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Lee C, Hwang Y, Kang HG, Lee SJ. Electron Transfer to Hydroxylase through Component Interactions in Soluble Methane Monooxygenase. J Microbiol Biotechnol 2022; 32:287-293. [PMID: 35131957 PMCID: PMC9628860 DOI: 10.4014/jmb.2201.01029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
The hydroxylation of methane (CH4) is crucial to the field of environmental microbiology, owing to the heat capacity of methane, which is much higher than that of carbon dioxide (CO2). Soluble methane monooxygenase (sMMO), a member of the bacterial multicomponent monooxygenase (BMM) superfamily, is essential for the hydroxylation of specific substrates, including hydroxylase (MMOH), regulatory component (MMOB), and reductase (MMOR). The diiron active site positioned in the MMOH α-subunit is reduced through the interaction of MMOR in the catalytic cycle. The electron transfer pathway, however, is not yet fully understood due to the absence of complex structures with reductases. A type II methanotroph, Methylosinus sporium 5, successfully expressed sMMO and hydroxylase, which were purified for the study of the mechanisms. Studies on the MMOH-MMOB interaction have demonstrated that Tyr76 and Trp78 induce hydrophobic interactions through π-π stacking. Structural analysis and sequencing of the ferredoxin domain in MMOR (MMOR-Fd) suggested that Tyr93 and Tyr95 could be key residues for electron transfer. Mutational studies of these residues have shown that the concentrations of flavin adenine dinucleotide (FAD) and iron ions are changed. The measurements of dissociation constants (Kds) between hydroxylase and mutated reductases confirmed that the binding affinities were not significantly changed, although the specific enzyme activities were significantly reduced by MMOR-Y93A. This result shows that Tyr93 could be a crucial residue for the electron transfer route at the interface between hydroxylase and reductase.
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Affiliation(s)
- Chaemin Lee
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Yunha Hwang
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hyun Goo Kang
- Department of Neurology, Research Institute of Clinical Medicine of Jeonbuk National University and Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea,Corresponding authors H.G. Kang Phone: +82-63-250-1590 Fax: +82-63-251-9363 E-mail:
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea,Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea,
S.J. Lee Phone: +82-63-270-3412 Fax: +82-63-270-3407 E-mail:
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2
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Lettau E, Zill D, Späth M, Lorent C, Singh P, Lauterbach L. Catalytic and spectroscopic properties of the halotolerant soluble methane monooxygenase reductase from Methylomonas methanica MC09. Chembiochem 2021; 23:e202100592. [PMID: 34905639 PMCID: PMC9305295 DOI: 10.1002/cbic.202100592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Indexed: 11/10/2022]
Abstract
The soluble methane monooxygenase receives electrons from NADH via its reductase MmoC for oxidation of methane, which is itself an attractive C1 building block for a future bioeconomy. Herein, we present biochemical and spectroscopic insights into the reductase from the marine methanotroph Methylomonas methanica MC09. The presence of a flavin adenine dinucleotide (FAD) and [2Fe2S] cluster as its prosthetic group were revealed by reconstitution experiments, iron determination and electron paramagnetic resonance spectroscopy. As a true halotolerant enzyme, MmoC still showed 50 % of its specific activity at 2 M NaCl. We show that MmoC produces only trace amounts of superoxide, but mainly hydrogen peroxide during uncoupled turnover reactions. The characterization of a highly active reductase is an important step for future biotechnological applications of a halotolerant sMMO.
