1.14.13.25	evolution	enzyme sMMO belongs to the BMM superfamily	-, 764425	
1.14.13.25	evolution	methanotrophs produce two genetically unrelated MMOs: soluble MMO (sMMO) expressed by a subset of methanotrophs and membrane-bound, particulate MMO (pMMO) expressed by nearly all methanotrophs. Enzyme sMMO belongs to the larger bacterial multicomponent monooxygenase (BMM) family. In organisms that have genes for both sMMO and pMMO, expression levels are coupled to intracellular copper levels in a mechanism known as the copper switch, wherein sMMO is produced at low copper concentrations while pMMO expression is mildly upregulated and sMMO expression is downregulated when copper is available	-, 745389	
1.14.13.25	malfunction	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	764188	
1.14.13.25	metabolism	ammonia-supplied Methylosinus trichosporium OB3b containing soluble methane monooxygenase (sMMO) grow at the fastest rate, while the highest poly-beta-hydroxybutyrate content is obtained by transferring nitrate-supplied bacteria with the expression of particulate methane monooxygenase (pMMO) to nitrogen-free mineral salts (NFMS) + 0.005 mmol/l Cu medium	745453	
1.14.13.25	metabolism	enzyme is a self-sufficient cytochrome P450	-, 764329	
1.14.13.25	metabolism	methane hydroxylation through methane monooxygenases is a key aspect due to their control of the carbon cycle in the ecology system	-, 745535	
1.14.13.25	metabolism	Methyloceanibacter methanicus {R-67174} is capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase	-, 744797	
1.14.13.25	metabolism	Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most known methanotrophs but similar to Methylocella spp., possesses only a soluble methane monooxygenase	745039	
1.14.13.25	metabolism	the enzyme expresses the soluble enzyme form under copper limitation, and the membrane-bound particulate MMO at high copper-to-biomass ratio, analysis of the mechanism of the copper switch. Transcriptomic profiling of particulate MMO, EC 1.14.18.3, and soluble MMO, using Methylococcus capsulatus DNA microarrays. 137 ORFs are found to be differentially expressed between cells producing sMMO and pMMO, while only minor differences in gene expression are observed between the pMMO-producing cultures. Of these, 87 genes are upregulated during sMMO-producing cells, i.e. during copper-limited growth. Major changes takes place in the respiratory chain between pMMO-and sMMO-producing cells, and quinone are predominantly used as the electron donors for methane oxidation by pMMO. Proposed pathway of methane oxidation in Methylococcus capsulatus cells producing either sMMO or pMMO, overview	-, 745730	
1.14.13.25	metabolism	the high number of up-regulated genes in cells producing soluble methane monooxygenase shows that Methylococcus capsulatus is highly adapted to copper-limited growth	-, 745730	
1.14.13.25	additional information	analysis of structural and functional differences of sMMO and pMMO, EC 1.14.18.3, substrate/product/cofactor-active site interactions, docking analysis of interactions between cofactors and corresponding enzymes. Molecular simulations and modeling, overview. Structural architecture of sMMO. Enzyme sMMO requires three protein components for maximal catalytic activity: the hydroxylase (MMOH), the reductase (MMOR), and the regulatory protein (MMOB), structure-function relationships, detailed overview. MMOR consists of a NAD binding domain, an FAD-binding domain and a ferredoxin and plays a key role in the delivery of electrons within sMMO enzyme systems. The Fe2S2 domain appears to be the MMOH (methane monooxygenase hydroxylase) binding site, sMMOH docking simulations. MMOB acts as a controller of the methane-to-methanol conversion reaction	-, 746420	
1.14.13.25	additional information	enzyme sMMO contains a non-heme diiron active site, active site structure, overview. Enzyme sMMO requires three protein components for maximal catalytic activity: the hydroxylase (MMOH), the reductase (MMOR), and the regulatory protein (MMOB), detailed overview	-, 745389	
1.14.13.25	additional information	enzyme sMMO structural reorganization through subunits MMOH and MMOB including the dinuclear iron cluster, detailed overview	764976	
1.14.13.25	additional information	exogenous ligands bound to the diiron cluster of the sMMOH:MMOB complex induce conformational changes, structural analysis, overview. Bottlenecks between cavities are regulated by flexible residues. Bottleneck regulated by residues V105, F109, V285, and L289 is located between cavities 3 and 2. Cavity 2 is separated from the active site cavity 1 by another bottleneck controlled by residues L110, F188, L216, F282 and F286. Cavities 3 and 2 are connected in all of the Mt sMMOH and sMMOH:MMOB crystal structures. The MMOB binding-induced reorganization of the bottleneck residues L216 and L110 in sMMOH serves to isolate cavity 1 from cavity 2 in the complex. The pore is located between helices E and F and has been proposed to be involved in regulating the access of substrates and release of products (CH3OH) to and from the active site, respectively. The strictly conserved amino acids T213, N214, and E240 are considered the pore gating residues that regulate these processes. The pore is a uniquely polar region on the sMMOH surface as it is flanked by hydrophobic amino acids A210, V218, L237, L244, and M247 on helices E and F. The side chain of T213 lines the active site cavity and the hydroxyl moiety points towards the diiron cluster. Chemical reduction of the diiron cluster causes the middle of helix E to twist, resulting in T213 and N214 to shift 2.2 A and 3.2 A, respectively. The rotameric conformations of the hydrophobic residues V218, L244, and M247 are altered as well, helping to create a chemical environment that does not favor stable binding of water molecules to the region around the pore. MMOB binding to sMMOH causes structural rearrangement of the pore residues as well. The side chain of E240 is no longer solvent exposed, and instead, traverses the width of the Pore. This new conformation blocks the access of substrates through the Pore into the active site cavity. The side chain of T213 is shifted 2.2 A compared to its position in Mt sMMOHox and rotated about 180° compared to its position in Mt sMMOHred. This new conformation positions the side chain hydroxyl moiety of T213 to face away from the diiron cluster and form a hydrogen bond with E240. MMOB covers the pore while in complex with sMMOH, further limiting access to the active site by this route	764175	
