Structural and functional model of methane hydroxylase of membrane-bound methane monooxygenase from Methylococcus capsulatus (Bath)

Computer analysis of a wide range of primary sequences showed that -, -, and -peptides of membrane-bound methane hydroxylase contained 2, 7, and 6 transmembrane helices respectively. Conservative amino acid residues participating in complex formation were revealed. The - and -peptides are suggested to contain mononuclear copper ions with the ligand environment mainly consisting of His residues. The Cu sites are located in the hydrophilic region and are responsible for ESR signals. The active site of -peptide in which the activation of O₂ and oxidation of CH₄ occur is localized in the hydrophobic region close to the membrane surface. This site is formed by the amino acid residues of four transmembrane helices and one loop between them and is suggested to be a binuclear Cu—Fe or Fe—Fe center. The Cu site of -peptide transfers electrons to the active site of -peptide, and the Cu site of -peptide is either involved in this process or only stabilizes the protein structure.     

Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.

The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.     

Fourier transform infrared characterization of the azido complex of methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath)

The azido complex formed in oxidized methane monooxygenase from Methylococcus capsulatus (Bath) was investigated with resonance Raman and FTIR techniques. These experiments show the presence of a nuas(NNN) at approximately 2077 cm-1 which splits to two components at 2059 and 2073 cm-1 with 15N14N2. The vibrational data are assigned to an azido complex bound terminally to one iron(III) at the diiron center. When the azido complex is illuminated at 15 K, a new nuas(NNN) is observed at 2136 cm-1 which is assigned to a photodissociated HN3 within the substrate pocket. We propose a model where an aqua ligand engages a hydrogen bond interaction with the 1N atom of the azido group and acts as at a proton donor during the photolysis process.     

Mutational and structural analyses of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath).

BACKGROUND: The soluble methane monooxygenase (sMMO) system in methanotrophic bacteria uses three protein components to catalyze the selective oxidation of methane to methanol. The coupling protein B (MMOB) both activates the carboxylate-bridged diiron center in the hydroxylase (MMOH) for substrate oxidation and couples the reaction to electron transfer from NADH through the sMMO reductase. Although the X-ray structure of the hydroxylase is known, little structural information is available regarding protein B. RESULTS: Wild-type protein B from Methylococcus capsulatus (Bath) is very susceptible to degradation. The triple mutant protein B, Gly10-->Ala, Gly13-->Gln, Gly16-->Ala is resistant to degradation. Analyzing wild-type and mutant forms of protein B using size exclusion chromatography and circular dichroism spectroscopy suggests that the amino terminus of MMOB (Ser1-Ala25) is responsible for the proteolytic sensitivity and unusual mobility of the protein. We used the stable triple glycine protein B mutant to generate an affinity column for the hydroxylase and investigated the interaction between MMOH and MMOB. These results suggest the interaction is dominated by hydrophobic contacts. CONCLUSIONS: A structural model is presented for protein B that explains both its proclivity for degradation and its anomalous behavior during size exclusion chromatography. The model is consistent with previously published biophysical data, including the NMR structure of the phenol hydroxylase regulatory protein P2. Furthermore, this model allows for detailed and testable predictions about the structure of protein B and the role of proposed recognition sites for the hydroxylase.     

Reactions of the peroxo intermediate of soluble methane monooxygenase hydroxylase with ethers

Soluble methane monooxygenase (sMMO) isolated from Methylococcus capsulatus (Bath) utilizes a carboxylate-bridged diiron center and dioxygen to catalyze the conversion of methane to methanol. Previous studies revealed that a di(mu-oxo)diiron(IV) intermediate termed Q is responsible for the catalytic activity with hydrocarbons. In addition, the peroxodiiron(III) intermediate (H(peroxo)) that precedes Q formation in the catalytic cycle has been demonstrated to react with propylene, but its reactivity has not been extensively investigated. Given the burgeoning interest in the existence of multiple oxidants in metalloenzymes, a more exhaustive study of the reactivity of H(peroxo) was undertaken. The kinetics of single turnover reactions of the two intermediates with ethyl vinyl ether and diethyl ether were monitored by single- and double-mixing stopped-flow optical spectroscopy. For both substrates, the rate constants for reaction with H(peroxo) are greater than those for Q. An analytical model for explaining the transient kinetics is described and used successfully to fit the observed data. Activation parameters were determined through temperature-dependent studies, and the kinetic isotope effects for the reactions with diethyl ether were measured. The rate constants indicate that H(peroxo) is a more electrophilic oxidant than Q. We propose that H(peroxo) reacts via two-electron transfer mechanisms, and that Q reacts by single-electron transfer steps.     