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Affiliation(s)
- Elisabeth Lettau
- Rheinisch-Westfälische Technische Hochschule Aachen: Rheinisch-Westfalische Technische Hochschule Aachen, Institute of Applied Microbiology, GERMANY
| | - Domenic Zill
- Rheinisch Westfalische Technische Hochschule Aachen Fakultat fur Mathematik Informatik und Naturwissenschaften, Institute of Applied Microbiology, GERMANY
| | - Marta Späth
- Technische Universität Berlin: Technische Universitat Berlin, Institute of Chemistry, GERMANY
| | - Christian Lorent
- Technische Universität Berlin: Technische Universitat Berlin, Institute of Chemistry, GERMANY
| | - Praveen Singh
- Rheinisch-Westfälische Technische Hochschule Aachen: Rheinisch-Westfalische Technische Hochschule Aachen, Institute of Applied Microbiology, GERMANY
| | - Lars Lauterbach
- Technische Universitat Berlin, Chemistry, Strasse des 17. Juni 135, Max-Volmer-Laboratorium, Sekr. PC 14, 10623, Berlin, Germany, GERMANY
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3
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Abstract
Aerobic life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O2 activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O2 activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
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5
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Biocatalytic Oxidations of Substrates through Soluble Methane Monooxygenase from Methylosinus sporium 5. Catalysts 2018. [DOI: 10.3390/catal8120582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Methane, an important greenhouse gas, has a 20-fold higher heat capacity than carbon dioxide. Earlier, through advanced spectroscopy and structural studies, the mechanisms underlying the extremely stable C–H activation of soluble methane monooxygenase (sMMO) have been elucidated in Methylosinus trichosporium OB3b and Methylococcus capsulatus Bath. Here, sMMO components—including hydroxylase (MMOH), regulatory (MMOB), and reductase (MMOR)—were expressed and purified from a type II methanotroph, Methylosinus sporium strain 5 (M. sporium 5), to characterize its hydroxylation mechanism. Two molar equivalents of MMOB are necessary to achieve catalytic activities and oxidized a broad range of substrates including alkanes, alkenes, halogens, and aromatics. Optimal activities were observed at pH 7.5 for most substrates possibly because of the electron transfer environment in MMOR. Substitution of MMOB or MMOR from another type II methanotroph, Methylocystis species M, retained specific enzyme activities, demonstrating the successful cross-reactivity of M. sporium 5. These results will provide fundamental information for further enzymatic studies to elucidate sMMO mechanisms.
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6
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A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Berstis L, Beckham GT, Crowley MF. Electronic coupling through natural amino acids. J Chem Phys 2015; 143:225102. [PMID: 26671404 DOI: 10.1063/1.4936588] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Laura Berstis
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Gregg T. Beckham
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Michael F. Crowley
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
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8
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Wang W, Liang AD, Lippard SJ. Coupling Oxygen Consumption with Hydrocarbon Oxidation in Bacterial Multicomponent Monooxygenases. Acc Chem Res 2015; 48:2632-9. [PMID: 26293615 PMCID: PMC4624108 DOI: 10.1021/acs.accounts.5b00312] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A fundamental goal in catalysis is the coupling of multiple reactions to yield a desired product. Enzymes have evolved elegant approaches to address this grand challenge. A salient example is the biological conversion of methane to methanol catalyzed by soluble methane monooxygenase (sMMO), a member of the bacterial multicomponent monooxygenase (BMM) superfamily. sMMO is a dynamic protein complex of three components: a hydroxylase, a reductase, and a regulatory protein. The active site, a carboxylate-rich non-heme diiron center, is buried inside the 251 kDa hydroxylase component. The enzyme processes four substrates: O2, protons, electrons, and methane. To couple O2 activation to methane oxidation, timely control of substrate access to the active site is critical. Recent studies of sMMO, as well as its homologues in the BMM superfamily, have begun to unravel the mechanism. The emerging and unifying picture reveals that each substrate gains access to the active site along a specific pathway through the hydroxylase. Electrons and protons are delivered via a three-amino-acid pore located adjacent to the diiron center; O2 migrates via a series of hydrophobic cavities; and hydrocarbon substrates reach the active site through a channel or linked set of cavities. The gating of these pathways mediates entry of each substrate to the diiron active site in a timed sequence and is coordinated by dynamic interactions with the other component proteins. The result is coupling of dioxygen consumption with hydrocarbon oxidation, avoiding unproductive oxidation of the reductant rather than the desired hydrocarbon. To initiate catalysis, the reductase delivers two electrons to the diiron(III) center by binding over the pore of the hydroxylase. The regulatory component then displaces the reductase, docking onto the same surface of the hydroxylase. Formation of the hydroxylase-regulatory component complex (i) induces