1
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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2
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Andrade LS, Lima HH, Silva CT, Amorim WL, Poço JG, López-Castillo A, Kirillova MV, Carvalho WA, Kirillov AM, Mandelli D. Metal–organic frameworks as catalysts and biocatalysts for methane oxidation: The current state of the art. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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3
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Cutsail GE, Banerjee R, Rice DB, McCubbin Stepanic O, Lipscomb JD, DeBeer S. Determination of the iron(IV) local spin states of the Q intermediate of soluble methane monooxygenase by Kβ X-ray emission spectroscopy. J Biol Inorg Chem 2022; 27:573-582. [PMID: 35988092 PMCID: PMC9470658 DOI: 10.1007/s00775-022-01953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022]
Abstract
Soluble methane monooxygenase (sMMO) facilitates the conversion of methane to methanol at a non-heme FeIV2 intermediate MMOHQ, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent FeIV sites in catalysis; however, MMOHQ is unique as Nature’s only identified FeIV2 intermediate. Previous 57Fe Mössbauer spectroscopic studies have shown that MMOHQ employs antiferromagnetic coupling of the two FeIV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (Sloc) of each of the irons by most spectroscopic techniques. Here, we use Fe Kβ X-ray emission spectroscopy (XES) to characterize the local spin states of the key intermediates of the sMMO catalytic cycle, including MMOHQ trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOHQ is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOHQ spectrum with those of known Sloc = 1 and Sloc = 2 FeIV sites in chemical and biological models reveal that MMOHQ possesses Sloc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.
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Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany.
| | - Rahul Banerjee
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Derek B Rice
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
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4
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Mahor D, Cong Z, Weissenborn MJ, Hollmann F, Zhang W. Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization. CHEMSUSCHEM 2022; 15:e202101116. [PMID: 34288540 DOI: 10.1002/cssc.202101116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/18/2021] [Indexed: 06/13/2023]
Abstract
The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.
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Affiliation(s)
- Durga Mahor
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- Indian Institute of Science Education and Research Berhampur, Odisha, 760010, India
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Martin J Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale), Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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5
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Jones JC, Banerjee R, Semonis MM, Shi K, Aihara H, Lipscomb JD. X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry 2022; 61:21-33. [PMID: 34910460 PMCID: PMC8727504 DOI: 10.1021/acs.biochem.1c00673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Full activity of soluble methane monooxygenase (sMMO) depends upon the formation of a 1:1 complex of the regulatory protein MMOB with each alpha subunit of the (αβγ)2 hydroxylase, sMMOH. Previous studies have shown that mutations in the core region of MMOB and in the N- and C-termini cause dramatic changes in the rate constants for steps in the sMMOH reaction cycle. Here, X-ray crystal structures are reported for the sMMOH complex with two double variants within the core region of MMOB, DBL1 (N107G/S110A), and DBL2 (S109A/T111A), as well as two variants in the MMOB N-terminal region, H33A and H5A. DBL1 causes a 150-fold decrease in the formation rate constant of the reaction cycle intermediate P, whereas DBL2 accelerates the reaction of the dinuclear Fe(IV) intermediate Q with substrates larger than methane by three- to fourfold. H33A also greatly slows P formation, while H5A modestly slows both formation of Q and its reactions with substrates. Complexation with DBL1 or H33A alters the position of sMMOH residue R245, which is part of a conserved hydrogen-bonding network encompassing the active site diiron cluster where P is formed. Accordingly, electron paramagnetic resonance spectra of sMMOH:DBL1 and sMMOH:H33A complexes differ markedly from that of sMMOH:MMOB, showing an altered electronic environment. In the sMMOH:DBL2 complex, the position of M247 in sMMOH is altered such that it enlarges a molecular tunnel associated with substrate entry into the active site. The H5A variant causes only subtle structural changes despite its kinetic effects, emphasizing the precise alignment of sMMOH and MMOB required for efficient catalysis.
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Affiliation(s)
- Jason C. Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Manny M. Semonis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, U. S. A.,Corresponding Author:
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6
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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7
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Jacobs AB, Banerjee R, Deweese DE, Braun A, Babicz JT, Gee LB, Sutherlin KD, Böttger LH, Yoda Y, Saito M, Kitao S, Kobayashi Y, Seto M, Tamasaku K, Lipscomb JD, Park K, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of the Fe(IV) 2 Intermediate Q in Methane Monooxygenase and Its Reactivity. J Am Chem Soc 2021; 143:16007-16029. [PMID: 34570980 PMCID: PMC8631202 DOI: 10.1021/jacs.1c05436] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.
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Affiliation(s)
- Ariel B. Jacobs
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Dory E. Deweese
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Leland B. Gee
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578 Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, 590-0494
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo, 679-5148, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California, 94305, United States,Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, 94025, United States
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8
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Jones JC, Banerjee R, Shi K, Semonis MM, Aihara H, Pomerantz WCK, Lipscomb JD. Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR. Biochemistry 2021; 60:1995-2010. [PMID: 34100595 PMCID: PMC8345336 DOI: 10.1021/acs.biochem.1c00293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar KD values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.
