl Radical, a Potential Interstellar Precursor of Natural Amino Acids. J Phys Chem Lett 2021; 12:6744-6751. [PMID: 34264091 DOI: 10.1021/acs.jpclett.1c01306] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The reaction of H atoms with glycine was investigated at 3.1 K in para-H2, a quantum-solid host. The reaction was followed by IR spectroscopy, with the spectral analysis aided by quantum chemical computations. Comparison of the experimental IR spectrum with computed anharmonic frequencies and intensities proved that, regardless of the reactant glycine conformation, Cα-glycyl radical is formed in an H-atom-abstraction process with great selectivity. The product of the second H-atom abstraction, iminoacetic acid, was also observed in a smaller amount. The Cα-glycyl radical is sensitive to UV light and decomposes to iminoacetic acid and H atom upon 280 nm radiation. Since the reactive radical center is located on the Cα-atom, it is suggested that natural α-amino acids can be formed from glycine via the Cα-glycyl radical by non-energetic mechanisms in the solid phase of the interstellar medium.
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Affiliation(s)
- Anita Schneiker
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
| | - Sándor Góbi
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
| | - Prasad Ramesh Joshi
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Gábor Bazsó
- Wigner Research Centre for Physics, P. O. Box 49, H-1525 Budapest, Hungary
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 300093, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - György Tarczay
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, ELTE Eötvös Loránd University, H-1518 Budapest, Hungary
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4
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Selvaraj B, Buckel W, Golding BT, Ullmann GM, Martins BM. Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme. J Mol Microbiol Biotechnol 2016; 26:76-91. [DOI: 10.1159/000440882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.
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Heider J, Szaleniec M, Martins BM, Seyhan D, Buckel W, Golding BT. Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes. J Mol Microbiol Biotechnol 2016; 26:29-44. [PMID: 26959246 DOI: 10.1159/000441656] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The pathway of anaerobic toluene degradation is initiated by a remarkable radical-type enantiospecific addition of the chemically inert methyl group to the double bond of a fumarate cosubstrate to yield (R)-benzylsuccinate as the first intermediate, as catalyzed by the glycyl radical enzyme benzylsuccinate synthase. In recent years, it has become clear that benzylsuccinate synthase is the prototype enzyme of a much larger family of fumarate-adding enzymes, which play important roles in the anaerobic metabolism of further aromatic and even aliphatic hydrocarbons. We present an overview on the biochemical properties of benzylsuccinate synthase, as well as its recently solved structure, and present the results of an initial structure-based modeling study on the reaction mechanism. Moreover, we compare the structure of benzylsuccinate synthase with those predicted for different clades of fumarate-adding enzymes, in particular the paralogous enzymes converting p-cresol, 2-methylnaphthalene or n-alkanes.
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Affiliation(s)
- Johann Heider
- Laboratory of Microbial Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
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Abstract
Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.
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Peck SC, Chekan JR, Ulrich EC, Nair SK, van der Donk WA. A common late-stage intermediate in catalysis by 2-hydroxyethyl-phosphonate dioxygenase and methylphosphonate synthase. J Am Chem Soc 2015; 137:3217-20. [PMID: 25699631 PMCID: PMC4487810 DOI: 10.1021/jacs.5b00282] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
2-Hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are nonheme iron oxygenases that both catalyze the carbon-carbon bond cleavage of 2-hydroxyethylphosphonate but generate different products. Substrate labeling experiments led to a mechanistic hypothesis in which the fate of a common intermediate determined product identity. We report here the generation of a bifunctional mutant of HEPD (E176H) that exhibits the activity of both HEPD and MPnS. The product distribution of the mutant is sensitive to a substrate isotope effect, consistent with an isotope-sensitive branching mechanism involving a common intermediate. The X-ray structure of the mutant was determined and suggested that the introduced histidine does not coordinate the active site metal, unlike the iron-binding glutamate it replaced.