conformational changes of pore residues that may bring protons to the active site; (ii) connects hydrophobic cavities in the hydroxylase leading from the exterior to the diiron active site, providing a pathway for O2 and methane, in the case of sMMO, to the reduced diiron center for O2 activation and substrate hydroxylation; (iii) closes the pore, as well as a channel in the case of four-component BMM enzymes, restricting proton access to the diiron center during formation of "Fe2O2" intermediates required for hydrocarbon oxidation; and (iv) inhibits undesired electron transfer to the Fe2O2 intermediates by blocking reductase binding during O2 activation. This mechanism is quite different from that adopted by cytochromes P450, a large class of heme-containing monooxygenases that catalyze reactions very similar to those catalyzed by the BMM enzymes. Understanding the timed enzyme control of substrate access has implications for designing artificial catalysts. To achieve multiple turnovers and tight coupling, synthetic models must also control substrate access, a major challenge considering that nature requires large, multimeric, dynamic protein complexes to accomplish this feat.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexandria D. Liang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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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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10
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Mukherjee P, Biswas S, Sen P. Real Time Quantification of Ultrafast Photoinduced Bimolecular Electron Transfer Rate: Direct Probing of the Transient Intermediate. J Phys Chem B 2015; 119:11253-61. [DOI: 10.1021/acs.jpcb.5b03105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Puspal Mukherjee
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Somnath Biswas
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Pratik Sen
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
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11
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Sazinsky MH, Lippard SJ. Methane Monooxygenase: Functionalizing Methane at Iron and Copper. Met Ions Life Sci 2015; 15:205-56. [DOI: 10.1007/978-3-319-12415-5_6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Liang A, Lippard SJ. Component interactions and electron transfer in toluene/o-xylene monooxygenase. Biochemistry 2014; 53:7368-75. [PMID: 25402597 PMCID: PMC4255640 DOI: 10.1021/bi500892n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/28/2014] [Indexed: 01/19/2023]
Abstract
The multicomponent protein toluene/o-xylene monooxygenase (ToMO) activates molecular oxygen to oxidize aromatic hydrocarbons. Prior to dioxygen activation, two electrons are injected into each of two diiron(III) units of the hydroxylase, a process that involves three redox active proteins: the ToMO hydroxylase (ToMOH), Rieske protein (ToMOC), and an NADH oxidoreductase (ToMOF). In addition to these three proteins, a small regulatory protein is essential for catalysis (ToMOD). Through steady state and pre-steady state kinetics studies, we show that ToMOD attenuates electron transfer from ToMOC to ToMOH in a concentration-dependent manner. At substoichiometric concentrations, ToMOD increases the rate of turnover, which we interpret to be a consequence of opening a pathway for oxygen transport to the catalytic diiron center in ToMOH. Excess ToMOD inhibits steady state catalysis in a manner that depends on ToMOC concentration. Through rapid kinetic assays, we demonstrate that ToMOD attenuates formation of the ToMOC-ToMOH complex. These data, coupled with protein docking studies, support a competitive model in which ToMOD and ToMOC compete for the same binding site on the hydroxylase. These results are discussed in the context of other studies of additional proteins in the superfamily of bacterial multicomponent monooxygenases.
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Affiliation(s)
- Alexandria
Deliz Liang
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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13
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Wang W, Iacob RE, Luoh RP, Engen JR, Lippard SJ. Electron transfer control in soluble methane monooxygenase. J Am Chem Soc 2014; 136:9754-62. [PMID: 24937475 PMCID: PMC4105053 DOI: 10.1021/ja504688z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The
hydroxylation or epoxidation of hydrocarbons by bacterial multicomponent
monooxygenases (BMMs) requires the interplay of three or four protein
components. How component protein interactions control catalysis,
however, is not well understood. In particular, the binding sites
of the reductase components on the surface of their cognate hydroxylases
and the role(s) that the regulatory proteins play during intermolecular
electron transfer leading to the hydroxylase reduction have been enigmatic.
Here we determine the reductase binding site on the hydroxylase of
a BMM enzyme, soluble methane monooxygenase (sMMO) from Methylococcus
capsulatus (Bath). We present evidence that the ferredoxin
domain of the reductase binds to the canyon region of the hydroxylase,
previously determined to be the regulatory protein binding site as
well. The latter thus inhibits reductase binding to the hydroxylase
and, consequently, intermolecular electron transfer from the reductase
to the hydroxylase diiron active site. The binding competition between
the regulatory protein and the reductase may serve as a control mechanism
for regulating electron transfer, and other BMM enzymes are likely
to adopt the same mechanism.
