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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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2
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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3
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When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nat Rev Microbiol 2021; 19:774-785. [PMID: 34183820 PMCID: PMC9191689 DOI: 10.1038/s41579-021-00583-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
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4
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Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 PMCID: PMC8683613 DOI: 10.1016/j.jbc.2021.101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
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5
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Calvey GD, Katz AM, Zielinski KA, Dzikovski B, Pollack L. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers. Anal Chem 2020; 92:13864-13870. [PMID: 32955854 PMCID: PMC8367009 DOI: 10.1021/acs.analchem.0c02569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mix-and-inject serial crystallography is an emerging technique that utilizes X-ray free-electron lasers (XFELs) and microcrystalline samples to capture atomically detailed snapshots of biomolecules as they function. Early experiments have yielded exciting results; however, there are limited options to characterize reactions in crystallo in advance of the beamtime. Complementary measurements are needed to identify the best conditions and timescales for observing structural intermediates. Here, we describe the interface of XFEL compatible mixing injectors with rapid freeze-quenching and X-band EPR spectroscopy, permitting characterization of reactions in crystals under the same conditions as an XFEL experiment. We demonstrate this technology by tracking the reaction of azide with microcrystalline myoglobin, using only a fraction of the sample required for a mix-and-inject experiment. This spectroscopic method enables optimization of sample and mixer conditions to maximize the populations of intermediate states, eliminating the guesswork of current mix-and-inject experiments.
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Affiliation(s)
- George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Kara A Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
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6
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Khademian M, Imlay JA. Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Mol Microbiol 2020; 114:333-347. [PMID: 32301184 DOI: 10.1111/mmi.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Bacteroides thetaiotaomicron was examined to determine whether its obligate anaerobiosis is imposed by endogenous reactive oxygen species or by molecular oxygen itself. Previous analyses established that aerated B. thetaiotaomicron loses some enzyme activities due to a high rate of endogenous superoxide formation. However, the present study establishes that another key step in central metabolism is poisoned by molecular oxygen itself. Pyruvate dissimilation was shown to depend upon two enzymes, pyruvate:formate lyase (PFL) and pyruvate:ferredoxin oxidoreductase (PFOR), that lose activity upon aeration. PFL is a glycyl-radical enzyme whose vulnerability to oxygen is already understood. The rate of PFOR damage was unaffected by the level of superoxide or peroxide, showing that molecular oxygen itself is the culprit. The cell cannot repair PFOR, which amplifies the impact of damage. The rates of PFOR and fumarase inactivation are similar, suggesting that superoxide dismutase is calibrated so the oxygen- and superoxide-sensitive enzymes are equally sensitive to aeration. The physiological purpose of PFL and PFOR is to degrade pyruvate without disrupting the redox balance, and they do so using catalytic mechanisms that are intrinsically vulnerable to oxygen. In this way, the anaerobic excellence and oxygen sensitivity of B. thetaiotaomicron are two sides of the same coin.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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7
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Hanževački M, Banhatti RD, Čondić-Jurkić K, Smith AS, Smith DM. Exploring Reactive Conformations of Coenzyme A during Binding and Unbinding to Pyruvate Formate-Lyase. J Phys Chem A 2019; 123:9345-9356. [PMID: 31580071 DOI: 10.1021/acs.jpca.9b06913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme that converts pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. Recently, we showed that the acetylation of the PFL active site in the first half-reaction induces subtle conformational changes, leading to the opening of a potential channel for CoA entry. Entry of CoA into the active site is crucial for the second half-reaction, involving the acetyl transfer to CoA, and the completion of the catalytic cycle. Using steered molecular dynamics (SMD) simulations, performed on acetylated and nonacetylated monomeric PFL model systems, we first of all investigate the possible entry/exit pathways of CoA with respect to the active site through the previously identified channel. We then perform umbrella sampling simulations on multiple snapshots from SMD trajectories as well as unrestrained molecular dynamics simulations starting from the final structures obtained from entry SMD, with a view to identifying possible bound states of CoA in the near vicinity of the active site. Detailed study of the unrestrained dissociation processes reveals the presence of stable and reactive bound states of CoA close to the active site, one of which is in an ideal position for triggering the second half-reaction. Examination of the spatial distributions associated with the reactive bound states allows us to discuss the free energy barriers. Umbrella sampling, performed on snapshots from unrestrained dynamics confirms the above findings. The significance of the results for the catalysis are discussed for both acetylated and nonacetylated systems.