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Affiliation(s)
- Spencer C. Peck
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Jonathan R. Chekan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois 61801, United States
| | - Emily C. Ulrich
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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9
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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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10
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Lanz ND, Booker SJ. Auxiliary iron-sulfur cofactors in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1316-34. [PMID: 25597998 DOI: 10.1016/j.bbamcr.2015.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022]
Abstract
A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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The ferredoxin-like domain of the activating enzyme is required for generating a lasting glycyl radical in 4-hydroxyphenylacetate decarboxylase. J Biol Inorg Chem 2014; 19:1317-26. [PMID: 25156152 DOI: 10.1007/s00775-014-1189-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
4-Hydroxyphenylacetate decarboxylase-activating enzyme (4Hpad-AE) uses S-adenosylmethionine (SAM or AdoMet) and a [4Fe-4S] ²⁺/⁺cluster (RS cluster) to generate a stable glycyl radical on the decarboxylase. 4Hpad-AE might bind up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert C-terminal to the RS cluster-binding motif. Except for the AEs of pyruvate formate-lyase and anaerobic ribonucleotide reductase, all glycyl radical-activating enzymes possess a similar ferredoxin-like domain, whose functional role is still poorly understood. To assess the role of the putative ferredoxin clusters from 4Hpad-AE, we combined biochemical and spectroscopic methods to characterize a truncated version of the protein (Δ66-AE) devoid of the ferredoxin-like domain. We found that Δ66-AE is stable, harbors a fully active RS cluster and can activate the decarboxylase. From the similar cleavage rates for S-adenosylmethionine of Δ66-AE and wild-type AE, we infer the reactivity of the RS cluster is unperturbed by the absence of the ferredoxin-like domain. Thus, the auxiliary clusters are not required as electron conduit to the RS cluster for effective reductive cleavage of SAM. The activation of the decarboxylase by Δ66-AE is almost as fast as with wild-type AE, but the generated glycyl radical is short living. We postulate that the ferredoxin-like domain is not required for SAM-dependent glycyl radical generation in the decarboxylase, but is necessary for producing a lasting glycyl radical.
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12
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The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant. Proc Natl Acad Sci U S A 2014; 111:E3756-65. [PMID: 25157154 DOI: 10.1073/pnas.1414396111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO2. Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism.
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Wei Y, Mathies G, Yokoyama K, Chen J, Griffin R, Stubbe J. A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase. J Am Chem Soc 2014; 136:9001-13. [PMID: 24827372 PMCID: PMC4073831 DOI: 10.1021/ja5030194] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/28/2022]
Abstract
The class III ribonucleotide reductases (RNRs) are glycyl radical (G•) enzymes that provide the balanced pool of deoxynucleotides required for DNA synthesis and repair in many facultative and obligate anaerobic bacteria and archaea. Unlike the class I and II RNRs, where reducing equivalents for the reaction are delivered by a redoxin (thioredoxin, glutaredoxin, or NrdH) via a pair of conserved active site cysteines, the class III RNRs examined to date use formate as the reductant. Here, we report that reaction of the Escherichia coli class III RNR with CTP (substrate) and ATP (allosteric effector) in the absence of formate leads to loss of the G• concomitant with stoichiometric formation of a new radical species and a "trapped" cytidine derivative that can break down to cytosine. Addition of formate to the new species results in recovery of 80% of the G• and reduction of the cytidine derivative, proposed to be 3'-keto-deoxycytidine, to dCTP and a small amount of cytosine. The structure of the new radical has been identified by 9.5 and 140 GHz EPR spectroscopy on isotopically labeled varieties of the protein to be a thiosulfuranyl radical [RSSR2]•, composed of a cysteine thiyl radical stabilized by an interaction with a methionine residue. The presence of a stable radical species on the reaction pathway rationalizes the previously reported [(3)H]-(k(cat)/K(M)) isotope effect of 2.3 with [(3)H]-formate, requiring formate to exchange between the active site and solution during nucleotide reduction. Analogies with the disulfide anion radical proposed to provide the reducing equivalent to the 3'-keto-deoxycytidine intermediate by the class I and II RNRs provide further evidence for the involvement of thiyl radicals in the reductive half-reaction catalyzed by all RNRs.
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Affiliation(s)
- Yifeng Wei
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Guinevere Mathies
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Kenichi Yokoyama
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Jiahao Chen
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Robert
G. Griffin
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - JoAnne Stubbe
- Departments of Chemistry and Biology and Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
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14
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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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15
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Shisler KA, Broderick JB. Glycyl radical activating enzymes: structure, mechanism, and substrate interactions. Arch Biochem Biophys 2014; 546:64-71. [PMID: 24486374 PMCID: PMC4083501 DOI: 10.1016/j.abb.2014.01.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/20/2022]
Abstract
The glycyl radical enzyme activating enzymes (GRE-AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe-4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE-AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE-AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE-AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States.