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Affiliation(s)
- Weixue Wang
- Departments of †Chemistry and §Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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14
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Lee SJ, McCormick MS, Lippard SJ, Cho US. Control of substrate access to the active site in methane monooxygenase. Nature 2013; 494:380-4. [PMID: 23395959 PMCID: PMC3596810 DOI: 10.1038/nature11880] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 12/21/2012] [Indexed: 11/16/2022]
Abstract
Methanotrophs consume methane as their major carbon source and have an essential role in the global carbon cycle by limiting escape of this greenhouse gas to the atmosphere. These bacteria oxidize methane to methanol by soluble and particulate methane monooxygenases (MMOs). Soluble MMO contains three protein components, a 251-kilodalton hydroxylase (MMOH), a 38.6-kilodalton reductase (MMOR), and a 15.9-kilodalton regulatory protein (MMOB), required to couple electron consumption with substrate hydroxylation at the catalytic diiron centre of MMOH. Until now, the role of MMOB has remained ambiguous owing to a lack of atomic-level information about the MMOH-MMOB (hereafter termed H-B) complex. Here we remedy this deficiency by providing a crystal structure of H-B, which reveals the manner by which MMOB controls the conformation of residues in MMOH crucial for substrate access to the active site. MMOB docks at the α(2)β(2) interface of α(2)β(2)γ(2) MMOH, and triggers simultaneous conformational changes in the α-subunit that modulate oxygen and methane access as well as proton delivery to the diiron centre. Without such careful control by MMOB of these substrate routes to the diiron active site, the enzyme operates as an NADH oxidase rather than a monooxygenase. Biological catalysis involving small substrates is often accomplished in nature by large proteins and protein complexes. The structure presented in this work provides an elegant example of this principle.
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Affiliation(s)
- Seung Jae Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael S. McCormick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Uhn-Soo Cho
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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15
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Tinberg CE, Song WJ, Izzo V, Lippard SJ. Multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas sp. OX1. Biochemistry 2011; 50:1788-98. [PMID: 21366224 PMCID: PMC3059347 DOI: 10.1021/bi200028z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. In this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate (phenol; NADH) consumption and product (catechol; H(2)O(2)) generation. Single-turnover experiments revealed that only complete systems containing all three or four protein components are capable of oxidizing phenol, a major substrate for both enzymes. Under ideal conditions, the hydroxylated product yield was ∼50% of the diiron centers for both systems, suggesting that these enzymes operate by half-sites reactivity mechanisms. Single-turnover studies indicated that the PH and ToMO electron-transfer components exert regulatory effects on substrate oxidation processes taking place at the hydroxylase actives sites, most likely through allostery. Steady state NADH consumption assays showed that the regulatory proteins facilitate the electron-transfer step in the hydrocarbon oxidation cycle in the absence of phenol. Under these conditions, electron consumption is coupled to H(2)O(2) formation in a hydroxylase-dependent manner. Mechanistic implications of these results are discussed.
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Affiliation(s)
- Christine E. Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Woon Ju Song
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Viviana Izzo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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16
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Bailey LJ, McCoy JG, Phillips GN, Fox BG. Structural consequences of effector protein complex formation in a diiron hydroxylase. Proc Natl Acad Sci U S A 2008; 105:19194-8. [PMID: 19033467 PMCID: PMC2614738 DOI: 10.1073/pnas.0807948105] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Indexed: 11/18/2022] Open
Abstract
Carboxylate-bridged diiron hydroxylases are multicomponent enzyme complexes responsible for the catabolism of a wide range of hydrocarbons and as such have drawn attention for their mechanism of action and potential uses in bioremediation and enzymatic synthesis. These enzyme complexes use a small molecular weight effector protein to modulate the function of the hydroxylase. However, the origin of these functional changes is poorly understood. Here, we report the structures of the biologically relevant effector protein-hydroxylase complex of toluene 4-monooxygenase in 2 redox states. The structures reveal a number of coordinated changes that occur up to 25 A from the active site and poise the diiron center for catalysis. The results provide a structural basis for the changes observed in a number of the measurable properties associated with effector protein binding. This description provides insight into the functional role of effector protein binding in all carboxylate-bridged diiron hydroxylases.