Multiple polypeptide forms observed in two-dimensional gels of Methylococcus capsulatus (Bath) polypeptides are generated during the separation procedure

We have examined two-dimensional electrophoresis (2-DE) gel maps of polypeptides from the Gram-negative bacterium Methylococcus capsulatus (Bath) and found the same widespread trains of spots as often reported in 2-DE gels of polypeptides of other Gram-negative bacteria. Some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-DE, and not by covalent post-translational modifications. The trains were found to be regenerated when rerunning individual polypeptide spots. The polypeptides analysed giving this type of trains were all found to be classified as stable polypeptides according to the instability index of Guruprasad et al. (Protein Eng. 1990, 4, 155-161). The phenomenon most likely reflects conformational equilibria of polypeptides arising from the experimental conditions used, and is a clear drawback of the standard 2-DE procedure, making the gel picture unnecessarily complex to analyse.     

Component B binding to the soluble methane monooxygenase hydroxylase by saturation-recovery EPR spectroscopy of spin-labeled MMOB

Spin-labeled Cys89 of the soluble methane monooxygenase regulatory protein (MMOB) from Methylococcus capsulatus (Bath) binds within 15 +/- 4 A of the hydroxylase (MMOH) diiron center, placing the MMOB docking site in the MMOH "canyon" region on iron-coordinating helices E and F of the alpha-subunit.     

Intermolecular electron-transfer reactions in soluble methane monooxygenase: a role for hysteresis in protein function

Electron transfer from reduced nicotinamide adenine dinucleotide (NADH) to the hydroxylase component (MMOH) of soluble methane monooxygenase (sMMO) primes its non-heme diiron centers for reaction with dioxygen to generate high-valent iron intermediates that convert methane to methanol. This intermolecular electron-transfer step is facilitated by a reductase (MMOR), which contains [2Fe-2S] and flavin adenine dinucleotide (FAD) prosthetic groups. To investigate interprotein electron transfer, chemically reduced MMOR was mixed rapidly with oxidized MMOH in a stopped-flow apparatus, and optical changes associated with reductase oxidation were recorded. The reaction proceeds via four discrete kinetic phases corresponding to the transfer of four electrons into the two dinuclear iron sites of MMOH. Pre-equilibrating the hydroxylase with sMMO auxiliary proteins MMOB or MMOD severely diminishes electron-transfer throughput from MMOR, primarily by shifting the bulk of electron transfer to the slowest pathway. The biphasic reactions for electron transfer to MMOH from several MMOR ferredoxin analogues are also inhibited by MMOB and MMOD. These results, in conjunction with the previous finding that MMOB enhances electron-transfer rates from MMOR to MMOH when preformed MMOR-MMOH-MMOB complexes are allowed to react with NADH [Gassner, G. T.; Lippard, S. J. Biochemistry 1999, 38, 12768-12785], suggest that isomerization of the initial ternary complex is required for maximal electron-transfer rates. To account for the slow electron transfer observed for the ternary precomplex in this work, a model is proposed in which conformational changes imparted to the hydroxylase by MMOR are retained throughout the catalytic cycle. Several electron-transfer schemes are discussed with emphasis on those that invoke multiple interconverting MMOH populations.     