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16
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Feliks M, Martins BM, Ullmann GM. Catalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations. J Am Chem Soc 2013; 135:14574-85. [DOI: 10.1021/ja402379q] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikolaj Feliks
- Computational
Biochemistry, University of Bayreuth, Universitätsstrasse 30,
BGI, 95447 Bayreuth, Germany
| | - Berta M. Martins
- Structural Biology/Biochemistry
− Radical Enzymes, Humboldt-Universität zu Berlin, Unter den
Linden 6, 10099 Berlin, Germany
| | - G. Matthias Ullmann
- Computational
Biochemistry, University of Bayreuth, Universitätsstrasse 30,
BGI, 95447 Bayreuth, Germany
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17
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Bharadwaj VS, Dean AM, Maupin CM. Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study. J Am Chem Soc 2013; 135:12279-88. [DOI: 10.1021/ja404842r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vivek S. Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - Anthony M. Dean
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
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18
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Selvaraj B, Pierik AJ, Bill E, Martins BM. 4-Hydroxyphenylacetate decarboxylase activating enzyme catalyses a classical S-adenosylmethionine reductive cleavage reaction. J Biol Inorg Chem 2013; 18:633-43. [DOI: 10.1007/s00775-013-1008-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
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19
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The catalytic mechanism for aerobic formation of methane by bacteria. Nature 2013; 497:132-6. [DOI: 10.1038/nature12061] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/08/2013] [Indexed: 11/08/2022]
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20
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Lanz ND, Booker SJ. Identification and function of auxiliary iron-sulfur clusters in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1196-212. [PMID: 22846545 DOI: 10.1016/j.bbapap.2012.07.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Radical SAM (RS) enzymes use a 5'-deoxyadenosyl 5'-radical generated from a reductive cleavage of S-adenosyl-l-methionine to catalyze over 40 distinct reaction types. A distinguishing feature of these enzymes is a [4Fe-4S] cluster to which each of three iron ions is ligated by three cysteinyl residues most often located in a Cx(3)Cx(2)C motif. The α-amino and α-carboxylate groups of SAM anchor the molecule to the remaining iron ion, which presumably facilitates its reductive cleavage. A subset of RS enzymes contains additional iron-sulfur clusters, - which we term auxiliary clusters - most of which have unidentified functions. Enzymes in this subset are involved in cofactor biosynthesis and maturation, post-transcriptional and post-translational modification, enzyme activation, and antibiotic biosynthesis. The additional clusters in these enzymes have been proposed to function in sulfur donation, electron transfer, and substrate anchoring. This review will highlight evidence supporting the presence of multiple iron-sulfur clusters in these enzymes as well as their predicted roles in catalysis. This article is part of a special issue entitled: Radical SAM enzymes and radical enzymology.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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21
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Feliks M, Ullmann GM. Glycerol Dehydratation by the B12-Independent Enzyme May Not Involve the Migration of a Hydroxyl Group: A Computational Study. J Phys Chem B 2012; 116:7076-87. [DOI: 10.1021/jp301165b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikolaj Feliks
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
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22
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Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T. Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme. J Am Chem Soc 2011; 133:14666-74. [DOI: 10.1021/ja203344x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Berta M. Martins
- Institute für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Martin Blaser
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Mikolaj Feliks
- Structural Biology/Bioinformatics, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Thorsten Selmer
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- AG Biotechnologie/Enzymtechnologie, Fachhochschule Aachen-Jülich, D-52428 Jülich, Germany
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23
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Hioe J, Savasci G, Brand H, Zipse H. The stability of Cα peptide radicals: why glycyl radical enzymes? Chemistry 2011; 17:3781-9. [PMID: 21341321 DOI: 10.1002/chem.201002620] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 11/06/2022]
Abstract
The conformational space of dipeptide models derived from glycine, alanine, phenylalanine, proline, tyrosine, and cysteine has been searched extensively and compared with the corresponding C(α) dipeptide radicals at the G3(MP2)-RAD level of theory. The results indicate that the (least-substituted) glycine dipeptide radical is the thermochemically most stable of these species. Analysis of the structural parameters indicates that this is due to repulsive interactions between the C(α) substituents and peptide units in the radical. A comparison of the conformational preferences of dipeptide radicals and their closed-shell parents also indicates that radical stability is a strongly conformation-dependent property.