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Affiliation(s)
- Marko Hanževački
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - Radha Dilip Banhatti
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Karmen Čondić-Jurkić
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia.,PULS Group, Department of Physics, Interdisciplinary Center for Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg , Cauerstraße 3 , 91058 Erlangen , Germany
| | - David M Smith
- Group for Computational Life Sciences, Division for Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
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8
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Imlay JA, Sethu R, Rohaun SK. Evolutionary adaptations that enable enzymes to tolerate oxidative stress. Free Radic Biol Med 2019; 140:4-13. [PMID: 30735836 PMCID: PMC6684875 DOI: 10.1016/j.freeradbiomed.2019.01.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Biochemical mechanisms emerged and were integrated into the metabolic plan of cellular life long before molecular oxygen accumulated in the biosphere. When oxygen levels finaly rose, they threatened specific types of enzymes: those that use organic radicals as catalysts, and those that depend upon iron centers. Nature has found ways to ensure that such enzymes are still used by contemporary organisms. In some cases they are restricted to microbes that reside in anoxic habitats, but in others they manage to function inside aerobic cells. In the latter case, it is frequently true that the ancestral enzyme has been modified to fend off poisoning. In this review we survey a range of protein adaptations that permit radical-based and low-potential iron chemistry to succeed in oxic environments. In many cases, accessory domains shield the vulnerable radical or metal center from oxygen. In others, the structures of iron cofactors evolved to less oxidizable forms, or alternative metals replaced iron altogether. The overarching view is that some classes of biochemical mechanism are intrinsically incompatible with the presence of oxygen. The structural modification of target enzymes is an under-recognized response to this problem.
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Affiliation(s)
- James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA.
| | - Ramakrishnan Sethu
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Sanjay Kumar Rohaun
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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9
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Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
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Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
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10
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Cousin FJ, Lynch DB, Chuat V, Bourin MJB, Casey PG, Dalmasso M, Harris HMB, McCann A, O'Toole PW. A long and abundant non-coding RNA in Lactobacillus salivarius. Microb Genom 2017; 3:e000126. [PMID: 29114404 PMCID: PMC5643018 DOI: 10.1099/mgen.0.000126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/21/2017] [Indexed: 01/12/2023] Open
Abstract
Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq)transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.
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Affiliation(s)
- Fabien J Cousin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Denise B Lynch
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Victoria Chuat
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maxence J B Bourin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Pat G Casey
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hugh M B Harris
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Angela McCann
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- 2APC Microbiome Institute, University College Cork, Cork, Ireland.,1School of Microbiology, University College Cork, Cork, Ireland
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11
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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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12
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Rajakovich LJ, Nørgaard H, Warui DM, Chang WC, Li N, Booker SJ, Krebs C, Bollinger JM, Pandelia ME. Rapid Reduction of the Diferric-Peroxyhemiacetal Intermediate in Aldehyde-Deformylating Oxygenase by a Cyanobacterial Ferredoxin: Evidence for a Free-Radical Mechanism. J Am Chem Soc 2015; 137:11695-709. [PMID: 26284355 DOI: 10.1021/jacs.5b06345] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aldehyde-deformylating oxygenase (ADO) is a ferritin-like nonheme-diiron enzyme that catalyzes the last step in a pathway through which fatty acids are converted into hydrocarbons in cyanobacteria. ADO catalyzes conversion of a fatty aldehyde to the corresponding alk(a/e)ne and formate, consuming four electrons and one molecule of O2 per turnover and incorporating one atom from O2 into the formate coproduct. The source of the reducing equivalents in vivo has not been definitively established, but a cyanobacterial [2Fe-2S] ferredoxin (PetF), reduced by ferredoxin-NADP(+) reductase (FNR) using NADPH, has been implicated. We show that both the diferric form of Nostoc punctiforme ADO and its (putative) diferric-peroxyhemiacetal intermediate are reduced much more rapidly by Synechocystis sp. PCC6803 PetF than by the previously employed chemical reductant, 1-methoxy-5-methylphenazinium methyl sulfate. The yield of formate and alkane per reduced PetF approaches its theoretical upper limit when reduction of the intermediate is carried out in the presence of FNR. Reduction of the intermediate by either system leads to accumulation of a substrate-derived peroxyl radical as a result of off-pathway trapping of the C2-alkyl radical intermediate by excess O2, which consequently diminishes the yield of the hydrocarbon product. A sulfinyl radical located on residue Cys71 also accumulates with short-chain aldehydes. The detection of these radicals under turnover conditions provides the most direct evidence to date for a free-radical mechanism. Additionally, our results expose an inefficiency of the enzyme in processing its radical intermediate, presenting a target for optimization of bioprocesses exploiting this hydrocarbon-production pathway.