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Affiliation(s)
- Lucas J. Bailey
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - Jason G. McCoy
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
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17
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Murray LJ, García-Serres R, McCormick MS, Davydov R, Naik S, Kim SH, Hoffman BM, Huynh BH, Lippard SJ. Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase. Biochemistry 2007; 46:14795-809. [PMID: 18044971 PMCID: PMC2494530 DOI: 10.1021/bi7017128] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At its carboxylate-bridged diiron active site, the hydroxylase component of toluene/o-xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. In an I100W variant of this enzyme, we characterized the formation and decay of two species formed by addition of dioxygen to the reduced, diiron(II) state by rapid-freeze quench (RFQ) EPR, Mössbauer, and ENDOR spectroscopy. The dependence of the formation and decay rates of this mixed-valent transient on pH and the presence of phenol, propylene, or acetylene was investigated by double-mixing stopped-flow optical spectroscopy. Modification of the alpha-subunit of the hydroxylase after reaction of the reduced protein with dioxygen-saturated buffer was investigated by tryptic digestion coupled mass spectrometry. From these investigations, we conclude that (i) a diiron(III,IV)-W* transient, kinetically linked to a preceding diiron(III) intermediate, arises from the one-electron oxidation of W100, (ii) the tryptophan radical is deprotonated, (iii) rapid exchange of either a terminal water or hydroxide ion with water occurs at the ferric ion in the diiron(III,IV) cluster, and (iv) the diiron(III,IV) core and W* decay to the diiron(III) product by a common mechanism. No transient radical was observed by stopped-flow optical spectroscopy for reactions of the reduced hydroxylase variants I100Y, L208F, and F205W with dioxygen. The absence of such species, and the deprotonated state of the tryptophanyl radical in the diiron(III,IV)-W* transient, allow for a conservative estimate of the reduction potential of the diiron(III) intermediate as lying between 1.1 and 1.3 V. We also describe the X-ray crystal structure of the I100W variant of ToMOH.
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Affiliation(s)
- Leslie J. Murray
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
| | | | - Michael S. McCormick
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
| | - Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Sunil Naik
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Sun-Hee Kim
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Boi Hanh Huynh
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
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18
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Wu CH, Jiang W, Krebs C, Stubbe J. YfaE, a ferredoxin involved in diferric-tyrosyl radical maintenance in Escherichia coli ribonucleotide reductase. Biochemistry 2007; 46:11577-88. [PMID: 17880186 DOI: 10.1021/bi7012454] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. The class I RNRs are composed of a 1:1 complex of two homodimeric subunits: alpha and beta. beta contains the diferric-tyrosyl radical (Y*) cofactor essential for the reduction process. In vivo, the mechanism of Y* regeneration from the diferric-beta2 (met-beta2) or apo-beta2 is still unclear. Y* regenerations from met-beta2 and apo-beta2 have been designated the maintenance and biosynthetic pathways, respectively. To understand these two pathways, 181 genomes that contain nrdAnrdB (genes encoding alpha and beta) were examined. In 29% of the cases, an open reading frame annotated 2Fe2S ferredoxin (YfaE in Escherichia coli) is located next to nrdB. Thus, YfaE has been cloned, expressed, resolubilized, reconstituted anaerobically with Fe2+, Fe3+, and S2-, and characterized by Mössbauer, EPR, and visible spectroscopies. Titration of met-beta2 with [2Fe2S]1+-YfaE anaerobically results in the formation of an equilibrium mixture of diferrous-beta2 and [2Fe2S]2+-YfaE with one Fe reduced/YfaE oxidized. At the end point of the titration, O2 is added to the mixture and the diferrous-beta2 rapidly undergoes reaction to form the diferric-Y* with a stoichiometry of 2Fe/Y* and a specific activity correlated to the amount of Y*. The reducing equivalent required for diferric-Y* cofactor biosynthesis is supplied by beta. Under anaerobic conditions, stopped flow kinetics have been used to monitor the disappearance of the diferric cluster and the formation of [2Fe2S]2+-YfaE. The titrations and kinetic studies provide the first evidence for a protein involved in the maintenance pathway and likely the biosynthetic pathway.
