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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 PMCID: PMC7457426 DOI: 10.1021/jacs.0c05613] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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, Sweden
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jason C. Jones
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Cindy C. Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Esra Bozkurt
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, 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, UK
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Stephen Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - 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 U.S.A
| | - Franklin D. Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025 U.S.A
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, 94025 U.S.A
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0FA, UK
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391 U.S.A
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 U.S.A
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
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Iwasaki T, Kappl R, Bracic G, Shimizu N, Ohmori D, Kumasaka T. ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization. J Biol Inorg Chem 2011; 16:923-35. [PMID: 21647778 DOI: 10.1007/s00775-011-0793-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 05/16/2011] [Indexed: 12/11/2022]
Abstract
The crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB), probably involved in the de novo iron-sulfur cluster biosynthesis (ISC) system of Pseudomonas putida JCM 20004, was determined at 1.90-Å resolution and displayed a novel tail-to-tail dimeric form. P. putida FdxB lacks the consensus free cysteine usually present near the cluster of ISC-like ferredoxins, indicating its primarily electron transfer role in the iron-sulfur cluster. Orientation-selective electron-nuclear double resonance spectroscopic analysis of reduced FdxB in conjunction with the crystal structure has identified the innermost Fe2 site with a high positive spin population as the nonreducible iron retaining the Fe(3+) valence and the outermost Fe1 site as the reduced iron with a low negative spin density. The average g (max) direction is skewed, forming an angle of about 27.3° (±4°) with the normal of the [2Fe-2S] plane, whereas the g (int) and g (min) directions are distributed in the cluster plane, presumably tilted by the same angle with respect to this plane. These results are related to those for other [2Fe-2S] proteins in different electron transport chains (e.g. adrenodoxin) and suggest a significant distortion of the electronic structure of the reduced [2Fe-2S] cluster under the influence of the protein environment around each iron site in general.
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Affiliation(s)
- Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.
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Tumanova LV, Tukhvatullin IA, Burbaev DS, Gvozdev RI, Andersson KK. The binuclear iron site of membrane-bound methane hydroxylase from Methylococcus capsulatus (Strain M). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 34:194-203. [DOI: 10.1134/s1068162008020064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dutta TK, Chakraborty J, Roy M, Ghosal D, Khara P, Gunsalus IC. Cloning and characterization of a p-cymene monooxygenase from Pseudomonas chlororaphis subsp. aureofaciens. Res Microbiol 2010; 161:876-82. [DOI: 10.1016/j.resmic.2010.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/05/2010] [Indexed: 10/18/2022]
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Davydov R, Hoffman BM. EPR and ENDOR studies of Fe(II) hemoproteins reduced and oxidized at 77 K. J Biol Inorg Chem 2007; 13:357-69. [PMID: 18058139 DOI: 10.1007/s00775-007-0328-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 11/14/2007] [Indexed: 11/24/2022]
Abstract
gamma-irradiation of frozen solutions of Fe(II) hemoproteins at 77 K generates both electron paramagnetic resonance (EPR) active singly reduced and oxidized heme centers trapped in the conformation of the Fe(II) precursors. The reduction products of pentacoordinate (S = 2) Fe(II) globins, peroxidases and cytochrome P450cam show EPR and electron-nuclear double resonance (ENDOR) spectra characteristic of (3d 7) Fe(I) species. In addition, cryoreduced Fe(II) alpha-chains of hemoglobin and myoglobin exhibit an S = 3/2 spin state produced by antiferromagnetic coupling between a porphyrin anion radical and pentacoordinate (S = 2) Fe(II). The spectra of cryoreduced forms of Fe(II) hemoglobin alpha-chains and deoxymyoglobin reveal that the Fe(II) precursors adopt multiple conformational substates. Reduction of hexacoordinate Fe(II) cytochrome c and cytochrome b5 as well as carboxy complexes of deoxyglobins produces only Fe(II) porphyrin pi-anion radical species. The low-valent hemoprotein intermediates produced by cryoreduction convert to the Fe(II) states at T > 200 K. Cryogenerated Fe(III) cytochrome c and cytochrome b5 have spectra similar to these for the resting Fe(III) states, whereas the spectra of the products of cryooxidation of pentacoordinate Fe(II) globins and peroxidases are different. Cryooxidation of CO-Fe(II) globins generates Fe(III) hemes with quantum-mechanically admixed S = 3/2, 5/2 ground states. The trapped Fe(III) species relax to the equilibrium ferric states upon annealing at T > 190 K. Both cryooxidized and reduced centers provide very sensitive EPR/ENDOR structure probes of the EPR-silent Fe(II) state.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Tech K148, Evanston, IL 60208-3113, USA.