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Affiliation(s)
- Jason C. Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Manny M. Semonis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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9
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Schulz CE, Castillo RG, Pantazis DA, DeBeer S, Neese F. Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations. J Am Chem Soc 2021; 143:6560-6577. [PMID: 33884874 PMCID: PMC8154522 DOI: 10.1021/jacs.1c01180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The determination
of the diiron core intermediate structures involved
in the catalytic cycle of soluble methane monooxygenase (sMMO), the
enzyme that selectively catalyzes the conversion of methane to methanol,
has been a subject of intense interest within the bioinorganic scientific
community. Particularly, the specific geometry and electronic structure
of the intermediate that precedes methane binding, known as intermediate
Q (or MMOHQ), has been debated for over 30 years. Some
reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer
Fe–Fe distance. The lack of consensus calls for a thorough
re-examination and reinterpretation of the spectroscopic data available
on the MMOHQ intermediate. Herein, we report extensive
simulations based on a hybrid quantum mechanics/molecular mechanics
approach (QM/MM) approach that takes into account the complete enzyme
to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum
chemical approaches are used to correlate specific structural motifs
with geometric parameters for comparison with crystallographic and
EXAFS data, as well as with spectroscopic data from Mössbauer
spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy
(HERFD XAS), and resonance Raman 16O–18O difference spectroscopy. The results provide strong support for
an open-core-type configuration in MMOHQ, with the most
likely topology involving mono-oxo-bridged Fe ions and alternate terminal
Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen
bonding. The implications of an open-core intermediate Q on the reaction
mechanism of sMMO are discussed.
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Affiliation(s)
- Christine E Schulz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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10
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Pullin J, Wilson MT, Clémancey M, Blondin G, Bradley JM, Moore GR, Le Brun NE, Lučić M, Worrall JAR, Svistunenko DA. Iron Oxidation in Escherichia coli Bacterioferritin Ferroxidase Centre, a Site Designed to React Rapidly with H 2O 2 but Slowly with O 2. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:8442-8450. [PMID: 38529354 PMCID: PMC10962548 DOI: 10.1002/ange.202015964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/05/2021] [Indexed: 11/09/2022]
Abstract
Both O2 and H2O2 can oxidize iron at the ferroxidase center (FC) of Escherichia coli bacterioferritin (EcBfr) but mechanistic details of the two reactions need clarification. UV/Vis, EPR, and Mössbauer spectroscopies have been used to follow the reactions when apo-EcBfr, pre-loaded anaerobically with Fe2+, was exposed to O2 or H2O2. We show that O2 binds di-Fe2+ FC reversibly, two Fe2+ ions are oxidized in concert and a H2O2 molecule is formed and released to the solution. This peroxide molecule further oxidizes another di-Fe2+ FC, at a rate circa 1000 faster than O2, ensuring an overall 1:4 stoichiometry of iron oxidation by O2. Initially formed Fe3+ can further react with H2O2 (producing protein bound radicals) but relaxes within seconds to an H2O2-unreactive di-Fe3+ form. The data obtained suggest that the primary role of EcBfr in vivo may be to detoxify H2O2 rather than sequester iron.
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Affiliation(s)
- Jacob Pullin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Martin Clémancey
- Université Grenoble AlpesCNRS, CEA, IRIGLaboratoire de Chimie et Biologie des Métaux, UMR 524917 rue des Martyrs38000GrenobleFrance
| | - Geneviève Blondin
- Université Grenoble AlpesCNRS, CEA, IRIGLaboratoire de Chimie et Biologie des Métaux, UMR 524917 rue des Martyrs38000GrenobleFrance
| | - Justin M. Bradley
- School of ChemistryUniversity of East AngliaNorwich Research Park NorwichNorfolkNR4 7TJUK
| | - Geoffrey R. Moore
- School of ChemistryUniversity of East AngliaNorwich Research Park NorwichNorfolkNR4 7TJUK
| | - Nick E. Le Brun
- School of ChemistryUniversity of East AngliaNorwich Research Park NorwichNorfolkNR4 7TJUK
| | - Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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11
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Pullin J, Wilson MT, Clémancey M, Blondin G, Bradley JM, Moore GR, Le Brun NE, Lučić M, Worrall JAR, Svistunenko DA. Iron Oxidation in Escherichia coli Bacterioferritin Ferroxidase Centre, a Site Designed to React Rapidly with H 2 O 2 but Slowly with O 2. Angew Chem Int Ed Engl 2021; 60:8361-8369. [PMID: 33482043 PMCID: PMC8049013 DOI: 10.1002/anie.202015964] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/05/2021] [Indexed: 01/08/2023]
Abstract
Both O2 and H2O2 can oxidize iron at the ferroxidase center (FC) of Escherichia coli bacterioferritin (EcBfr) but mechanistic details of the two reactions need clarification. UV/Vis, EPR, and Mössbauer spectroscopies have been used to follow the reactions when apo‐EcBfr, pre‐loaded anaerobically with Fe2+, was exposed to O2 or H2O2. We show that O2 binds di‐Fe2+ FC reversibly, two Fe2+ ions are oxidized in concert and a H2O2 molecule is formed and released to the solution. This peroxide molecule further oxidizes another di‐Fe2+ FC, at a rate circa 1000 faster than O2, ensuring an overall 1:4 stoichiometry of iron oxidation by O2. Initially formed Fe3+ can further react with H2O2 (producing protein bound radicals) but relaxes within seconds to an H2O2‐unreactive di‐Fe3+ form. The data obtained suggest that the primary role of EcBfr in vivo may be to detoxify H2O2 rather than sequester iron.