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Affiliation(s)
- Chia-Hung Wu
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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Murray LJ, Lippard SJ. Substrate trafficking and dioxygen activation in bacterial multicomponent monooxygenases. Acc Chem Res 2007; 40:466-74. [PMID: 17518435 DOI: 10.1021/ar600040e] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-heme carboxylate-bridged diiron centers in the hydroxylase components of the bacterial multicomponent monooxygenases process four substrates during catalysis: electrons, protons, dioxygen, and hydrocarbons. Understanding how protein-protein interactions mediate the transport of these substrates to the diiron center to achieve the selective oxidation of the hydrocarbon is a significant challenge. In this Account, we summarize our current knowledge of these processes with a focus on the methane monooxygenase system. We also describe recent results for the toluene/ o-xylene monooxygenase and phenol hydroxylase systems from Pseudomonas sporium OX1. The observation in these latter systems of a diiron(III) oxygenated intermediate having different Mössbauer parameters from analogous species in other carboxylate-bridged diiron proteins is discussed. The results indicate that the ability of the protein framework to tune the reactivity of the diiron center at structurally similar active sites is substantially more complex than previously recognized.
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Affiliation(s)
- Leslie J Murray
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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20
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Romakh VB, Therrien B, Süss-Fink G, Shul'pin GB. Synthesis, Molecular Structure, and Catalytic Potential of the Tetrairon Complex [Fe4(N3O2-L)4(μ-O)2]4+ (L = 1-Carboxymethyl-4,7-dimethyl-1,4,7-triazacyclononane). Inorg Chem 2007; 46:3166-75. [PMID: 17373788 DOI: 10.1021/ic062207k] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of iron sulfate with 1-carboxymethyl-4,7-dimethyl-1,4,7-triazacyclononane (L) and hydrogen peroxide in aqueous ethanol gives a brown dinuclear complex considered to be [Fe2(N3O-L)2(mu-O)(mu-OOCCH3)] + (1), which converts upon standing in acetonitrile solution into the green tetranuclear complex [Fe4(N3O2-L)4(mu-O)2]4+ (2). A single-crystal X-ray structure analysis of [2][PF6]4.5MeCN reveals 2 to contain four iron(III) centers, each of which is coordinated to three nitrogen atoms of a triazacyclononane ligand and is bridged by one oxo and two carboxylato bridges, a structural feature known from the active center of methane monooxygenase. Accordingly, complex 2 was found to catalyze the oxidative functionalization of methane with hydrogen peroxide in aqueous solution to give methanol, methyl hydroperoxide, and formic acid; the total turnover numbers attain 24 catalytic cycles within 4 h. To gain more insight into the catalytic process, the catalytic potential of 2 was also studied for the oxidation of higher alkanes, cycloalkanes, and isopropanol in acetonitrile, as well as in aqueous solution. The bond selectivities of the oxidation of linear and branched alkanes suggest a ferroxy radical pathway.
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Affiliation(s)
- Vladimir B Romakh
- Institut de Chimie, Université de Neuchâtel, CH-2009 Neuchâtel, Switzerland, and Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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21
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Sazinsky MH, Dunten PW, McCormick MS, DiDonato A, Lippard SJ. X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase. Biochemistry 2006; 45:15392-404. [PMID: 17176061 PMCID: PMC1829208 DOI: 10.1021/bi0618969] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenol hydroxylase (PH) belongs to a family of bacterial multicomponent monooxygenases (BMMs) with carboxylate-bridged diiron active sites. Included are toluene/o-xylene (ToMO) and soluble methane (sMMO) monooxygenase. PH hydroxylates aromatic compounds, but unlike sMMO, it cannot oxidize alkanes despite having a similar dinuclear iron active site. Important for activity is formation of a complex between the hydroxylase and a regulatory protein component. To address how structural features of BMM hydroxylases and their component complexes may facilitate the catalytic mechanism and choice of substrate, we determined X-ray structures of native and SeMet forms of the PH hydroxylase (PHH) in complex with its regulatory protein (PHM) to 2.3 A resolution. PHM binds in a canyon on one side of the (alphabetagamma)2 PHH dimer, contacting alpha-subunit helices A, E, and F approximately 12 A above the diiron core. The structure of the dinuclear iron center in PHH resembles that of mixed-valent MMOH, suggesting an Fe(II)Fe(III) oxidation state. Helix E, which comprises part of the iron-coordinating four-helix bundle, has more pi-helical character than analogous E helices in MMOH and ToMOH lacking a bound regulatory protein. Consequently, conserved active site Thr and Asn residues translocate to the protein surface, and an approximately 6 A pore opens through the four-helix bundle. Of likely functional significance is a specific hydrogen bond formed between this Asn residue and a conserved Ser side chain on PHM. The PHM protein covers a putative docking site on PHH for the PH reductase, which transfers electrons to the PHH diiron center prior to O2 activation, suggesting that the regulatory component may function to block undesired reduction of oxygenated intermediates during the catalytic cycle. A series of hydrophobic cavities through the PHH alpha-subunit, analogous to those in MMOH, may facilitate movement of the substrate to and/or product from the active site pocket. Comparisons between the ToMOH and PHH structures provide insights into their substrate regiospecificities.