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Affiliation(s)
- Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Hanne Nørgaard
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Douglas M Warui
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wei-chen Chang
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Ning Li
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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13
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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14
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Zhang Y, Dai Z, Krivoruchko A, Chen Y, Siewers V, Nielsen J. Functional pyruvate formate lyase pathway expressed with two different electron donors in Saccharomyces cerevisiae at aerobic growth. FEMS Yeast Res 2015; 15:fov024. [DOI: 10.1093/femsyr/fov024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2015] [Indexed: 11/14/2022] Open
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15
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Tan L, Tureček F, Francisco JS, Xia Y. Probing the radical and base dual properties of peptide sulfinyl radicals via mass spectrometry. J Phys Chem A 2014; 118:11828-35. [PMID: 25428214 DOI: 10.1021/jp510362p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heteroatom-centered radicals are known to play critical roles in atmospheric chemistry, organic synthesis, and biology. While most studies have focused on the radical reactivity such as hydrogen abstraction, the base properties of heteroatom-centered radicals have long been overlooked, despite the profound consequences, such as their ability to participate in hydrogen-bonding networks. In this study, we use the sulfinyl radical (-SO(•)) as a model to show that the dual properties of heteroatom-centered radicals, that is, their ability to function as a radical and a base, can coexist in peptides and be differentiated by examining the loss of hydrosulfinyl radical (SOH) upon unimolecular dissociation of the peptide sulfinyl radical ions in the gas phase. The loss of SOH can result from two channels; one involves hydrogen atom abstraction, which reflects the radical property; the other is initiated by proton transfer to the sulfinyl radical, manifesting its base property. Tuning of the two properties of peptide sulfinyl radicals can be achieved by varying the chemical properties of the neighboring functional groups, which demonstrates the influence of the local chemical environment on the behavior of the radical species. The experimental approach established in this study to probe the dual chemical property of the peptide sulfinyl radical can be potentially applied to studying other types of heteroatom-centered radical species of biological significance.
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Affiliation(s)
- Lei Tan
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
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16
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Doi Y, Ikegami Y. Pyruvate formate-lyase is essential for fumarate-independent anaerobic glycerol utilization in the Enterococcus faecalis strain W11. J Bacteriol 2014; 196:2472-80. [PMID: 24769696 PMCID: PMC4054171 DOI: 10.1128/jb.01512-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/22/2014] [Indexed: 11/20/2022] Open
Abstract
Although anaerobic glycerol metabolism in Enterococcus faecalis requires exogenous fumarate for NADH oxidation, E. faecalis strain W11 can metabolize glycerol in the absence of oxygen without exogenous fumarate. In this study, metabolic end product analyses and reporter assays probing the expression of enzymes involved in pyruvate metabolism were performed to investigate this fumarate-independent anaerobic metabolism of glycerol in W11. Under aerobic conditions, the metabolic end products of W11 cultured with glycerol were similar to those of W11 cultured with glucose. However, when W11 was cultured anaerobically, most of the glucose was converted to l-lactate, but glycerol was converted to ethanol and formate. During anaerobic culture with glycerol, the expression of the l-lactate dehydrogenase and pyruvate dehydrogenase E1αβ genes in W11 was downregulated, whereas the expression of the pyruvate formate-lyase (Pfl) and aldehyde/alcohol dehydrogenase genes was upregulated. These changes in the expression levels caused the change in the composition of end products. A pflB gene disruptant (Δpfl mutant) of W11 could barely utilize glycerol under anaerobic conditions, but the growth of the Δpfl mutant cultured with either glucose or dihydroxyacetone (DHA) under anaerobic conditions was the same as that of W11. Glucose metabolism and DHA generates one NADH molecule per pyruvate molecule, whereas glycerol metabolism in the dehydrogenation pathway generates two NADH molecules per pyruvate molecule. These findings demonstrate that NADH generated from anaerobic glycerol metabolism in the absence of fumarate is oxidized through the Pfl-ethanol fermentation pathway. Thus, Pfl is essential to avoid the accumulation of excess NADH during fumarate-independent anaerobic glycerol metabolism.