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Sazinsky MH, LeMoine B, Orofino M, Davydov R, Bencze KZ, Stemmler TL, Hoffman BM, Argüello JM, Rosenzweig AC. Characterization and structure of a Zn2+ and [2Fe-2S]-containing copper chaperone from Archaeoglobus fulgidus. J Biol Chem 2007; 282:25950-9. [PMID: 17609202 PMCID: PMC2859431 DOI: 10.1074/jbc.m703311200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial CopZ proteins deliver copper to P1B-type Cu+-ATPases that are homologous to the human Wilson and Menkes disease proteins. The genome of the hyperthermophile Archaeoglobus fulgidus encodes a putative CopZ copper chaperone that contains an unusual cysteine-rich N-terminal domain of 130 amino acids in addition to a C-terminal copper binding domain with a conserved CXXC motif. The N-terminal domain (CopZ-NT) is homologous to proteins found only in extremophiles and is the only such protein that is fused to a copper chaperone. Surprisingly, optical, electron paramagnetic resonance, and x-ray absorption spectroscopic data indicate the presence of a [2Fe-2S] cluster in CopZ-NT. The intact CopZ protein binds two copper ions, one in each domain. The 1.8 A resolution crystal structure of CopZ-NT reveals that the [2Fe-2S] cluster is housed within a novel fold and that the protein also binds a zinc ion at a four-cysteine site. CopZ can deliver Cu+ to the A. fulgidus CopA N-terminal metal binding domain and is capable of reducing Cu2+ to Cu+. This unique fusion of a redox-active domain with a CXXC-containing copper chaperone domain is relevant to the evolution of copper homeostatic mechanisms and suggests new models for copper trafficking.
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Affiliation(s)
- Matthew H. Sazinsky
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Benjamin LeMoine
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Maria Orofino
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Roman Davydov
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Krisztina Z. Bencze
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Brian M. Hoffman
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - José M. Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Amy C. Rosenzweig
- Department of Biochemistry, Molecular Biology, and Cell Biology and Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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Zhang J, Wallar BJ, Popescu CV, Renner DB, Thomas DD, Lipscomb JD. Methane monooxygenase hydroxylase and B component interactions. Biochemistry 2006; 45:2913-26. [PMID: 16503646 DOI: 10.1021/bi052256t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interaction of the soluble methane monooxygenase regulatory component (MMOB) and the active site-bearing hydroxylase component (MMOH) is investigated using spin and fluorescent probes. MMOB from Methylosinus trichosporium OB3b is devoid of cysteine. Consequently, site-directed mutagenesis was used to incorporate single cysteine residues, allowing specific placement of the probe molecules. Sixteen MMOB Cys mutants were prepared and labeled with the EPR spin probe 4-maleimido-2,2,6,6-tetramethyl-1-piperidinyloxy (MSL). Spectral evaluation of probe mobility and accessibility to the hydrophilic spin-relaxing agent NiEDDA showed that both properties decrease dramatically for a subset of the spin labels as the complex with MMOH forms, thereby defining the likely interaction surface on MMOB. This surface contains MMOB residue T111 thought to play a role in substrate access into the MMOH active site. The surface also contains several hydrophilic residues and is ringed by charged residues. The surface of MMOB opposite the proposed binding surface is highly charged, consistent with solvent exposure. Probes of both of the disordered N- and C-terminal regions remain highly mobile and exposed to solvent in the MMOH complex. Spin-labeling studies show that residue A62 of MMOB is located in a position where it can be used to monitor MMOH-MMOB complex formation without perturbing the process. Accordingly, steady-state kinetic assays show that it can be changed to Cys (A62C) and labeled with the fluorescent probes 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) or 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (1,5-IAEDANS) without loss of the ability of MMOB to promote turnover. The BADAN fluorescence is partially quenched and red shifted as the complex with MMOH forms, allowing affinity measurements. It is shown that the high affinity of labeled MMOB (K(D) = 13.5 nM at pH 6.6, 25 degrees C) for the oxidized MMOH decreases substantially with increasing pH and increasing ionic strength but is nearly unaffected by addition of nonionic detergents. Similarly, the fluorescence anisotropy of the 1,5-IAEDANS-labeled A62C-MMOH complex is perturbed by salts but not nonionic detergents. This suggests that the MMOB-MMOH complex is stabilized by electrostatic interactions consistent with the characteristics of the proposed binding surface. Reduction of MMOH results in a 2-3 order of magnitude decrease in the affinity of the BADAN-labeled A62C-MMOB-MMOH complex, consistent with previous indications of structural change associated with reduction of the active site dinuclear iron cluster. Utilizing BADAN-labeled MMOB, the association and dissociation rate constants for the MMOB-MMOH binding reaction were determined and found to be consistent with a two-step process, possibly involving rapid association followed by a slower conformational change. The latter may be related to the regulation of substrate access into the active site of MMOH.