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Affiliation(s)
- Jacob Pullin
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Martin Clémancey
- Université Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000, Grenoble, France
| | - Geneviève Blondin
- Université Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000, Grenoble, France
| | - Justin M Bradley
- School of Chemistry, University of East Anglia, Norwich Research Park Norwich, Norfolk, NR4 7TJ, UK
| | - Geoffrey R Moore
- School of Chemistry, University of East Anglia, Norwich Research Park Norwich, Norfolk, NR4 7TJ, UK
| | - Nick E Le Brun
- School of Chemistry, University of East Anglia, Norwich Research Park Norwich, Norfolk, NR4 7TJ, UK
| | - Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
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12
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Fuller ME, Rezes RT, Hedman PC, Jones JC, Sturchio NC, Hatzinger PB. Biotransformation of the insensitive munition constituents 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN) by aerobic methane-oxidizing consortia and pure cultures. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124341. [PMID: 33144007 DOI: 10.1016/j.jhazmat.2020.124341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/22/2020] [Accepted: 10/17/2020] [Indexed: 06/11/2023]
Abstract
We present the first report of biotransformation of 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN), replacements for the explosives 1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT), respectively, by methane-oxidizing cultures under aerobic conditions. Two consortia, dominated by Methylosinus spp., degraded both compounds with transient production of reduced NTO products, and non-stoichiometric production of reduced DNAN products. No release of inorganic nitrogen was observed with either compound, indicating that NTO and DNAN may be utilized as nitrogen sources by these consortia. The pure culture Methylosinus trichosporium OB3b also degraded both compounds. Degradation was observed in the presence of acetylene (a known inhibitor of methane monooxygenase; MMO) when methanol was supplied, indicating that MMO was not involved. Furthermore, studies with purified soluble MMO (sMMO) from OB3b indicated that neither compound was a substrate for sMMO. Degradation was inhibited by 2-iodosobenzoic acid, but not by dicoumarol, suggesting involvement of an oxygen- and dicoumarol-insensitive (nitro)reductase. These results indicate methanotrophs can aerobically degrade NTO and DNAN via one or more (nitro)reductases, with sMMO serving a supporting role deriving reducing equivalents from methane. This finding is important because methanotrophic bacteria are widely dispersed, and may represent a previously unrecognized route of NTO and DNAN biotransformation in aerobic environments.
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Affiliation(s)
- Mark E Fuller
- Aptim Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA.
| | - Rachael T Rezes
- Aptim Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
| | - Paul C Hedman
- Aptim Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
| | | | | | - Paul B Hatzinger
- Aptim Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
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13
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Abstract
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
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Affiliation(s)
- Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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14
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Srinivas V, Banerjee R, Lebrette H, Jones JC, Aurelius O, Kim IS, Pham CC, Gul S, Sutherlin KD, Bhowmick A, John J, Bozkurt E, Fransson T, Aller P, Butryn A, Bogacz I, Simon P, Keable S, Britz A, Tono K, Kim KS, Park SY, Lee SJ, Park J, Alonso-Mori R, Fuller FD, Batyuk A, Brewster AS, Bergmann U, Sauter NK, Orville AM, Yachandra VK, Yano J, Lipscomb JD, Kern J, Högbom M. High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. J Am Chem Soc 2020; 142:14249-14266. [PMID: 32683863 DOI: 10.1021/jacs.0c05613] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Esra Bozkurt
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-gun 679 5198, Japan
| | - Kyung Sook Kim
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang-Youn Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Allen M Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
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15
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Jones JC, Banerjee R, Shi K, Aihara H, Lipscomb JD. Structural Studies of the Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel. Biochemistry 2020; 59:2946-2961. [PMID: 32692178 DOI: 10.1021/acs.biochem.0c00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The metalloenzyme soluble methane monooxygenase (sMMO) consists of hydroxylase (sMMOH), regulatory (MMOB), and reductase components. When sMMOH forms a complex with MMOB, the rate constants are greatly increased for the sequential access of O2, protons, and CH4 to an oxygen-bridged diferrous metal cluster located in the buried active site. Here, we report high-resolution X-ray crystal structures of the diferric and diferrous states of both sMMOH and the sMMOH:MMOB complex using the components from Methylosinus trichosporium OB3b. These structures are analyzed for O2 access routes enhanced when the complex forms. Previously reported, lower-resolution structures of the sMMOH:MMOB complex from the sMMO of Methylococcus capsulatus Bath revealed a series of cavities through sMMOH postulated to serve as the O2 conduit. This potential role is evaluated in greater detail using the current structures. Additionally, a search for other potential O2 conduits in the M. trichosporium OB3b sMMOH:MMOB complex revealed a narrow molecular tunnel, termed the W308-tunnel. This tunnel is sized appropriately for O2 and traverses the sMMOH-MMOB interface before accessing the active site. The kinetics of reaction of O2 with the diferrous sMMOH:MMOB complex in solution show that use of the MMOB V41R variant decreases the rate constant for O2 binding >25000-fold without altering the component affinity. The location of Val41 near the entrance to the W308-tunnel is consistent with the tunnel serving as the primary route for the transfer of O2 into the active site. Accordingly, the crystal structures show that formation of the diferrous sMMOH:MMOB complex restricts access through the chain of cavities while opening the W308-tunnel.