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Affiliation(s)
- Yuki Doi
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science, Okayama, Okayama, Japan
| | - Yuki Ikegami
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Okayama University of Science, Okayama, Okayama, Japan
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17
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Stinson CA, Xia Y. Radical induced disulfide bond cleavage within peptides via ultraviolet irradiation of an electrospray plume. Analyst 2013; 138:2840-6. [DOI: 10.1039/c3an00303e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Tan L, Xia Y. Gas-phase peptide sulfinyl radical ions: formation and unimolecular dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2011-2019. [PMID: 22911098 DOI: 10.1007/s13361-012-0465-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
A variety of peptide sulfinyl radical (RSO•) ions with a well-defined radical site at the cysteine side chain were formed at atmospheric pressure (AP), sampled into a mass spectrometer, and investigated via collision-induced dissociation (CID). The radical ion formation was based on AP reactions between oxidative radicals and peptide ions containing single inter-chain disulfide bond or free thiol group generated from nanoelectrospray ionization (nanoESI). The radical induced reactions allowed large flexibility in forming peptide radical ions independent of ion polarity (protonated or deprotonated) or charge state (singly or multiply charged). More than 20 peptide sulfinyl radical ions in either positive or negative ion mode were subjected to low energy collisional activation on a triple-quadrupole/linear ion trap mass spectrometer. The competition between radical- and charge-directed fragmentation pathways was largely affected by the presence of mobile protons. For peptide sulfinyl radical ions with reduced proton mobility (i.e., singly protonated, containing basic amino acid residues), loss of 62 Da (CH(2)SO), a radical-initiated dissociation channel, was dominant. For systems with mobile protons, this channel was suppressed, while charge-directed amide bond cleavages were preferred. The polarity of charge was found to significantly alter the radical-initiated dissociation channels, which might be related to the difference in stability of the product ions in different ion charge polarities.
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Affiliation(s)
- Lei Tan
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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19
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Zhu Y, Song J, Xu Z, Sun J, Zhang Y, Li Y, Ma Y. Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis. Biotechnol Bioeng 2012; 110:914-23. [DOI: 10.1002/bit.24739] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/31/2012] [Accepted: 09/26/2012] [Indexed: 11/09/2022]
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20
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Engineering a synthetic dual-organism system for hydrogen production. Appl Environ Microbiol 2009; 75:1867-75. [PMID: 19201964 DOI: 10.1128/aem.02009-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular hydrogen produced biologically from renewable biomass is an attractive replacement for fossil fuels. One potential route for biological hydrogen production is the conversion of biomass into formate, which can subsequently be processed into hydrogen by Escherichia coli. Formate is also a widely used commodity chemical, making its bioproduction even more attractive. Here we demonstrate the implementation of a formate-overproducing pathway in Saccharomyces cerevisiae, a well-established industrial organism. By expressing the anaerobic enzyme pyruvate formate lyase from E. coli, we engineered a strain of yeast that overproduced formate relative to undetectable levels in the wild type. The addition of a downstream enzyme, AdhE of E. coli, resulted in an additional 4.5-fold formate production increase as well as an increase in growth rate and biomass yield. Overall, an 18-fold formate increase was achieved in a strain background whose formate degradation pathway had been deleted. Finally, as a proof of concept, we were able to produce hydrogen from this formate-containing medium by using E. coli as a catalyst in a two-step process. With further optimizations, it may be feasible to use S. cerevisiae on a larger scale as the foundation for yeast-based biohydrogen.
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21
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Zhu J, Shalel-Levanon S, Bennett G, San KY. The YfiD protein contributes to the pyruvate formate-lyase flux in an Escherichia coli arcA mutant strain. Biotechnol Bioeng 2007; 97:138-43. [PMID: 17013945 DOI: 10.1002/bit.21219] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The product of yfiD gene is similar to pyruvate formate-lyase (PFL) activase and it has been reported to activate PFL by replacing the glycyl radical domain. To quantitate the effect of YfiD on the cell metabolism in microaerobic cultures, glucose-limited chemostat cultures were conducted with Escherichia coli yfiD mutant and yfiDarcA mutant strains. The microaerobic condition was controlled by purging the culture media with 2.5% O(2) in N(2). The intracellular metabolic flux distributions in these cultures were estimated based on C-13 labeling experiments. By comparing with the flux distributions in wild-type E. coli and the arcA mutant, it was shown that YfiD contributes to about 18% of the PFL flux in the arcA mutant, but it did not contribute to the PFL flux in wild-type E. coli. It was also shown that the cell used both PFL and pyruvate dehydrogenase (PDH) to supplement the acetyl-coenzyme A (AcCoA) pool under microaerobic conditions. The flux through PDH was about 22-30% of the total flux toward AcCoA in the wild-type, the yfiD mutant and yfiDarcA mutant strains. Relatively higher lactate production was seen in the yfiDarcA mutant than the other strains, which was due to the lower total flux through PFL and PDH toward AcCoA in this strain.