Product binding to the diiron(III) and mixed-valence diiron centers of methane monooxygenase hydroxylase studied by (1,2)H and (19)F ENDOR spectroscopy

The binding of ethanol and 1,1,1-trifluoroethanol (TFE) to both the H(mv) and H(ox) forms of soluble methane monooxygenase (sMMO) in solution has been studied by Q-band (35 GHz) CW and pulsed ENDOR spectroscopy of (1)H, (2)H and (19)F nuclei of exogenous ligands. As part of this investigation we introduce (19)F, in this case from bound TFE, as a new probe for the binding of small molecules to a metalloenzyme active site. The H(mv) form was prepared in solution by chemical reduction of H(ox). For study of H(ox) itself, frozen solutions were subjected to gamma-irradiation in the frozen solution state at 77 K, which affords an EPR-visible mixed-valent diiron center, denoted (H(ox))(mv), held in the geometry of the diiron(III) state. The (19)F and (2)H ENDOR spectra of bound TFE together with (1,2)H ENDOR spectra of bound ethanol indicate that the alcohols bind close to the Fe(II) ion of the mixed-valence cluster in H(mv) and in a bridging or semi-bridging fashion to H(ox). DMSO does not affect the binding of either of the ethanols or of methanol to H(ox), nor of ethanol or methanol to H(mv). It does, however, displace TFE from the diiron site in H(mv). These results provide the first evidence that crystal structures of sMMO hydroxylase into which product alcohols were introduced by diffusion represent the structures in solution.     

Intermediate Q from soluble methane monooxygenase hydroxylates the mechanistic substrate probe norcarane: evidence for a stepwise reaction.

Norcarane is a valuable mechanistic probe for enzyme-catalyzed hydrocarbon oxidation reactions because different products or product distributions result from concerted, radical, and cation based reactions. Soluble methane monooxygenase (sMMO) from Methylosinus trichosporium OB3b catalyzes the oxidation of norcarane to afford 3-hydroxymethylcyclohexene and 3-cycloheptenol, compounds characteristic of radical and cationic intermediates, respectively, in addition to 2- and 3-norcaranols. Past single turnover transient kinetic studies have identified several optically distinct intermediates from the catalytic cycle of the hydroxylase component of sMMO. Thus, the reaction between norcarane and key reaction intermediates can be directly monitored. The presence of norcarane increases the rate of decay of only one intermediate, the high-valent bis-mu-oxo Fe(IV)(2) cluster-containing species compound Q, showing that it is responsible for the majority of the oxidation chemistry. The observation of products from both radical and cationic intermediates from norcarane oxidation catalyzed by sMMO is consistent with a mechanism in which an initial substrate radical intermediate is formed by hydrogen atom abstraction. This intermediate then undergoes either oxygen rebound, intramolecular rearrangement followed by oxygen rebound, or loss of a second electron to yield a cationic intermediate to which OH(-) is transferred. The estimated lower limit of 20 ps for the lifetime of the putative radical intermediate is in accord with values determined from previous studies of sterically hindered sMMO probes.     

Synthetic analogue of the [Fe(2)(mu-OH)(2)(mu-O(2)CR)](3+) core of soluble methane monooxygenase hydroxylase via synthesis and dioxygen reactivity of carboxylate-bridged diiron(II) complexes

We describe the synthesis and dioxygen reactivity of diiron(II) tetracarboxylate complexes [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(N,N-Me(2)en)(2)] (2) and [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(N,N-Bn(2)en)(2)] (6), where Ar(Tol)CO(2)(-) = 2,6-di(p-tolyl)benzoate. These complexes were prepared as models for the diiron(II) center in the hydroxylase component of soluble methane monooxygenase (MMOH). Compound 6 reacts with dioxygen to afford PhCHO in approximately 60(5)% yield, following oxidative N-dealkylation of the pendant benzyl group on the diamine ligand. The diiron(III) complex [Fe(2)(mu-OH)(2)(mu-O(2)CAr(Tol))(O(2)CAr(Tol))(3)(N-Bnen)(N,N-Bn(2)en)] (8) was isolated from the reaction mixture. The 4.2 K M?ssbauer spectrum of 8 displays a single quadrupole doublet with parameters delta = 0.48(2) mm s(-1) and Delta E(Q) = 0.61(2) mm s(-1). The [Fe(2)(mu-OH)(2)(mu-O(2)CR)](3+) core structure in 8 matches that of the fully oxidized form of MMOH. The conversion of 6 to 8 closely parallels the chemistry of MMOH in which an O(2)-derived oxygen atom is inserted into the C-H bond of methane. Several reaction pathways are considered to account for this novel chemical transformation, and these are compared with mechanistic frameworks previously developed for related cytochrome P450 and copper(I) dioxygen chemistry.     