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Affiliation(s)
- Johnny Hioe
- Department of Chemistry, LMU München, Butenandtstrasse 5-13, 81377 München, Germany
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24
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Abouelatta AI, Campanali AA, Ekkati AR, Shamoun M, Kalapugama S, Kodanko JJ. Oxidation of the Natural Amino Acids by a Ferryl Complex: Kinetic and Mechanistic Studies with Peptide Model Compounds. Inorg Chem 2009; 48:7729-39. [DOI: 10.1021/ic900527c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ahmed I. Abouelatta
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
| | - Ashley A. Campanali
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
| | - Anil R. Ekkati
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
| | - Mark Shamoun
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
| | - Suneth Kalapugama
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
| | - Jeremy J. Kodanko
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202
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25
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Siu CK, Zhao J, Laskin J, Chu IK, Hopkinson AC, Siu KWM. Kinetics for tautomerizations and dissociations of triglycine radical cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:996-1005. [PMID: 19254850 DOI: 10.1016/j.jasms.2009.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 05/27/2023]
Abstract
Fragmentations of tautomers of the alpha-centered radical triglycine radical cation, [GGG(*)](+), [GG(*)G](+), and [G(*)GG](+), are charge-driven, giving b-type ions; these are processes that are facilitated by a mobile proton, as in the fragmentation of protonated triglycine (Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012). By contrast, radical centers are less mobile. Two mechanisms have been examined theoretically utilizing density functional theory and Rice-Ramsperger-Kassel-Marcus modeling: (1) a direct hydrogen-atom migration between two alpha-carbons, and (2) a two-step proton migration involving canonical [GGG](*+) as an intermediate. Predictions employing the latter mechanism are in good agreement with results of recent CID experiments (Chu, I. K. et al. J. Am. Chem. Soc. 2008, 130, 7862-7872).
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Affiliation(s)
- Chi-Kit Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
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26
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Fani R, Fondi M. Origin and evolution of metabolic pathways. Phys Life Rev 2009; 6:23-52. [PMID: 20416849 DOI: 10.1016/j.plrev.2008.12.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 11/27/2008] [Accepted: 12/01/2008] [Indexed: 10/21/2022]
Abstract
The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less-dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Among these gene elongations, gene and operon duplications undoubtedly played a major role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence giving rise to new genes coding for new metabolic abilities. Gene duplication has been invoked in the different schemes proposed to explain why and how the extant metabolic pathways have arisen and shaped. Both the analysis of completely sequenced genomes and directed evolution experiments strongly support one of them, i.e. the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis and nitrogen fixation, suggested that other different hypothesis, i.e. the retrograde hypothesis or the semi-enzymatic theory, may account for the arisal of some metabolic routes.
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Affiliation(s)
- Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Evolutionary Biology, Via Romana 17-19, University of Florence, Italy
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27
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Condic-Jurkic K, Zipse H, Smith DM. A compound QM/MM procedure: Comparative performance on a pyruvate formate-lyase model system. J Comput Chem 2009; 31:1024-35. [DOI: 10.1002/jcc.21389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Mamantov A. Possible New Reaction Mechanisms of Dideoxynucleosides as Anti-Aids Drugs. PROGRESS IN REACTION KINETICS AND MECHANISM 2008. [DOI: 10.3184/146867807x310783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Evidence is presented that a major class of drugs, the dideoxynucleosides (ddNs) and nucleoside/nucleotide analogues, may inhibit the symptoms of acquired immunodeficiency syndrome (AIDS) by initiation of inactivation at the ribonucleotide reductase (RNR) enzyme stage and/or inactivation of reverse transcriptase enzyme or at a stage more initial than that of the currently accepted DNA chain termination hypothesis. For example, it has been previously shown that ribonucleotide diphosphate reductase (RDPR) and ribonucleotide triphosphate reductase (RTPR) are inactivated with 2′-chloro-2 ‘-deoxyuridine 5′-diphosphate-([3′-3H]ClUDP) and triphosphate ([3′-3H]ClUTP) by reaction with an intermediate furanone, Scheme 2. RDPR has also been inactivated by 2‘-azido-2‘-deoxyuridine 5‘-diphosphate (N3UDP). Furthermore, addition of hydroxyurea to RNR can inhibit DNA synthesis which results in a rapid depletion of limiting deoxynucleotide triphosphate (dNTP) pools. There are similar perturbations of dNTP pools upon interaction of human RNR with 3‘-azido-2‘,3 ‘-dideoxythymidine (AZT), in human cell studies involving AZT/HIV and in adenosine/coformycin experiments in relation to inherited immunodeficiency, Table 1. Also, the herein proposed reduction mechanisms of nucleotides by RNR ( e.g., a single electron transfer from the nucleotide base to the phenol moiety of the tyrosyl radical of RNR via a pathway involving the thiyl radical of a cysteine residue) can also account for the chemistry of some antiretroviral drugs, the ddNs. Analyses are presented that the RNR reductions of regular unsubstituted nucleotides may occur predominantly via initial 2’ C-H abstraction instead of the originally proposed 3’ C-H abstraction mechanism. Also, it is noted that the fate of the phenol moiety of the tyrosyl unit in some RNR reactions with 2‘-halo-2‘-deoxynucleotides is not clear. The proposed reaction mechanisms may provide guidance for the development of potentially effective anti-AIDS drugs.