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Affiliation(s)
- Matthew H Sazinsky
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Sazinsky MH, Lippard SJ. Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins. Acc Chem Res 2006; 39:558-66. [PMID: 16906752 DOI: 10.1021/ar030204v] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial multicomponent monooxygenases (BMMs) catalyze the O2-dependent hydroxylation of hydrocarbons at a carboxylate-bridged diiron center similar to those that occur in a variety of dimetallic oxygen-utilizing enzymes. BMMs have found numerous biodegradation and biocatalytic applications. Recent investigations have begun to reveal how BMMs perform their C-H bond activation chemistry and why these enzymes may be mechanistically different from other related diiron proteins. The structures of the BMM component proteins and of complexes between them provide insights into the tuning of the dinuclear iron center and the enzyme mechanism. Selected findings are compared and contrasted with the properties of other carboxylate-bridged diiron proteins, revealing common structural and functional themes.
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Affiliation(s)
- Matthew H Sazinsky
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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Baddam S, Bowler BE. Tuning the Rate and pH Accessibility of a Conformational Electron Transfer Gate. Inorg Chem 2006; 45:6338-46. [PMID: 16878944 DOI: 10.1021/ic0603712] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods to fine-tune the rate of a fast conformational electron transfer (ET) gate involving a His-heme alkaline conformer of iso-1-cytochrome c (iso-1-Cytc) and to adjust the pH accessibility of a slow ET gate involving a Lys-heme alkaline conformer are described. Fine-tuning the fast ET gate employs a strategy of making surface mutations in a substructure unfolded in the alkaline conformer. To make the slow ET gate accessible at neutral pH, the strategy involves mutations at buried sequence positions which are expected to more strongly perturb the stability of native versus alkaline iso-1-Cytc. To fine-tune the rate of the fast His 73-heme ET gate, we mutate the surface-exposed Lys 79 to Ala (A79H73 variant). This mutation also simplifies ET gating by removing Lys 79, which can serve as a ligand in the alkaline conformer of iso-1-Cytc. To adjust the pH accessibility of the slow Lys 73-heme ET gate, we convert the buried side chain Asn 52 to Gly and also mutate Lys 79 to Ala to simplify ET gating (A79G52 variant). ET kinetics is studied as a function of pH using hexaammineruthenium(II) chloride (a6Ru2+) to reduce the variants. Both variants show fast direct ET reactions dependent on [a6Ru2+] and slower gated ET reactions that are independent of [a6Ru2+]. The observed gated ET rates correlate well with rates for the alkaline-to-native state conformational change measured independently. Together with the previously reported H73 variant (Baddam, S.; Bowler, B. E. J. Am. Chem. Soc. 2005, 127, 9702-9703), the A79H73 variant allows His 73-heme-mediated ET gating to be fine-tuned from 75 to 200 ms. The slower Lys 73-heme (15-20 s time scale) ET gate for the A79G52 variant is now accessible over the pH range 6-8.
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Affiliation(s)
- Saritha Baddam
- Department of Chemistry and Biochemistry, University of Denver, 2190 East Iliff Avenue, Denver, CO 80208-2436, USA
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