X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior

We report the X-ray crystal structures of native and manganese(II)-reconstituted toluene/o-xylene monooxygenase hydroxylase (ToMOH) from Pseudomonas stutzeri OX1 to 1.85 and 2.20 A resolution, respectively. The structures reveal that reduction of the dimetallic active site is accompanied by a carboxylate shift and alteration of the coordination environment for dioxygen binding and activation. A rotamer shift in a strategically placed asparagine 202 accompanies dimetallic center reduction and is proposed to influence protein component interactions. This rotamer shift is conserved between ToMOH and the corresponding residue in methane monooxygenase hydroxylase (MMOH). Previously unidentified hydrophobic pockets similar to those present in MMOH are assigned.     

Energetics of oxidized and reduced methane monooxygenase active site clusters in the protein environment

Using the density functional optimized active site geometries obtained in the accompanying paper (Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5251), a combined density functional and electrostatics approach has been applied to further address attendant uncertainties in the protonation states of the bridging ligands for MMOH(ox). The acidities (pK(a)s) associated with the bridging H(2)O ligand in Methylococcus capsulatus and corresponding energetics of each active site cluster interacting with the protein environment have been evaluated. The pK(a) calculations in combination with the results of the gas phase DFT studies allow the active site cluster in Methylosinustrichosporium to be best described as a diiron unit bridged by 2OH(-) ligands having an overall neutral net cluster charge. The presence of the exogenous acetate in M. capsulatus reveals a diiron unit bridged by 1OH(-) and 1H2O which asymmetrically shares its proton with a second-shell acetate in a very short strong AcO..H...OH hydrogen bond. For all MMOH(ox) and MMOH(red) active sites examined, significant Fe-ligand covalency is evident from the ESP atom charges, consistent with very strong ligand --> metal charge transfer from the muOH(-) and mu-carboxylato bridging ligands. The magnitude of electrostatic interaction of the individual protein residues in the active domain with the active site has been assessed via an energy decomposition scheme. Important second-shell residues are highlighted for the next level of quantum mechanics based calculations or alternatively for site-directed mutagenesis studies. Finally, from the known structural and spectroscopic evidence and the DFT studies, a possible mechanism is suggested for the conversion of MMOH(ox) into MMOH(red) that involves a combination of protein residues and solvent-derived ligands from the second coordination sphere.     

甲烷单加氧酶活性化合物的体外重构

甲烷氧化菌中甲烷单加氧酶既能催化甲烷转化为甲醇,也能降解小分子含氯有机物.将甲烷单加氧酶组分进行基因重组表达,利用表达的组分重构酶活性化合物,测定了重构化合物的丙烯环氧化活性及对三氯乙烯和三氯甲烷的降解.结果显示:经过30℃、220 r/min、20 min降解,约有52%的三氯乙烯被降解;在32℃、220 r/min、8 h反应条件下,约有26%的三氯甲烷被降解;表明甲烷单加氧酶亚基组分表达正确,能够在微生物体外重构活性化合物.     

Models for the trinuclear copper(II) cluster in the particulate methane monooxygenase from methanotrophic bacteria: Synthesis,spectroscopic and theoretical characterization of trinuclear copper(II) complexes

Three trinuclear Cu(II) complexes [Cu₃(tacp)(μ₃-Cl)₂](Cl)₄ (1), [Cu₃(tacp)(μ₃-Br)₂](Br)₄ (2) and [Cu₃(tacp)(μ₃-OH)₂](Cl)₄ (3) (tacp, 1,10,19-trioxa-4,7,13,16,22,25-hexaazacycloheptaeicosane) are synthesized to model the oxidized tricopper cluster implicated in the particulate methane monooxygenase from Methylococcus capsulatus (Bath). In the enzyme, the three Cu(II) ions are coupled by weak ferromagnetic interactions. The Cu(II) ions in 1 and 2 are shown to be ferromagnetically coupled from magnetic susceptibility and electron paramagnetic resonance (EPR) measurements. EPR suggests anti-ferromagnetic interactions among the Cu(II) ions in 3. Density functional theory calculations reproduce well the geometric, electronic and magnetic properties observed in these complexes and provide insights into the spin-coupling interactions mediated by the bridging ligands.     