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16
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Semrau JD, DiSpirito AA. Methanobactin: A Novel Copper-Binding Compound Produced by Methanotrophs. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-23261-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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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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18
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Cutsail GE, Banerjee R, Zhou A, Que L, Lipscomb JD, DeBeer S. High-Resolution Extended X-ray Absorption Fine Structure Analysis Provides Evidence for a Longer Fe···Fe Distance in the Q Intermediate of Methane Monooxygenase. J Am Chem Soc 2018; 140:16807-16820. [PMID: 30398343 DOI: 10.1021/jacs.8b10313] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Despite decades of intense research, the core structure of the methane C-H bond breaking diiron(IV) intermediate, Q, of soluble methane monooxygenase remains controversial, with conflicting reports supporting either a "diamond" diiron core structure or an open core structure. Early extended X-ray absorption fine structure (EXAFS) data assigned a short 2.46 Å Fe-Fe distance to Q (Shu et al. Science 1997, 275, 515 ) that is inconsistent with several theoretical studies and in conflict with our recent high-resolution Fe K-edge X-ray absorption spectroscopy (XAS) studies (Castillo et al. J. Am. Chem. Soc. 2017, 139, 18024 ). Herein, we revisit the EXAFS of Q using high-energy resolution fluorescence-detected extended X-ray absorption fine structure (HERFD-EXAFS) studies. The present data show no evidence for a short Fe-Fe distance, but rather a long 3.4 Å diiron distance, as observed in open core synthetic model complexes. The previously reported 2.46 Å feature plausibly arises from a background metallic iron contribution from the experimental setup, which is eliminated in HERFD-EXAFS due to the increased selectivity. Herein, we explore the origin of the short diiron feature in partial-fluorescent yield EXAFS measurements and discuss the diagnostic features of background metallic scattering contribution to the EXAFS of dilute biological samples. Lastly, differences in sample preparation and resultant sample inhomogeneity in rapid-freeze quenched samples for EXAFS analysis are discussed. The presented approaches have broad implications for EXAFS studies of all dilute iron-containing samples.
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Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55455 , United States.,Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ang Zhou
- Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,Department of Chemistry , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455 , United States
| | - Lawrence Que
- Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,Department of Chemistry , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455 , United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55455 , United States.,Center for Metals in Biocatalysis , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
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19
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Komor AJ, Jasniewski AJ, Que L, Lipscomb JD. Diiron monooxygenases in natural product biosynthesis. Nat Prod Rep 2018; 35:646-659. [PMID: 29552683 PMCID: PMC6051903 DOI: 10.1039/c7np00061h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2017 The participation of non-heme dinuclear iron cluster-containing monooxygenases in natural product biosynthetic pathways has been recognized only recently. At present, two families have been discovered. The archetypal member of the first family, CmlA, catalyzes β-hydroxylation of l-p-aminophenylalanine (l-PAPA) covalently linked to the nonribosomal peptide synthetase (NRPS) CmlP, thereby effecting the first step in the biosynthesis of chloramphenicol by Streptomyces venezuelae. CmlA houses the diiron cluster in a metallo-β-lactamase protein fold instead of the 4-helix bundle fold of nearly every other diiron monooxygenase. CmlA couples O2 activation and substrate hydroxylation via a structural change caused by formation of the l-PAPA-loaded CmlP:CmlA complex. The other new diiron family is typified by two enzymes, AurF and CmlI, which catalyze conversion of aryl-amine substrates to aryl-nitro products with incorporation of oxygen from O2. AurF from Streptomyces thioluteus catalyzes the formation of p-nitrobenzoate from p-aminobenzoate as a precursor to the biostatic compound aureothin, whereas CmlI from S. venezuelae catalyzes the ultimate aryl-amine to aryl-nitro step in chloramphenicol biosynthesis. Both enzymes stabilize a novel type of peroxo-intermediate as the reactive species. The rare 6-electron N-oxygenation reactions of CmlI and AurF involve two progressively oxidized pathway intermediates. The enzymes optimize efficiency by utilizing one of the reaction pathway intermediates as an in situ reductant for the diiron cluster, while simultaneously generating the next pathway intermediate. For CmlI, this reduction allows mid-pathway regeneration of the peroxo intermediate required to complete the biosynthesis. CmlI ensures specificity by carrying out the multistep aryl-amine oxygenation without dissociating intermediate products.