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Affiliation(s)
- Jiangfeng Zhu
- Department of Bioengineering, Rice University, Houston, Texas, USA
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22
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Atteia A, van Lis R, Gelius-Dietrich G, Adrait A, Garin J, Joyard J, Rolland N, Martin W. Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria. J Biol Chem 2006; 281:9909-18. [PMID: 16452484 DOI: 10.1074/jbc.m507862200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyruvate formate-lyase (PFL) catalyzes the non-oxidative conversion of pyruvate to formate and acetyl-CoA. PFL and its activating enzyme (PFL-AE) are common among strict anaerobic and microaerophilic prokaryotes but are very rare among eukaryotes. In a proteome survey of isolated Chlamydomonas reinhardtii mitochondria, we found several PFL-specific peptides leading to the identification of cDNAs for PFL and PFL-AE, establishing the existence of a PFL system in this photosynthetic algae. Anaerobiosis and darkness led to increased PFL transcripts but had little effect on protein levels, as determined with antiserum raised against C. reinhardtii PFL. Protein blots revealed the occurrence of PFL in both chloroplast and mitochondria purified from aerobically grown cells. Mass spectrometry sequencing of C. reinhardtii mitochondrial proteins, furthermore, identified peptides for phosphotransacetylase and acetate kinase. The phosphotransacetylase-acetate kinase pathway is a common route of ATP synthesis or acetate assimilation among prokaryotes but is novel among eukaryotes. In addition to PFL and pyruvate dehydrogenase, the algae also expresses pyruvate:ferredoxin oxidoreductase and bifunctional aldehyde/alcohol dehydrogenase. Among eukaryotes, the oxygen producer C. reinhardtii has the broadest repertoire of pyruvate-, ethanol-, and acetate-metabolizing enzymes described to date, many of which were previously viewed as specific to anaerobic eukaryotic lineages.
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Affiliation(s)
- Ariane Atteia
- Institute of Botany, University of Düsseldorf, 40225 Düsseldorf, Germany.
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Cherepanov AV, De Vries S. Microsecond freeze-hyperquenching: development of a new ultrafast micro-mixing and sampling technology and application to enzyme catalysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1656:1-31. [PMID: 15136155 DOI: 10.1016/j.bbabio.2004.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 02/17/2004] [Accepted: 02/17/2004] [Indexed: 11/21/2022]
Abstract
A novel freeze-quench instrument with a characteristic <<dead-time>> of 137 +/- 18 micros is reported. The prototype has several key features that distinguish it from conventional freeze-quench devices and provide a significant improvement in time resolution: (a) high operating pressures (up to 400 bar) result in a sample flow with high linear rates (up to 200 m s(-1)); (b) tangential micro-mixer with an operating volume of approximately 1 nl yields short mixing times (up to 20 micros); (c) fast transport between the mixer and the cryomedium results in short reaction times: the ageing solution exits the mixer as a free-flowing jet, and the chemical reaction occurs "in-flight" on the way to the cryomedium; (d) a small jet diameter (approximately 20 microm) and a high jet velocity (approximately 200 m s(-1)) provide high sample-cooling rates, resulting in a short cryofixation time (up to 30 micros). The dynamic range of the freeze-quench device is between 130 micros and 15 ms. The novel tangential micro-mixer efficiently mixes viscous aqueous solutions, showing more than 95% mixing at eta < or = 4 (equivalent to protein concentrations up to 250 mg ml(-1)), which makes it an excellent tool for the preparation of pre-steady state samples of concentrated protein solutions for spectroscopic structure analysis. The novel freeze-quench device is characterized using the reaction of binding of azide to metmyoglobin from horse heart. Reaction samples are analyzed using 77 K optical absorbance spectroscopy, and X-band EPR spectroscopy. A simple procedure of spectral analysis is reported that allows (a) to perform a quantitative analysis of the reaction kinetics and (b) to identify and characterize novel reaction intermediates. The reduction of dioxygen by the bo3-type quinol oxidase from Escherichia coli is assayed using the MHQ technique. In these pilot experiments, low-temperature optical absorbance measurements show the rapid oxidation of heme o3 in the first 137 micros of the reaction, accompanied by the formation of an oxo-ferryl species. X-band EPR spectroscopy shows that a short-living radical intermediate is formed during the oxidation of heme o3. The radical decays within approximately 1 ms concomitant with the oxidation of heme b, and can be attributed to the PM reaction intermediate converting to the oxoferryl intermediate F. The general field of application of the freeze-quench methodology is discussed.