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Affiliation(s)
- Andrew Mamantov
- Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency, 1200 Pennsylvania Avenue, Washington, DC 20460, USA
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29
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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30
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Moran D, Jacob R, Wood G, Coote M, Davies M, O'Hair R, Easton C, Radom L. Rearrangements in Model Peptide-Type Radicalsvia Intramolecular Hydrogen-Atom Transfer. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690210] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
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32
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Abstract
Ribonucleotide reductases (RNRs) transform RNA building blocks to DNA building blocks by catalyzing the substitution of the 2'OH-group of a ribonucleotide with a hydrogen by a mechanism involving protein radicals. Three classes of RNRs employ different mechanisms for the generation of the protein radical. Recent structural studies of members from each class have led to a deeper understanding of their catalytic mechanism and allosteric regulation by nucleoside triphosphates. The main emphasis of this review is on regulation of RNR at the molecular and cellular level. Conformational transitions induced by nucleotide binding determine the regulation of substrate specificity. An intricate interplay between gene activation, enzyme inhibition, and protein degradation regulates, together with the allosteric effects, enzyme activity and provides the appropriate amount of deoxynucleotides for DNA replication and repair. In spite of large differences in the amino acid sequences, basic structural features are remarkably similar and suggest a common evolutionary origin for the three classes.
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Affiliation(s)
- Pär Nordlund
- Division of Biophysics and 2Division of Biochemistry, Medical Nobel Institute, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.
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33
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Uppsten M, Färnegårdh M, Domkin V, Uhlin U. The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action. J Mol Biol 2006; 359:365-77. [PMID: 16631785 DOI: 10.1016/j.jmb.2006.03.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 03/01/2006] [Accepted: 03/16/2006] [Indexed: 11/20/2022]
Abstract
Ribonucleotide reductase is an indispensable enzyme for all cells, since it catalyses the biosynthesis of the precursors necessary for both building and repairing DNA. The ribonucleotide reductase class I enzymes, present in all mammals as well as in many prokaryotes and DNA viruses, are composed mostly of two homodimeric proteins, R1 and R2. The reaction involves long-range radical transfer between the two proteins. Here, we present the first crystal structure of a ribonucleotide reductase R1/R2 holocomplex. The biological relevance of this complex is based on the binding of the R2 C terminus in the hydrophobic cleft of R1, an interaction proven to be crucial for enzyme activity, and by the fact that all conserved amino acid residues in R2 are facing the R1 active sites. We suggest that the asymmetric R1/R2 complex observed in the 4A crystal structure of Salmonella typhimurium ribonucleotide reductase represents an intermediate stage in the reaction cycle, and at the moment of reaction the homodimers transiently form a tight symmetric complex.
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Affiliation(s)
- Malin Uppsten
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Box 590, SE-751 24 Uppsala, Sweden
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34
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Selmer T, Pierik AJ, Heider J. New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria. Biol Chem 2005; 386:981-8. [PMID: 16218870 DOI: 10.1515/bc.2005.114] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
During the last decade, an increasing number of new enzymes containing glycyl radicals in their active sites have been identified and biochemically characterised. These include benzylsuccinate synthase (Bss), 4-hydroxyphenylacetate decarboxylase (Hpd) and the coenzyme B12-independent glycerol dehydratase (Gdh). These are involved in metabolic pathways as different as anaerobic toluene metabolism, fermentative production of p-cresol and glycerol fermentation. Some features of these newly discovered enzymes are described and compared with those of the previously known glycyl radical enzymes pyruvate formate-lyase (Pfl) and anaerobic ribonucleotide reductase (Nrd). Among the new enzymes, Bss and Hpd share the presence of small subunits, the function of which in the catalytic mechanisms is still enigmatic, and both enzymes contain metal centres in addition to the glycyl radical prosthetic group. The activating enzymes of the novel systems also deviate from the standard type, containing at least one additional Fe-S cluster. Finally, the available whole-genome sequences of an increasing number of strictly or facultative anaerobic bacteria revealed the presence of many more hitherto unknown glycyl radical enzyme (GRE) systems. Recent studies suggest that the particular types of these enzymes represent the ends of different evolutionary lines, which emerged early in evolution and diversified to yield remarkably versatile biocatalysts for chemical reactions that are otherwise difficult to perform in anoxic environments.