Determination by X-ray absorption spectroscopy of the Fe-Fe separation in the oxidized form of the hydroxylase of methane monooxygenase alone and in the presence of MMOD

The diiron active site in the hydroxylase of Methylococcus capsulatus (Bath) methane monooxygenase (MMOH) has been studied in the oxidized form by X-ray absorption spectroscopy (XAS). Previous investigations by XAS and X-ray crystallography have identified two different distances (3.0 and 3.4 angstroms) between the two Fe atoms in the dinuclear site. The present study has employed a systematic extended X-ray absorption fine structure (EXAFS) fitting methodology, utilizing known and simulated active site and relevant model structures, to determine unambiguously the Fe-Fe separation in the oxidized form of MMOH. Consistent and unique fits were only possible for an Fe-Fe distance of 3.0 angstroms. This methodology was then applied to study potential changes in the active site local structure in the presence of MMOD, a protein of unknown function in multicomponent MMO. Fe K-edge and EXAFS analyses revealed negligible changes in the diiron site electronic and geometric structure upon addition of MMOD to oxidized MMOH.     

Stopped-flow Fourier transform infrared spectroscopy of nitromethane oxidation by the diiron(IV) intermediate of methane monooxygenase

The hydroxylase component (MMOH) of soluble methane monooxygenase from Methylococcus capsulatus (Bath) was reduced to the diiron(II) form and then allowed to react with dioxygen to generate the diiron(IV) intermediate Q in the first phase of a double-mixing stopped-flow experiment. CD3NO2 was then introduced in the second phase of the experiment, which was carried out in D2O at 25 degrees C. The kinetics of the reaction of the substrate with Q were monitored by stopped-flow Fourier transform infrared spectroscopy, observing the disappearance of the asymmetric NO2 bending vibration at 1548 cm-1. The data were fit to a single-exponential function, which yielded a kobs of 0.45 +/- 0.07 s-1. This result is in quantitative agreement with a kobs of 0.39 +/- 0.01 s-1 obtained by observing the disappearance of Q by double-mixing stopped-flow optical spectroscopy at its absorption maximum of 420 nm. These results provide for the first time direct monitoring of the hydroxylation of a methane-derived substrate in the MMOH reaction pathway and demonstrate that Q decay occurs concomitantly with substrate consumption.     

Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): a DFT and QM/MM study

Methane hydroxylation at the mononuclear and dinuclear copper sites of pMMO is discussed using quantum mechanical and QM/MM calculations. Possible mechanisms are proposed with respect to the formation of reactive copper-oxo and how they activate methane. Dioxygen is incorporated into the Cu(I) species to give a Cu(II)-superoxo species, followed by an H-atom transfer from a tyrosine residue near the monocopper active site. A resultant Cu(II)-hydroperoxo species is next transformed into a Cu(III)-oxo species and a water molecule by the abstraction of an H-atom from another tyrosine residue. This process is accessible in energy under physiological conditions. Dioxygen is also incorporated into the dicopper site to form a (mu-eta(2):eta(2)-peroxo)dicopper species, which is then transformed into a bis(mu-oxo)dicopper species. The formation of this species is more favorable in energy than that of the monocopper-oxo species. The reactivity of the Cu(III)-oxo species is sufficient for the conversion of methane to methanol if it is formed in the protein environment. Since the sigma orbital localized in the Cu-O bond region is singly occupied in the triplet state, this orbital plays a role in the homolytic cleavage of a C-H bond of methane. The reactivity of the bis(mu-oxo)dicopper species is also sufficient for the conversion of methane to methanol. The mixed-valent bis(mu-oxo)Cu(II)Cu(III) species is reactive to methane because the amplitude of the sigma singly occupied MO localized on the bridging oxo moieties plays an essential role in C-H activation.