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Affiliation(s)
- Anna J Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Andrew J Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Lawrence Que
- Department of Chemistry, 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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20
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Castillo RG, Banerjee R, Allpress CJ, Rohde GT, Bill E, Que L, Lipscomb JD, DeBeer S. High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase. J Am Chem Soc 2017; 139:18024-18033. [PMID: 29136468 PMCID: PMC5729100 DOI: 10.1021/jacs.7b09560] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.
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Affiliation(s)
- Rebeca G. Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Caleb J. Allpress
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Gregory T. Rohde
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
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21
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Potential for cometabolic biodegradation of 1,4-dioxane in aquifers with methane or ethane as primary substrates. Biodegradation 2017; 28:453-468. [PMID: 29022194 DOI: 10.1007/s10532-017-9808-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/28/2017] [Indexed: 10/18/2022]
Abstract
The objective of this research was to evaluate the potential for two gases, methane and ethane, to stimulate the biological degradation of 1,4-dioxane (1,4-D) in groundwater aquifers via aerobic cometabolism. Experiments with aquifer microcosms, enrichment cultures from aquifers, mesophilic pure cultures, and purified enzyme (soluble methane monooxygenase; sMMO) were conducted. During an aquifer microcosm study, ethane was observed to stimulate the aerobic biodegradation of 1,4-D. An ethane-oxidizing enrichment culture from these samples, and a pure culture capable of growing on ethane (Mycobacterium sphagni ENV482) that was isolated from a different aquifer also biodegraded 1,4-D. Unlike ethane, methane was not observed to appreciably stimulate the biodegradation of 1,4-D in aquifer microcosms or in methane-oxidizing mixed cultures enriched from two different aquifers. Three different pure cultures of mesophilic methanotrophs also did not degrade 1,4-D, although each rapidly oxidized 1,1,2-trichloroethene (TCE). Subsequent studies showed that 1,4-D is not a substrate for purified sMMO enzyme from Methylosinus trichosporium OB3b, at least not at the concentrations evaluated, which significantly exceeded those typically observed at contaminated sites. Thus, our data indicate that ethane, which is a common daughter product of the biotic or abiotic reductive dechlorination of chlorinated ethanes and ethenes, may serve as a substrate to enhance 1,4-D degradation in aquifers, particularly in zones where these products mix with aerobic groundwater. It may also be possible to stimulate 1,4-D biodegradation in an aerobic aquifer through addition of ethane gas. Conversely, our results suggest that methane may have limited importance in natural attenuation or for enhancing biodegradation of 1,4-D in groundwater environments.
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22
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Weitz AC, Giri N, Caranto JD, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures. J Am Chem Soc 2017; 139:12009-12019. [PMID: 28756660 PMCID: PMC5898632 DOI: 10.1021/jacs.7b06546] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.
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Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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23
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Banerjee R, Komor AJ, Lipscomb JD. Use of Isotopes and Isotope Effects for Investigations of Diiron Oxygenase Mechanisms. Methods Enzymol 2017; 596:239-290. [PMID: 28911774 DOI: 10.1016/bs.mie.2017.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Isotope effects of four broad and overlapping categories have been applied to the study of the mechanisms of chemical reaction and regulation of nonheme diiron cluster-containing oxygenases. The categories are: (a) mass properties that allow substrate-to-product conversions to be tracked, (b) atomic properties that allow specialized spectroscopies, (c) mass properties that impact primarily vibrational spectroscopies, and (d) bond dissociation energy shifts that permit dynamic isotope effect studies of many types. The application of these categories of isotope effects is illustrated using the soluble methane monooxygenase system and CmlI, which catalyzes the multistep arylamine to arylnitro conversion in the biosynthetic pathway for chloramphenicol.
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Affiliation(s)
| | - Anna J Komor
- University of Minnesota, Minneapolis, MN, United States
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24
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Miller EK, Trivelas NE, Maugeri PT, Blaesi EJ, Shafaat HS. Time-Resolved Investigations of Heterobimetallic Cofactor Assembly in R2lox Reveal Distinct Mn/Fe Intermediates. Biochemistry 2017; 56:3369-3379. [PMID: 28574263 DOI: 10.1021/acs.biochem.7b00403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly mechanism of the Mn/Fe ligand-binding oxidases (R2lox), a family of proteins that are homologous to the nonheme diiron carboxylate enzymes, has been investigated using time-resolved techniques. Multiple heterobimetallic intermediates that exhibit unique spectral features, including visible absorption bands and exceptionally broad electron paramagnetic resonance signatures, are observed through optical and magnetic resonance spectroscopies. On the basis of comparison to known diiron species and model compounds, the spectra have been attributed to (μ-peroxo)-MnIII/FeIII and high-valent Mn/Fe species. Global spectral analysis coupled with isotopic substitution and kinetic modeling reveals elementary rate constants for the assembly of Mn/Fe R2lox under aerobic conditions. A complete reaction mechanism for cofactor maturation that is consistent with experimental data has been developed. These results suggest that the Mn/Fe cofactor can perform direct C-H bond abstraction, demonstrating the potential for potent chemical reactivity that remains unexplored.