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Affiliation(s)
- Jingyan Zhang
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Dalton H. The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria. Philos Trans R Soc Lond B Biol Sci 2005; 360:1207-22. [PMID: 16147517 PMCID: PMC1569495 DOI: 10.1098/rstb.2005.1657] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2000] [Accepted: 12/17/2004] [Indexed: 11/12/2022] Open
Abstract
Methane gas is produced from many natural and anthropogenic sources. As such, methane gas plays a significant role in the Earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. As with nearly all other naturally produced organic molecules on Earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. The microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. Although anaerobic methanotrophs are believed to exist, so far, none have been isolated in pure culture. Methanotrophs have been known to exist for over 100 years; however, it is only in the last 30 years that we have begun to understand their physiology and biochemistry. Their unique ability to use methane for growth is attributed to the presence of a multicomponent enzyme system-methane monooxygenase (MMO)-which has two distinct forms: soluble (sMMO) and membrane-associated (pMMO); however, both convert methane into the readily assimilable product, methanol. Our understanding of how bacteria are capable of effecting one of the most difficult reactions in chemistry-namely, the controlled oxidation of methane to methanol-has been made possible by the isolation, in pure form, of the enzyme components.The mechanism by which methane is activated by sMMO involves abstraction of a hydrogen atom from methane by a high-valence iron species (FeIV or possibly FeV) in the hydroxylase component of the MMO complex to form a methyl radical. The radical combines with a captive oxygen atom from dioxygen to form the reaction product, methanol, which is further metabolized by the cell to produce multicarbon intermediates. Regulation of the sMMO system relies on the remarkable properties of an effector protein, protein B. This protein is capable of facilitating component interactions in the presence of substrate, modifying the redox potential of the diiron species at the active site. These interactions permit access of substrates to the hydroxylase, coupling electron transfer by the reductase with substrate oxidation and affecting the rate and regioselectivity of the overall reaction. The membrane-associated form is less well researched than the soluble enzyme, but is known to contain copper at the active site and probably iron. From an applied perspective, methanotrophs have enjoyed variable successes. Whole cells have been used as a source of single-cell protein (SCP) since the 1970s, and although most plants have been mothballed, there is still one currently in production. Our earlier observations that sMMO was capable of inserting an oxygen atom from dioxygen into a wide variety of hydrocarbon (and some non-hydrocarbon) substrates has been exploited to either produce value added products (e.g. epoxypropane from propene), or in the bioremediation of pollutants such as chlorinated hydrocarbons. Because we have shown that it is now possible to drive the reaction using electricity instead of expensive chemicals, there is promise that the system could be exploited as a sensor for any of the substrates of the enzyme.
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Affiliation(s)
- Howard Dalton
- Department of Biological Sciences, University of Warwick, Coventry, UK.
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Baik MH, Newcomb M, Friesner RA, Lippard SJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev 2003; 103:2385-419. [PMID: 12797835 DOI: 10.1021/cr950244f] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Brazeau BJ, Lipscomb JD. Key amino acid residues in the regulation of soluble methane monooxygenase catalysis by component B. Biochemistry 2003; 42:5618-31. [PMID: 12741818 DOI: 10.1021/bi027429i] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The regulatory component MMOB of soluble methane monooxygenase (sMMO) has been hypothesized to control access of substrates into the active site of the hydroxylase component (MMOH) through formation of a size specific channel or region of increased structural flexibility tuned to methane and O(2). Accordingly, a decrease in the size of four MMOB residues (N107G/S109A/S110A/T111A, the Quad mutant) was shown to accelerate the reaction of substrates larger than methane with the reactive MMOH intermediate Q [Wallar, B. J., and Lipscomb, J. D. (2001) Biochemistry 40, 2220-2233]. Here, this hypothesis is tested by construction of single and double mutations involving the residues of the Quad mutant. It is shown that mutations of residues that extend into the core structure of MMOB alter many aspects of the MMOH catalyzed reaction but do not mimic the effects of the Quad mutant. In contrast, the MMOB residues that are thought to form part of the interface in the MMOH-MMOB complex increase active site accessibility as observed for the Quad mutant. In particular, the mutant T111A mimics most of the effects of the Quad mutant; thus, Thr111 is proposed to most directly control access. Unexpectedly, mutation of Thr111 to the larger Tyr greatly increases the rate constant for the reaction of larger substrates such as ethane, furan, and nitrobenzene with Q while decreasing the rate constant for the reaction with methane. Other steps in the cycle are dramatically slowed, the regiospecificity for nitrobenzene oxidation is altered, and 10-fold more T111Y than wild-type MMOB is required to maximize the rate of turnover. Thus, T111Y appears to make a more extensive change in local interface structure that allows hydrocarbons at least as large as ethane to bind and react with Q similarly. As a result, the bond cleavage rates for methane, ethane, and their deuterated analogues are shown for the first time to correlate with bond strength in accord with a mechanism in which C-H bond cleavage occurs during reaction of substrates with Q.