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Affiliation(s)
- Thorsten Selmer
- Laboratorium für Mikrobiologie, Philipps-Universität Marburg, D-35032 Marburg, Germany.
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35
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Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P. Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat Struct Mol Biol 2004; 11:1142-9. [PMID: 15475969 DOI: 10.1038/nsmb838] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Accepted: 08/13/2004] [Indexed: 11/08/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.
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Affiliation(s)
- Karl-Magnus Larsson
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
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36
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Hänzelmann P, Schindelin H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc Natl Acad Sci U S A 2004; 101:12870-5. [PMID: 15317939 PMCID: PMC516487 DOI: 10.1073/pnas.0404624101] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Indexed: 11/18/2022] Open
Abstract
The MoaA and MoaC proteins catalyze the first step during molybdenum cofactor biosynthesis, the conversion of a guanosine derivative to precursor Z. MoaA belongs to the S-adenosylmethionine (SAM)-dependent radical enzyme superfamily, members of which catalyze the formation of protein and/or substrate radicals by reductive cleavage of SAM by a [4Fe-4S] cluster. A defined in vitro system is described, which generates precursor Z and led to the identification of 5'-GTP as the substrate. The structures of MoaA in the apo-state (2.8 angstroms) and in complex with SAM (2.2 angstroms) provide valuable insights into its mechanism and help to define the defects caused by mutations in the human ortholog of MoaA that lead to molybdenum cofactor deficiency, a usually fatal disease accompanied by severe neurological symptoms. The central core of each subunit of the MoaA dimer is an incomplete triosephosphate isomerase barrel formed by the N-terminal part of the protein, which contains the [4Fe-4S] cluster typical for SAM-dependent radical enzymes. SAM is the fourth ligand to the cluster and binds to its unique Fe as an N/O chelate. The lateral opening of the incomplete triosephosphate isomerase barrel is covered by the C-terminal part of the protein containing an additional [4Fe-4S] cluster, which is unique to MoaA proteins. Both FeS clusters are separated by approximately 17 angstroms, with a large active site pocket between. The noncysteinyl-ligated unique Fe site of the C-terminal [4Fe-4S] cluster is proposed to be involved in the binding and activation of 5'-GTP.
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Affiliation(s)
- Petra Hänzelmann
- Department of Biochemistry, Center for Structural Biology, State University of New York, Stony Brook, NY 11794-5115, USA
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37
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Affiliation(s)
- Jing-Dong Guo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, ALBANOVA, SE−106 91 Stockholm, Sweden
| | - Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, ALBANOVA, SE−106 91 Stockholm, Sweden
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38
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Chang CJ, Chang MCY, Damrauer NH, Nocera DG. Proton-coupled electron transfer: a unifying mechanism for biological charge transport, amino acid radical initiation and propagation, and bond making/breaking reactions of water and oxygen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:13-28. [PMID: 15100012 DOI: 10.1016/j.bbabio.2003.08.010] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Accepted: 08/08/2003] [Indexed: 10/26/2022]
Abstract
Redox-driven proton pumps, radical initiation and propagation in biology, and small-molecule activation processes all involve the coupling of electron transfer to proton transport. A mechanistic framework in which to interpret these processes is being developed by examining proton-coupled electron transfer (PCET) in model and natural systems. Specifically, PCET investigations are underway on the following three fronts: (1) the elucidation of the PCET reaction mechanism by time-resolved laser spectroscopy of electron donors and acceptors juxtaposed by a proton transfer interface; (2) the role of amino acid radicals in biological catalysis with the radical initiation and transport processes of E. coli ribonucleotide reductase (RNR) as a focal point; and (3) the application of PCET towards small-molecule activation with emphasis on biologically relevant bond-breaking and bond-making processes involving oxygen and water. A review of recent developments in each of these areas is discussed.