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Affiliation(s)
| | | | | | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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25
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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Lawton TJ, Rosenzweig AC. Biocatalysts for methane conversion: big progress on breaking a small substrate. Curr Opin Chem Biol 2016; 35:142-149. [PMID: 27768948 DOI: 10.1016/j.cbpa.2016.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Abstract
Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature's most inert hydrocarbon have been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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28
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Jasniewski AJ, Knoot CJ, Lipscomb JD, Que L. A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme β-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase. Biochemistry 2016; 55:5818-5831. [PMID: 27668828 PMCID: PMC5258830 DOI: 10.1021/acs.biochem.6b00834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinuclear iron cluster that is reduced to the diferrous state (WTR) to initiate O2 activation. However, rapid O2 activation occurs only when WTR is bound to CmlP, the NRPS to which l-PAPA is covalently attached. Here the X-ray crystal structure of WTR is reported, which is very similar to that of the as-isolated diferric enzyme in which the irons are coordinately saturated. X-ray absorption spectroscopy is used to investigate the WTR cluster ligand structure as well as the structures of WTR in complex with a functional CmlP variant (CmlPAT) with and without l-PAPA attached. It is found that formation of the active WTR:CmlPAT-l-PAPA complex converts at least one iron of the cluster from six- to five-coordinate by changing a bidentately bound amino acid carboxylate to monodentate on Fe1. The only bidentate carboxylate in the structure of WTR is E377. The crystal structure of the CmlA variant E377D shows only monodentate carboxylate coordination. Reduced E377D reacts rapidly with O2 in the presence or absence of CmlPAT-l-PAPA, showing loss of regulation. However, this variant fails to catalyze hydroxylation, suggesting that E377 has the dual role of coupling regulation of O2 reactivity with juxtaposition of the substrate and the reactive oxygen species. The carboxylate shift in response to substrate binding represents a novel regulatory strategy for oxygen activation in diiron oxygenases.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Cory J Knoot
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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29
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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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Knoot CJ, Kovaleva EG, Lipscomb JD. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway. J Biol Inorg Chem 2016; 21:589-603. [PMID: 27229511 PMCID: PMC4994471 DOI: 10.1007/s00775-016-1363-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/16/2016] [Indexed: 11/28/2022]
Abstract
The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form.
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Affiliation(s)
- Cory J Knoot
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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31
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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32
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Rhodes CJ. The Role of ESR Spectroscopy in Advancing Catalytic Science: Some Recent Developments. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14297237081532] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent progress is surveyed in regard to the importance of molecular species containing unpaired electrons in catalytic systems, as revealed using ESR spectroscopy. The review begins with studies of enzymes and their role directly in biological systems, and then discusses investigations of various artificially created catalysts with potential human and environmental significance, including zeolites. Among the specific types of catalytic media considered are those for photocatalysis, water splitting, the degradation of environmental pollutants, hydrocarbon conversions, fuel cells, ionic liquids and sensor devices employing graphene. Studies of muonium-labelled radicals in zeolites are also reviewed, as a means for determining the dynamics of transient radicals in these nanoporous materials.
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33
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Liang AD, Lippard SJ. Single Turnover Reveals Oxygenated Intermediates in Toluene/o-Xylene Monooxygenase in the Presence of the Native Redox Partners. J Am Chem Soc 2015; 137:10520-3. [PMID: 26267757 DOI: 10.1021/jacs.5b07055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Toluene/o-xylene monooxygenase (ToMO) is a non-heme diiron protein that activates O2 for subsequent arene oxidation. ToMO utilizes four protein components, a catalytic hydroxylase, a regulatory protein, a Rieske protein, and a reductase. O2 activation and substrate hydroxylation in the presence of all four protein components is examined. These studies demonstrate the importance of native reductants by revealing reactivity unobserved when dithionite and mediators are used as the reductant. This reactivity is compared with that of other O2-activating diiron enzymes.
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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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34
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Abstract
Methane monooxygenases (MMOs) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. As potential targets for new gas-to-liquid methane bioconversion processes, MMOs have attracted intense attention in recent years. There are two distinct types of MMO, a soluble, cytoplasmic MMO (sMMO) and a membrane-bound, particulate MMO (pMMO). Both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mechanisms are completely different. This Current Topic review article focuses on the overall architectures, active site structures, substrate reactivities, protein-protein interactions, and chemical mechanisms of both MMOs, with an emphasis on fundamental aspects. In addition, recent advances, including new details of interactions between the sMMO components, characterization of sMMO intermediates, and progress toward understanding the pMMO metal centers are highlighted. The work summarized here provides a guide for those interested in exploiting MMOs for biotechnological applications.