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Affiliation(s)
- Brian J Brazeau
- Department of Biochemistry, Molecular Biology, and Biophysics, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Callaghan AJ, Smith TJ, Slade SE, Dalton H. Residues near the N-terminus of protein B control autocatalytic proteolysis and the activity of soluble methane mono-oxygenase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1835-43. [PMID: 11952785 DOI: 10.1046/j.1432-1033.2002.02829.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Soluble methane mono-oxygenase (sMMO) of Methylococcus capsulatus (Bath) catalyses the O2-dependent and NAD(P)H-dependent oxygenation of methane and numerous other substrates. During purification, the sMMO enzyme complex, which comprises three components and has a molecular mass in excess of 300 kDa, becomes inactivated because of cleavage of just 12 amino acids from the N-terminus of protein B, which is the smallest component of sMMO and the only one without prosthetic groups. Here we have shown that cleavage of protein B, to form the inactive truncated protein B', continued to occur when intact protein B was repeatedly separated from protein B' and all detectable contaminants, giving compelling evidence that the protein was cleaved autocatalytically. The rate of autocatalytic cleavage decreased when the residues flanking the cleavage site were mutated, but the position of cleavage was unaltered. Analysis of a series of incremental truncates showed that residue(s) essential for the activity of sMMO, and important in determining the stability of protein B, lay in the region Ser4-Tyr7. Protein B was shown to possess intrinsic nucleophilic activity, which we propose initiates the cleavage reaction via a novel mechanism. Proteins B and B' were detected in approximately equal amounts in the cell, showing that truncation of protein B is biologically relevant. Increasing the growth-medium copper concentration, which inactivates sMMO, did not alter the extent of in vivo cleavage, therefore the conditions under which cleavage of protein B may fulfil its proposed role as a regulator of sMMO remain to be identified.
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Mitchell KH, Studts JM, Fox BG. Combined participation of hydroxylase active site residues and effector protein binding in a para to ortho modulation of toluene 4-monooxygenase regiospecificity. Biochemistry 2002; 41:3176-88. [PMID: 11863457 DOI: 10.1021/bi012036p] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Toluene 4-monooxygenase (T4MO) is a diiron hydroxylase that exhibits high regiospecificity for para hydroxylation. This fidelity provides the basis for an assessment of the interplay between active site residues and protein complex formation in producing an essential biological outcome. The function of the T4MO catalytic complex (hydroxylase, T4moH, and effector protein T4moD) is evaluated with respect to effector protein concentration, the presence of T4MO electron-transfer components (Rieske ferredoxin, T4moC, and NADH oxidoreductase), and use of mutated T4moH isoforms with different hydroxylation regiospecificities. Steady-state kinetic analyses indicate that T4moC and T4moD form complexes of similar affinity with T4moH. At low T4moD concentrations, the steady-state hydroxylation rate is linearly dependent on T4moD-T4moH complex formation, whereas regiospecificity and the coupling efficiency between NADH consumption and hydroxylation are associated with intrinsic properties of the T4moD-T4moH complex. The optimized complex gives both efficient coupling and high regiospecificity with p-cresol representing >96% of total products from toluene. Similar coupling and regiospecificity for para hydroxylation are obtained with T3buV (an effector protein from a toluene 3-monooxygenase), demonstrating that effector protein binding does not uniquely determine or alter the regiospecificity of toluene hydroxylation. The omission of T4moD causes an approximately 20-fold decrease in hydroxylation rate, nearly complete uncoupling, and a decrease in regiospecificity so that p-cresol represents approximately 60% of total products. Similar shifts in regiospecificity are observed in oxidations of alternative substrates in the absence or upon the partial removal of either T4moD or T3buV from toluene oxidations. The mutated T4moH isoforms studied have apparent V(max)/K(M) specificities differing by approximately 2-4-fold and coupling efficiencies ranging from 88% to 95%, indicating comparable catalytic function, but also exhibit unique regiospecificity patterns for all substrates tested, suggesting unique substrate binding preferences within the active site. The G103L isoform has enhanced selectivity for ortho hydroxylation with all substrates tested except nitrobenzene, which gives only m-nitrophenol. The regiospecificity of the G103L isoform is comparable to that observed from naturally occurring variants of the toluene/benzene/o-xylene monooxygenase subfamily. Evolutionary and mechanistic implications of these findings are considered.