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Affiliation(s)
- Christopher J Chang
- Department of Chemistry, 6-335, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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39
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Cho KB, Pelmenschikov V, Gräslund A, Siegbahn PEM. Density Functional Calculations on Class III Ribonucleotide Reductase: Substrate Reaction Mechanism with Two Formates. J Phys Chem B 2004. [DOI: 10.1021/jp035280u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyung-Bin Cho
- Department of Biochemistry and Biophysics, and Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Vladimir Pelmenschikov
- Department of Biochemistry and Biophysics, and Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, and Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Biochemistry and Biophysics, and Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden
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40
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Uppsten M, Färnegårdh M, Jordan A, Eliasson R, Eklund H, Uhlin U. Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors. J Mol Biol 2003; 330:87-97. [PMID: 12818204 DOI: 10.1016/s0022-2836(03)00538-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The three-dimensional structure of the large subunit of the first member of a class Ib ribonucleotide reductase, R1E of Salmonella typhimurium, has been determined in its native form and together with three allosteric effectors. The enzyme contains the characteristic ten-stranded alpha/beta-barrel with catalytic residues at a finger loop in its center and with redox-active cysteine residues at two adjacent barrel strands. Structures where the redox-active cysteine residues are in reduced thiol form and in oxidized disulfide form have been determined revealing local structural changes. The R1E enzyme differs from the class Ia enzyme, Escherichia coli R1, by not having an overall allosteric regulation. This is explained from the structure by differences in the N-terminal domain, which is about 50 residues shorter and lacks the overall allosteric binding site. R1E has an allosteric substrate specificity regulation site and the binding site for the nucleotide effectors is located at the dimer interface similarly as for the class Ia enzymes. We have determined the structures of R1E in the absence of effectors and with dTTP, dATP and dCTP bound. The low affinity for ATP at the specificity site is explained by a tyrosine, which hinders nucleotides containing a 2'-OH group to bind.
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Affiliation(s)
- Malin Uppsten
- Department of Molecular Biosciences section of Structure Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, Sweden
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41
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Affiliation(s)
- Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden
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42
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Abstract
The evolution of enzymes and pathways is under debate. Recent studies show that recruitment of single enzymes from different pathways could be the driving force for pathway evolution. Other mechanisms of evolution, such as pathway duplication, enzyme specialization, de novo invention of pathways or retro-evolution of pathways, appear to be less abundant. Twenty percent of enzyme superfamilies are quite variable, not only in changing reaction chemistry or metabolite type but in changing both at the same time. These variable superfamilies account for nearly half of all known reactions. The most frequently occurring metabolites provide a helping hand for such changes because they can be accommodated by many enzyme superfamilies. Thus, a picture is emerging in which new pathways are evolving from central metabolites by preference, thereby keeping the overall topology of the metabolic network.
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Affiliation(s)
- Steffen Schmidt
- European Molecular Biology Laboratory Heidelberg, Postfach 102209, Germany
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Stubbe J, Nocera DG, Yee CS, Chang MCY. Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer? Chem Rev 2003; 103:2167-201. [PMID: 12797828 DOI: 10.1021/cr020421u] [Citation(s) in RCA: 666] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA.
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44
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Croft AK, Easton CJ, Radom L. Design of radical-resistant amino acid residues: a combined theoretical and experimental investigation. J Am Chem Soc 2003; 125:4119-24. [PMID: 12670233 DOI: 10.1021/ja029674v] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ab initio calculations have been used to design radical-resistant amino acid residues. Optimized structures of free and protected amino acids and their corresponding alpha-carbon-centered radicals were determined with B3-LYP/6-31G(d). Single-point RMP2/6-31G(d) calculations on these structures were then used to obtain radical stabilization energies, to examine the effect of steric repulsion between the side chains and amide carbonyl groups on the stability of alpha-carbon-centered peptide radicals. Relative to glycine, the destabilization for alanine and valine residues was found to be approximately 9 and 18 kJ mol(-1), respectively, which correlates with the reactivity of analogous amino acid residues in peptides toward hydrogen atom abstraction in conventional free radical reactions. To design amino acid residues that would resist radical reactions, strategies by which the steric effects could be magnified were considered. This resulted in the identification of tert-leucine and 3,3,3-trifluoroalanine as suitable molecules. With these amino acid residues, the destabilization of the alpha-carbon-centered radicals relative to that of glycine is increased substantially to approximately 36 and 41 kJ mol(-1), respectively. The theoretical predictions have been supported by experimental observations: a tert-leucine derivative was shown to be very slow to react with N-bromosuccinimide, while the corresponding trifluoroalanine derivative was found to be inert.