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Affiliation(s)
- Sarah Sirajuddin
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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35
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Abstract
A kinetic and spectroscopic characterization of the ferryl intermediate (APO-II) from APO, the heme-thiolate peroxygenase from Agrocybe aegerita, is described. APO-II was generated by reaction of the ferric enzyme with metachloroperoxybenzoic acid in the presence of nitroxyl radicals and detected with the use of rapid-mixing stopped-flow UV-visible (UV-vis) spectroscopy. The nitroxyl radicals served as selective reductants of APO-I, reacting only slowly with APO-II. APO-II displayed a split Soret UV-vis spectrum (370 nm and 428 nm) characteristic of thiolate ligation. Rapid-mixing, pH-jump spectrophotometry revealed a basic pKa of 10.0 for the Fe(IV)-O-H of APO-II, indicating that APO-II is protonated under typical turnover conditions. Kinetic characterization showed that APO-II is unusually reactive toward a panel of benzylic C-H and phenolic substrates, with second-order rate constants for C-H and O-H bond scission in the range of 10-10(7) M(-1)⋅s(-1). Our results demonstrate the important role of the axial cysteine ligand in increasing the proton affinity of the ferryl oxygen of APO intermediates, thus providing additional driving force for C-H and O-H bond scission.
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36
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Banerjee R, Proshlyakov Y, Lipscomb JD, Proshlyakov DA. Structure of the key species in the enzymatic oxidation of methane to methanol. Nature 2015; 518:431-4. [PMID: 25607364 PMCID: PMC4429310 DOI: 10.1038/nature14160] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Methane monooxygenase (MMO) catalyses the O2-dependent conversion of methane to methanol in methanotrophic bacteria, thereby preventing the atmospheric egress of approximately one billion tons of this potent greenhouse gas annually. The key reaction cycle intermediate of the soluble form of MMO (sMMO) is termed compound Q (Q). Q contains a unique dinuclear Fe(IV) cluster that reacts with methane to break an exceptionally strong 105 kcal mol(-1) C-H bond and insert one oxygen atom. No other biological oxidant, except that found in the particulate form of MMO, is capable of such catalysis. The structure of Q remains controversial despite numerous spectroscopic, computational and synthetic model studies. A definitive structural assignment can be made from resonance Raman vibrational spectroscopy but, despite efforts over the past two decades, no vibrational spectrum of Q has yet been obtained. Here we report the core structures of Q and the following product complex, compound T, using time-resolved resonance Raman spectroscopy (TR(3)). TR(3) permits fingerprinting of intermediates by their unique vibrational signatures through extended signal averaging for short-lived species. We report unambiguous evidence that Q possesses a bis-μ-oxo diamond core structure and show that both bridging oxygens originate from O2. This observation strongly supports a homolytic mechanism for O-O bond cleavage. We also show that T retains a single oxygen atom from O2 as a bridging ligand, while the other oxygen atom is incorporated into the product. Capture of the extreme oxidizing potential of Q is of great contemporary interest for bioremediation and the development of synthetic approaches to methane-based alternative fuels and chemical industry feedstocks. Insight into the formation and reactivity of Q from the structure reported here is an important step towards harnessing this potential.
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Affiliation(s)
- Rahul Banerjee
- 1] Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA [2] Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Yegor Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - John D Lipscomb
- 1] Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA [2] Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Denis A Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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37
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Makris TM, Vu VV, Meier KK, Komor AJ, Rivard BS, Münck E, Que L, Lipscomb JD. An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway. J Am Chem Soc 2015; 137:1608-17. [PMID: 25564306 PMCID: PMC4318726 DOI: 10.1021/ja511649n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces venezuelae CmlI catalyzes the six-electron oxygenation of the arylamine precursor of chloramphenicol in a nonribosomal peptide synthetase (NRPS)-based pathway to yield the nitroaryl group of the antibiotic. Optical, EPR, and Mössbauer studies show that the enzyme contains a nonheme dinuclear iron cluster. Addition of O(2) to the diferrous state of the cluster results in an exceptionally long-lived intermediate (t(1/2) = 3 h at 4 °C) that is assigned as a peroxodiferric species (CmlI-peroxo) based upon the observation of an (18)O(2)-sensitive resonance Raman (rR) vibration. CmlI-peroxo is spectroscopically distinct from the well characterized and commonly observed cis-μ-1,2-peroxo (μ-η(1):η(1)) intermediates of nonheme diiron enzymes. Specifically, it exhibits a blue-shifted broad absorption band around 500 nm and a rR spectrum with a ν(O-O) that is at least 60 cm(-1) lower in energy. Mössbauer studies of the peroxo state reveal a diferric cluster having iron sites with small quadrupole splittings and distinct isomer shifts (0.54 and 0.62 mm/s). Taken together, the spectroscopic comparisons clearly indicate that CmlI-peroxo does not have a μ-η(1):η(1)-peroxo ligand; we propose that a μ-η(1):η(2)-peroxo ligand accounts for its distinct spectroscopic properties. CmlI-peroxo reacts with a range of arylamine substrates by an apparent second-order process, indicating that CmlI-peroxo is the reactive species of the catalytic cycle. Efficient production of chloramphenicol from the free arylamine precursor suggests that CmlI catalyzes the ultimate step in the biosynthetic pathway and that the precursor is not bound to the NRPS during this step.