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Affiliation(s)
- Kevin H Mitchell
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706-1544, USA
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14
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Merkx M, Lippard SJ. Why OrfY? Characterization of MMOD, a long overlooked component of the soluble methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem 2002; 277:5858-65. [PMID: 11709550 DOI: 10.1074/jbc.m107712200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) has been studied intensively to understand the mechanism by which it catalyzes the remarkable oxidation of methane to methanol. The cluster of genes that encode for the three characterized protein components of sMMO (MMOH, MMOB, and MMOR) contains an additional open reading frame (orfY) of unknown function. In the present study, MMOD, the protein encoded by orfY, was overexpressed as a fusion protein in Escherichia coli. Pure MMOD was obtained in high yields after proteolytic cleavage and a two-step purification procedure. Western blot analysis of Methylococcus capsulatus (Bath) soluble cell extracts showed that MMOD is expressed in the native organism although at significantly lower levels than the other sMMO proteins. The cofactorless MMOD protein is a potent inhibitor of sMMO activity and binds to the hydroxylase protein (MMOH) with an affinity similar to that of MMOB and MMOR. The addition of up to 2 MMOD per MMOH results in changes in the optical spectrum of the hydroxylase that suggest the formation of a (micro-oxo)diiron(III) center in a fraction of the MMOH-MMOD complexes. Possible functions for MMOD are discussed, including a role in the assembly of the MMOH diiron center similar to that suggested for DmpK, a protein that shares some properties with MMOD.
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Affiliation(s)
- Maarten Merkx
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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15
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Brazeau BJ, Wallar BJ, Lipscomb JD. Unmasking of deuterium kinetic isotope effects on the methane monooxygenase compound Q reaction by site-directed mutagenesis of component B. J Am Chem Soc 2001; 123:10421-2. [PMID: 11604007 DOI: 10.1021/ja016632i] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B J Brazeau
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis University of Minnesota, Minneapolis 55455, USA
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16
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3773(20010803)40:15%3c2782::aid-anie2782%3e3.0.co;2-p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Aktivierung von Disauerstoff und Hydroxylierung von Methan durch lösliche Methan-Monooxygenase: eine Geschichte von zwei Eisenatomen und drei Proteinen. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010803)113:15<2860::aid-ange2860>3.0.co;2-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, Lippard SJ. Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins. Angew Chem Int Ed Engl 2001; 40:2782-2807. [PMID: 29711993 DOI: 10.1002/1521-3773(20010803)40:15<2782::aid-anie2782>3.0.co;2-p] [Citation(s) in RCA: 461] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2001] [Revised: 05/03/2001] [Indexed: 11/11/2022]
Affiliation(s)
- Maarten Merkx
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Daniel A Kopp
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Matthew H Sazinsky
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Jessica L Blazyk
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Jens Müller
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
| | - Stephen J Lippard
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue 18-590 Cambridge, MA 02139 (USA) Fax: (+1) 617-258-8150
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19
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Telser J, Davydov R, Horng YC, Ragsdale SW, Hoffman BM. Cryoreduction of methyl-coenzyme M reductase: EPR characterization of forms, MCR(ox1) and MCR (red1). J Am Chem Soc 2001; 123:5853-60. [PMID: 11414817 DOI: 10.1021/ja010428d] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the formation of methyl-coenzyme M (CH(3)S-CH(2)CH(2)SO(3)) from methane. The active site is a nickel tetrahydrocorphinoid cofactor, factor 430, which in inactive form contains EPR-silent Ni(II). Two such forms, denoted MCR(silent) and MCR(ox1)(-)(silent), were previously structurally characterized by X-ray crystallography. We describe here the cryoreduction of both of these MCR forms by gamma-irradiation at 77 K, which yields reduced protein maintaining the structure of the oxidized starting material. Cryoreduction of MCR(silent) yields an EPR signal that strongly resembles that of MCR(red1), the active form of MCR; and stepwise annealing to 260-270 K leads to formation of MCR(red1). Cryoreduction of MCR(ox1)(-)(silent) solutions shows that our preparative method for this state yields enzyme that contains two major forms. One behaves similarly to MCR(silent), as shown by the observation that both of these forms give essentially the same redlike EPR signals upon cryoreduction, both of which give MCR(red1) upon annealing. The other form is assigned to the crystallographically characterized MCR(ox1)(-)(silent) and directly gives MCR(ox1) upon cryoreduction. X-band spectra of these cryoreduced samples, and of conventionally prepared MCR(red1) and MCR(ox1), all show resolved hyperfine splitting from four equivalent nitrogen ligands with coupling constants in agreement with those determined in previous EPR studies and from (14)N ENDOR of MCR(red1) and MCR(ox1). These experiments have confirmed that all EPR-visible forms of MCR contain Ni(I) and for the first time generated in vitro the EPR-visible, enzymatically active MCR(red1) and the activate-able "ready" MCR(ox1) from "silent" precursors. Because the solution Ni(II) species we assign as MCR(ox1)(-)(silent) gives as its primary cryoreduction product the Ni(I) state MCR(ox1), previous crystallographic data on MCR(ox1)(-)(silent) allow us to identify the exogenous axial ligand in MCR(ox1) as the thiolate from CoM; the cryoreduction experiments further allow us to propose possible axial ligands in MCR(red1). The availability of model compounds for MCR(red1) and MCR(ox1) also is discussed.