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Affiliation(s)
- Alexey V Cherepanov
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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24
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Kumagai J, Masui K, Itagaki Y, Shiotani M, Kodama S, Watanabe M, Miyazaki T. Long-lived mutagenic radicals induced in mammalian cells by ionizing radiation are mainly localized to proteins. Radiat Res 2003; 160:95-102. [PMID: 12816528 DOI: 10.1667/rr3015] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have provided evidence that long-lived radicals, produced by ionizing radiation, are highly mutagenic and transforming in mammalian cells. Long-lived radicals are scavenged effectively by vitamin C or by epigallocatechin-3-O-gallate (EGCG). Long-lived radicals are not involved in lethality or in the induction of chromosome aberrations. We now report the results of experiments that define the relative amounts of long-lived radicals in DNA and proteins and identify the major protein radicals as sulfinyl radicals (R-CH2-S-O*). To make these assignments, yields of long-lived radicals in gamma-irradiated salmon sperm DNA and albumin were compared by ESR. ESR spectra of long-lived radicals produced in irradiated Syrian hamster embryo (SHE) cells were analyzed precisely and compared with ESR parameters obtained by density functional theory calculations. Long-lived radicals yields of 99.8% were produced in proteins. We also identified a new type of long-lived radical as H-added phenylalanine radicals. While our evidence does not rule out the possibility of important biological consequences of the low-level long-lived radicals created by radiation, it implicates radicals in proteins as playing a key role in genetic effects of ionizing radiation. We suggest that these novel radicals, wherever they reside, need to be considered in explanations of biological sequela of radiation.
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Affiliation(s)
- Jun Kumagai
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya 464-8603, Japan.
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25
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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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26
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Frey PA, Magnusson OT. S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin? Chem Rev 2003; 103:2129-48. [PMID: 12797826 DOI: 10.1021/cr020422m] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin--Madison, Madison, Wisconsin 53726, USA.
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27
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Chouchane S, Girotto S, Yu S, Magliozzo RS. Identification and characterization of tyrosyl radical formation in Mycobacterium tuberculosis catalase-peroxidase (KatG). J Biol Chem 2002; 277:42633-8. [PMID: 12205099 DOI: 10.1074/jbc.m207916200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic function of Mycobacterium tuberculosis catalase-peroxidase (KatG) and its role in activation of the anti-tuberculosis antibiotic isoniazid were investigated using rapid freeze-quench electron paramagnetic resonance (RFQ-EPR) experiments. The reaction of KatG with peroxyacetic acid was followed as a function of time using x-band EPR at 77 K. A doublet EPR signal appears within 6.4 ms after mixing and at time points through hundreds of milliseconds. Thereafter, a singlet signal develops and finally predominates after 1 s, with a total yield of radical approximately 0.5 spin/heme. Simulation of the spectra provided EPR parameters consistent with those for tyrosyl radicals. Changes in the hyperfine splitting and/or line width in spectra for l-3,3-[2H2]tyrosine-labeled, but not l-2,4,5,6,7-[2H5]tryptophan-labeled KatG confirmed this assignment. The initial rate of radical formation was unchanged using a 3-fold or 10-fold excess of peroxyacetic acid, consistent with a rate-determining step involving an intermediate. Although Compound I is likely to be the precursor of tyrosyl radical in KatG, neither its EPR signal nor its reduction to Compound II during formation of the radical(s) could be observed. The tyrosyl radical doublet signal was rapidly quenched by addition of isoniazid and benzoic hydrazide, but not by iproniazid, which binds poorly to KatG.
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Affiliation(s)
- Salem Chouchane
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, Brooklyn, New York 11210, USA
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28
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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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