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Affiliation(s)
- Thomas M. Makris
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Van V. Vu
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Anna J. Komor
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Brent S. Rivard
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
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38
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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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39
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Acheson JF, Bailey LJ, Elsen NL, Fox BG. Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system. Nat Commun 2014; 5:5009. [PMID: 25248368 PMCID: PMC4200526 DOI: 10.1038/ncomms6009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
Productive biomolecular recognition requires exquisite control of affinity and specificity. Accordingly, nature has devised many strategies to achieve proper binding interactions. Bacterial multicomponent monooxygenases provide a fascinating example, where a diiron hydroxylase must reversibly interact with both ferredoxin and catalytic effector in order to achieve electron transfer and O2 activation during catalysis. Because these two accessory proteins have distinct structures, and because the hydroxylase-effector complex covers the entire surface closest to the hydroxylase diiron centre, how ferredoxin binds to the hydroxylase has been unclear. Here we present high-resolution structures of toluene 4-monooxygenase hydroxylase complexed with its electron transfer ferredoxin and compare them with the hydroxylase-effector structure. These structures reveal that ferredoxin or effector protein binding produce different arrangements of conserved residues and customized interfaces on the hydroxylase in order to achieve different aspects of catalysis.
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Affiliation(s)
- Justin F Acheson
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Lucas J Bailey
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Nathaniel L Elsen
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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40
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Affiliation(s)
- John D Lipscomb
- From the Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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41
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Gelalcha FG. Biomimetic Iron-Catalyzed Asymmetric Epoxidations: Fundamental Concepts, Challenges and Opportunities. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300716] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Abstract
An overview is provided of the importance of molecular species containing unpaired electrons in catalytic systems, as revealed using ESR spectroscopy. The review aims to demonstrate the considerable extent of scientific progress that has been made in this broad topic during the past few decades. Studies of catalytically active surfaces, including zeolites, are surveyed, and the detection of radical species, formed as intermediates in their reactions, using matrix isolation and spin-trapping techniques. Radical cation formation in zeolites is discussed, and the employment of muon spin rotation and relaxation techniques to study the mobility of labelled radicals in various porous and catalytic media. Among the specific types of catalytic media considered are those for photocatalysis, water splitting, degradation of environmental pollutants, hydrocarbon conversions, fuel cells and sensor devices employing graphene. The review concludes with recent developments in the study of enzymes and their reactions, using ESR-based methods.
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43
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Aukema KG, Makris TM, Stoian SA, Richman JE, Münck E, Lipscomb JD, Wackett LP. Cyanobacterial aldehyde deformylase oxygenation of aldehydes yields n-1 aldehydes and alcohols in addition to alkanes. ACS Catal 2013; 3:2228-2238. [PMID: 24490119 PMCID: PMC3903409 DOI: 10.1021/cs400484m] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aldehyde-deformylating oxygenase (ADO) catalyzes O2-dependent release of the terminal carbon of a biological substrate, octadecanal, to yield formate and heptadecane in a reaction that requires external reducing equivalents. We show here that ADO also catalyzes incorporation of an oxygen atom from O2 into the alkane product to yield alcohol and aldehyde products. Oxygenation of the alkane product is much more pronounced with C9-10 aldehyde substrates, so that use of nonanal as the substrate yields similar amounts of octane, octanal, and octanol products. When using doubly-labeled [1,2-13C]-octanal as the substrate, the heptane, heptanal and heptanol products each contained a single 13C-label in the C-1 carbons atoms. The only one-carbon product identified was formate. [18O]-O2 incorporation studies demonstrated formation of [18O]-alcohol product, but rapid solvent exchange prevented similar determination for the aldehyde product. Addition of [1-13C]-nonanol with decanal as the substrate at the outset of the reaction resulted in formation of [1-13C]-nonanal. No 13C-product was formed in the absence of decanal. ADO contains an oxygen-bridged dinuclear iron cluster. The observation of alcohol and aldehyde products derived from the initially formed alkane product suggests a reactive species similar to that formed by methane monooxygenase (MMO) and other members of the bacterial multicomponent monooxygenase family. Accordingly, characterization by EPR and Mössbauer spectroscopies shows that the electronic structure of the ADO cluster is similar, but not identical, to that of MMO hydroxylase component. In particular, the two irons of ADO reside in nearly identical environments in both the oxidized and fully reduced states, whereas those of MMOH show distinct differences. These favorable characteristics of the iron sites allow a comprehensive determination of the spin Hamiltonian parameters describing the electronic state of the diferrous cluster for the first time for any biological system. The nature of the diiron cluster and the newly recognized products from ADO catalysis hold implications for the mechanism of C-C bond cleavage.
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Affiliation(s)
- Kelly G. Aukema
- BioTechnology Institute University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas M. Makris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Sebastian A. Stoian
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Jack E. Richman
- BioTechnology Institute University of Minnesota, St. Paul, Minnesota 55108
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence P. Wackett
- BioTechnology Institute University of Minnesota, St. Paul, Minnesota 55108
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
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