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Affiliation(s)
- J Telser
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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20
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Brazeau BJ, Lipscomb JD. Electron transfer and radical forming reactions of methane monooxygenase. Subcell Biochem 2001; 35:233-77. [PMID: 11192723 DOI: 10.1007/0-306-46828-x_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- B J Brazeau
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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21
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Krebs C, Davydov R, Baldwin J, Hoffman BM, Bollinger, JM, Huynh BH. Mössbauer and EPR Characterization of the S = 9/2 Mixed-Valence Fe(II)Fe(III) Cluster in the Cryoreduced R2 Subunit of Escherichia coli Ribonucleotide Reductase. J Am Chem Soc 2000. [DOI: 10.1021/ja000317z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carsten Krebs
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Roman Davydov
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jeff Baldwin
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Brian M. Hoffman
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger,
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Boi Hanh Huynh
- Contributions from the Department of Physics, Rollins Research Center, Emory University, Atlanta, Georgia 30322, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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22
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Cadieux E, Powlowski J. Characterization of active and inactive forms of the phenol hydroxylase stimulatory protein DmpM. Biochemistry 1999; 38:10714-22. [PMID: 10451366 DOI: 10.1021/bi990835q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stimulatory protein DmpM of phenol hydroxylase from methylphenol-degrading Pseudomonas sp. strain CF600 has been found to exist in two forms. DmpM purified from the native strain was mostly active in stimulating phenol hydroxylase activity, whereas an inactive form accumulated in a recombinant strain. Both forms exhibited a molecular mass of 10 361.3 +/- 1.3 Da by electrospray mass spectrometry, but nondenaturing gel filtration showed molecular masses of 31 600 Da for the inactive form and 11 500 Da for the active form. Cross-linking and sedimentation velocity results were consistent with the inactive form being a dimer. Partial thermal or chemical denaturation, or treatment with trifluoroethanol, readily activated dimeric DmpM. A combination of circular dichroism and fluorescence spectroscopies, activity assays, and native and urea gel electrophoresis were used to further characterize reactivation with urea. These results showed that dissociation of the dimeric form of DmpM precedes denaturation at low protein concentrations and results in activation. The same concentration of urea that effects dissociation also converts the monomeric form to a different conformation.
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Affiliation(s)
- E Cadieux
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
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23
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Telser J, Davydov R, Kim CH, Adams MWW, Hoffman BM. Investigation of the Unusual Electronic Structure of Pyrococcus furiosus 4Fe Ferredoxin by EPR Spectroscopy of Protein Reduced at Ambient and Cryogenic Temperatures. Inorg Chem 1999; 38:3550-3553. [PMID: 11671103 DOI: 10.1021/ic990209h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hyperthermophilic archaeon Pyrococcus furiosus contains a novel ferredoxin (Pf-Fd) in which, in the native 4Fe form, three of the Fe ions are coordinated to the protein by cysteinyl thiolato ligands, but the fourth Fe is coordinated by an aspartyl carboxylato ligand ([Fe(4)S(4)(cys)(3)(asp)](2)(-)(,3)(-)). Chemical reduction at ambient temperature of the oxidized 4Fe form (Pf-Fd 4Fe-ox, S = 0 ground state, with the cluster core indicated by [Fe(4)S(4)](2+)(ox)) produces a reduced 4Fe form (Pf-Fd 4Fe-red, with the cluster core indicated by [Fe(4)S(4)](+)(red)). Pf-Fd 4Fe-red, [Fe(4)S(4)](+)(red) core, in frozen solution exhibits S = (1)/(2) and (3)/(2) electronic states that are not in thermal equilibrium. The two spin states thus represent alternate ground states of the reduced cluster (cluster cores indicated by [Fe(4)S(4)](+)(red1) and [Fe(4)S(4)](+)(red2), respectively), rather than a ground and excited spin state. Low-temperature (77 K) reduction of 4Fe-ox in frozen solution by gamma-irradiation produces in high yield the reduced state of the cluster that is trapped in the structure of the oxidized parent cluster, and thus has a cluster core denoted by [Fe(4)S(4)](+)(ox). The [Fe(4)S(4)](+)(ox) form also exhibits non thermally converting S = (3)/(2) and (1)/(2) components in the same proportion as seen for [Fe(4)S(4)](+)(red). The EPR signal of the S = (3)/(2) component that results from cryoreduction ([Fe(4)S(4)](+)(ox2)) is indistinguishable, within experimental variability, from that seen in the ambient-temperature, chemically reduced protein ([Fe(4)S(4)](+)(red2)), and the signals of the two S = (1)/(2) components ([Fe(4)S(4)](+)(ox1) and [Fe(4)S(4)](+)(red1), respectively) closely resemble each other, although they are not identical. Previous NMR studies at ambient temperature showed evidence for only one species in fluid solution for both Pf-Fd 4Fe-ox and 4Fe-red. Taken together, the NMR and EPR results indicate that fluid solutions of either oxidized or reduced Pf-Fd contain only one conformer, but that frozen solutions of each contain two distinct conformers, with each one of the pair of oxidized protein forms having a corresponding reduced form. A shift in the coordination mode of the aspartyl carboxylato ligand is proposed to account for this conformational flexibility.