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Affiliation(s)
- Anna K Croft
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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45
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Duboc-Toia C, Hassan AK, Mulliez E, Ollagnier-de Choudens S, Fontecave M, Leutwein C, Heider J. Very high-field EPR study of glycyl radical enzymes. J Am Chem Soc 2003; 125:38-9. [PMID: 12515500 DOI: 10.1021/ja026690j] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work shows that very high-field EPR spectroscopy allows a rather accurate determination of the g-tensor of protein radicals, including C-centered ones, and thus may be used as a probe for distinguishing a tyrosyl-, a glycyl-, or a tryptophanyl-radical. In this paper, we report the first complete analysis of the g-tensor of glycyl radical enzymes (anaerobic ribonucleotide reductase, pyruvate formate lyase, and benzylsuccinate synthase), thus providing new information on their EPR properties. Because the g-anisotropy is small, the complete resolution of the g-tensor could be only obtained at very high field (18.8 T).
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Affiliation(s)
- Carole Duboc-Toia
- High Magnetic Field Laboratory of Grenoble, CNRS-MPI, 25 av. des Martyrs, 38042 Grenoble, France.
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46
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Becker A, Kabsch W. X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage. J Biol Chem 2002; 277:40036-42. [PMID: 12163496 DOI: 10.1074/jbc.m205821200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The glycyl radical enzyme pyruvate formate-lyase (PFL) synthesizes acetyl-CoA and formate from pyruvate and CoA. With the crystal structure of the non-radical form of PFL in complex with its two substrates, we have trapped the moment prior to pyruvate cleavage. The structure reveals how the active site aligns the scissile bond of pyruvate for radical attack, prevents non-radical side reactions of the pyruvate, and confines radical migration. The structure shows CoA in a syn conformation awaiting pyruvate cleavage. By changing to an anti conformation, without affecting the adenine binding mode of CoA, the thiol of CoA could pick up the acetyl group resulting from pyruvate cleavage.
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Affiliation(s)
- Andreas Becker
- Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany
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47
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Fontecave M, Mulliez E, Logan DT. Deoxyribonucleotide synthesis in anaerobic microorganisms: the class III ribonucleotide reductase. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2002; 72:95-127. [PMID: 12206460 DOI: 10.1016/s0079-6603(02)72068-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
For growth under oxygen-free atmosphere, some strict or facultative anaerobes depend on a class III ribonucleotide reductase for the synthesis of deoxyribonucleotides, the DNA precursors. Prototypes for this class of enzymes are ribonucleotide reductases from Escherichia coli and bacteriophage T4. This review article describes their structural and mechanistic properties as well as their complex allosteric regulation. Their evolutionnary relationship to class I and class II ribonucleotide reductases is also discussed.
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Affiliation(s)
- Marc Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, UMR CNRS/CEA/Université Joseph DRDC-CB, CEA Grenoble, France
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48
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Affiliation(s)
- Britt-Marie Sjöberg
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
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49
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Affiliation(s)
- Fahmi Himo
- Department of Molecular Biology, 10550 N. Torrey Pines Rd, TPC-15, The Scripps Research Institute, La Jolla, California 92037
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50
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Gerlt JA, Babbitt PC. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 2002; 70:209-46. [PMID: 11395407 DOI: 10.1146/annurev.biochem.70.1.209] [Citation(s) in RCA: 394] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The protein sequence and structure databases are now sufficiently representative that strategies nature uses to evolve new catalytic functions can be identified. Groups of divergently related enzymes whose members catalyze different reactions but share a common partial reaction, intermediate, or transition state (mechanistically diverse superfamilies) have been discovered, including the enolase, amidohydrolase, thiyl radical, crotonase, vicinal-oxygen-chelate, and Fe-dependent oxidase superfamilies. Other groups of divergently related enzymes whose members catalyze different overall reactions that do not share a common mechanistic strategy (functionally distinct suprafamilies) have also been identified: (a) functionally distinct suprafamilies whose members catalyze successive transformations in the tryptophan and histidine biosynthetic pathways and (b) functionally distinct suprafamilies whose members catalyze different reactions in different metabolic pathways. An understanding of the structural bases for the catalytic diversity observed in super- and suprafamilies may provide the basis for discovering the functions of proteins and enzymes in new genomes as well as provide guidance for in vitro evolution/engineering of new enzymes.
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Affiliation(s)
- J A Gerlt
- Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, USA.
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