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Affiliation(s)
- Joshua Telser
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
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24
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Gallagher SC, Callaghan AJ, Zhao J, Dalton H, Trewhella J. Global conformational changes control the reactivity of methane monooxygenase. Biochemistry 1999; 38:6752-60. [PMID: 10346895 DOI: 10.1021/bi982991n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present here X-ray scattering data that yield new structural information on the multicomponent enzyme methane monooxygenase and its components: a hydroxylase dimer, and two copies each of a reductase and regulatory protein B. Upon formation of the enzyme complex, the hydroxylase undergoes a dramatic conformational change that is observed in the scattering data as a fundamental change in shape of the scattering particle such that one dimension is narrowed (by 25% or 24 A) while the longest dimension increases (by 20% or 25 A). These changes also are reflected in a 13% increase in radius of gyration upon complex formation. Both the reductase and protein B are required for inducing the conformational change. We have modeled the scattering data for the complex by systematically modifying the crystal structure of the hydroxylase and using ellipsoids to represent the reductase and protein B components. Our model indicates that protein B plays a role in optimizing the interaction between the active centers of the reductase and hydroxylase components, thus, facilitating electron transfer between them. In addition, the model suggests reasons why the hydroxylase exists as a dimer and that a possible role for the outlying gamma-subunit may be to stabilize the complex through its interaction with the other components. We further show that proteolysis of protein B to form the inactive B' results in a conformational change and B' does not bind to the hydroxylase. The truncation thus could represent a regulatory mechanism for controlling the enzyme activity.
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Affiliation(s)
- S C Gallagher
- Chemical Science and Technology Division, Los Alamos National Laboratory, New Mexico 87544, USA
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25
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Dikanov SA, Davydov RM, Gräslund A, Bowman MK. Two-Dimensional ESEEM Spectroscopy of Nitrogen Hyperfine Couplings in Methemerythrin and Azidomethemerythrin. J Am Chem Soc 1998. [DOI: 10.1021/ja9742343] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergei A. Dikanov
- Contribution from Macromolecular Structure & Dynamics, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, the Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia, and the Department of Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Roman M. Davydov
- Contribution from Macromolecular Structure & Dynamics, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, the Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia, and the Department of Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Contribution from Macromolecular Structure & Dynamics, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, the Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia, and the Department of Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Michael K. Bowman
- Contribution from Macromolecular Structure & Dynamics, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, the Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia, and the Department of Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
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26
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Valentine AM, Tavares P, Pereira AS, Davydov R, Krebs C, Hoffman BM, Edmondson DE, Huynh BH, Lippard SJ. Generation of a Mixed-Valent Fe(III)Fe(IV) Form of Intermediate Q in the Reaction Cycle of Soluble Methane Monooxygenase, an Analog of Intermediate X in Ribonucleotide Reductase R2 Assembly. J Am Chem Soc 1998. [DOI: 10.1021/ja974169x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ann M. Valentine
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Pedro Tavares
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Alice S. Pereira
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Roman Davydov
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Carsten Krebs
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Brian M. Hoffman
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Dale E. Edmondson
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Boi Hanh Huynh
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
| | - Stephen J. Lippard
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Department of Chemistry, Northwestern University Evanston, Illinois 60208 Departments of Biochemistry, Chemistry, and Physics Emory University, Atlanta, Georgia 30322
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27
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Lloyd JS, Bhambra A, Murrell JC, Dalton H. Inactivation of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath) by proteolysis can be overcome by a Gly to Gln modification. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 248:72-9. [PMID: 9310362 DOI: 10.1111/j.1432-1033.1997.t01-1-00072.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The regulatory protein B of soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath), exists as a mixture of the full-length active form and truncated forms, B' and B". Electrospray ionisation mass spectrometry (ESI-MS) was used to identify a cleavage site between Met12 and Gly13, such that 12 amino acids were lost from the N-terminus of protein B. This truncate was designated B' and molecular masses were assigned to proteins B and B' of 15,852.6+/-0.4 Da and 14,629.5+/-0.3 Da, respectively. A cleavage site between Gln29 and Val30 was also identified such that 29 amino acids were lost from the N-terminus of protein B. This truncate was designated B" and had a molecular mass of 12,709.93+/-0.02 Da. Proteins B' and B" were found to be inactive in the sMMO system. Addition of protease inhibitors or the heterologous expression of protein B in various strains of lon-deficient or ompT-deficient Escherichia coli, did not inhibit B' formation. Expression of protein B as a glutathione S-transferase fusion protein and subsequent purification of protein B from E. coli using affinity chromatography resulted in preparations of protein B with higher enzyme activities than that of wild-type protein B. However, ESI-MS confirmed that protein B' was still present. Alteration of the Met12-Gly13 cleavage site to Met12-Gln13 revealed that the stability of G13Q at 20 degrees C and 37 degrees C was higher than that of wild-type preparations. ESI-MS indicated that protein B' was absent and could only be identified after prolonged incubation at room temperature. The amount of active protein B present in the cell may be controlled by protein B cleavage, thereby regulating electron transfer. Alternatively, it may allow protein B to maintain a certain conformation necessary for enzyme activity and this may control the activity of sMMO in response to the supply of methane to the cell.
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Affiliation(s)
- J S Lloyd
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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28
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Davydov RM, Davydov A, Ingemarson R, Thelander L, Ehrenberg A, Gräslund A. EPR study of the mixed-valent diiron sites in mouse and herpes simplex virus ribonucleotide reductases. Effect of the tyrosyl radical on structure and reactivity of the diferric center. Biochemistry 1997; 36:9093-100. [PMID: 9230041 DOI: 10.1021/bi9700375] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reduction of ribonucleotide reductase (EC 1.17.4.1) R2 proteins in a frozen glycerol-buffer solution at 77 K by mobile electrons generated by gamma-irradiation produces EPR-detectable iron sites in mixed-valent Fe(II)/Fe(III) states. The primary EPR signals give information about the ligand arrangement of the diferric form of the iron site, whereas secondary signals observed after annealing of the sample show the effects of structural relaxation. In recombinant metR2 proteins (without free radical) from mouse and herpes virus type 1, the mixed-valent sites trapped at 77 K give rise to axial S = 1/2 EPR spectra with g values in the range 1.79-1.94, observable at temperatures up to 110 K. The spectra are assigned to mu-oxo-bridged dinuclear iron sites. In mouse metR2, the primary EPR spectrum is a mixture of two components. Annealing the R2 samples to 160-170 K transforms the primary EPR signals into rhombic spectra, characterized by gav < 1.8, and observable only below 25 K. These spectra are assigned to partially relaxed forms with a mu-hydroxo bridge, formed by protonation of the oxo bridge. Further annealing at 220 K produces new rhombic EPR spectra, which are closely similar with those observed and found to be stable after chemical reduction at room temperature. The EPR signal of the primary mixed-valent iron site in active mouse R2 protein with a tyrosyl radical also has two components. Both are different from those observed in metR2. In herpes simplex virus type 1 protein R2, one primary mixed-valent component was observed for the met protein. The dose-yield curve for the mixed-valent state in active mouse R2 is sigmoidal in shape, indicating that the tyrosyl radical is reduced by mobile electrons before the iron site. Kinetic experiments on the reduction by dithionite on mouse R2 without and with radical show a significantly enhanced rate for reduction of the iron site in the protein without radical. The results suggest that in active mouse R2 only complete diferric sites with neighboring radicals give rise to the mixed-valent spectra, and that these sites may exist in two structurally distinct forms. The results on the mouse R2 proteins confirm and extend previous results obtained on the Escherichia coli protein R2 showing that the presence of the tyrosyl radical significantly affects not only the structure but also the reactivity of the iron site.
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Affiliation(s)
- R M Davydov
- Department of Biophysics, Stockholm University, Arrhenius Laboratory, Sweden
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