1.14.13.25	additional information	interaction analysis of sMMO subunits and structure-function analysis, detailed overview. Alterations of hydrogen bonding or solvent accessibility occur due to the conformational changes of isoalloxazine in FAD	-, 764425	
1.14.13.25	additional information	MmoC homology modeling using structure PDB ID 1KRH.1 and the crystal structure of the monomeric MMOH-MmoB complex from Methylococcus capsulatus (PDB ID 4GAM) as a templates	-, 764485	
1.14.13.25	additional information	significant conformational changes must be imparted within sMMOH by the binding of MMOB. Small-molecule tunnel analysis, overview	764188	
1.14.13.25	additional information	soluble methane monooxygenase component interactions monitored by 19F NMR spectroscopy. Modeling 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	764181	
1.14.13.25	additional information	structure comparisons of the enzymes from Methylosinus sporium strain 5 and Methylosinus trichosporium strain OB3b. MMOH-MMOD complex modeling, overview	-, 765765	
1.14.13.25	additional information	structure-spectroscopy correlations for intermediate Q of soluble methane monooxygenase, QM/MM calculations. Modeling of the MMOH oxidative and reductive state, Moessbauer parameters and electronic structure of MMOHox. The selection of plausible models include the following: (1) bis-mu-oxo bridged cores, (2) mu-OepsilonGlu243 bridged diamond cores, inspired from the MMOHred structure, as suggested recently, (3) mu-oxo bridged open cores, and (4) mu-OepsilonGlu243 bridged open cores. Closed- and open-core conformations for the key intermediate in sMMO. Optimized cores of eight MOHQ models are analyzed for molecular structure and electronic structure	764980	
1.14.13.25	physiological function	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 (alphabetagamma)2 hydroxylase, sMMOH	764188	
1.14.13.25	physiological function	in the enzyme complex of sMMO, Two molar equivalents of MMOB are necessary to achieve catalytic activities and oxidized a broad range of substrates including alkanes, alkenes, halogens, and aromatics. Optimal activities are observed at pH 7.5 for most substrates possibly because of the electron transfer environment in MMOR. The presence of iron at the diiron active site is required for the catalytic activity of the sMMO. Secretion of siderophores could be a defense mechanism of Methylosinus sporium strain 5 in growth condition of high bacterial concentrations and limited iron concentration. A possible explanation is that Methylosinus sporium strain 5 responds more sensitively than other type II methanotrophs because this methanotroph generates a brown-black pigment in response to a high cell:iron ratio. MMOR is an essential component for the catalytic cycle owing to its electron transfer abilities, which are accomplished by FAD-containing and [2Fe-2S] cluster ferredoxin domains to reduce diiron active sites in MMOH. NADH binds to the MMOR-FAD in MMOH to transfer hydride, and the conformational change of NADH-FAD generates charge transfer bands	-, 764425	
1.14.13.25	physiological function	MMO is an enzyme complex that can oxidize the C-H bonds in methane and other alkanes. As one of the oxidoreductase group,MMOplays a critical role in the first step of methanotrophs metabolism where methane is transformed into methanol	-, 746420	
1.14.13.25	physiological function	pMMO consists of two protein components (NADH-OR and pMH) and is coupled to the electron transport chain	-, 702501	
1.14.13.25	physiological function	soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the conversion of methane to methanol at ambient temperature and pressure. The enzyme consists of three protein components: a 245 kDa (alphabetagamma)2 hydroxylase (sMMOH), a 38 kDa flavin adenine dinucleotide (FAD) and 2Fe-2S cluster-containing reductase (MMOR), and a 15 kDa cofactorless regulatory component (MMOB). The sMMOH active site contains a dinuclear iron cluster, which serves to activate molecular oxygen for insertion into the C-H bond of methane. The resting state of sMMOH contains a diferric cluster (Fe3+Fe3+, sMMOHox) in which the irons are bridged by two solvent (OH- or H2O) molecules in addition to the carboxylate of Glu144. sMMOHox can form a complex with MMOR and receive two electrons to form the diferrous cluster (Fe2+Fe2+, sMMOHred) in which Glu243 shifts to bridge the irons via one carboxylate oxygen, one bridging solvent is lost, and the bond to the second solvent is weakened. In this new configuration, the diiron cluster can bind O2 between the irons upon dissociation of the weakly bound solvent. But O2 binding is observed to be very slow in the absence of the regulatory component MMOB. Binding of MMOB effects a 1000fold increase in the rate constant for the O2 binding to the diiron cluster to form the first spectroscopically distinct intermediate of the reaction cycle, termed P*. One cause of the decreased rate of O2 binding in the sMMOH active site in the absence of MMOB is the near closure of the molecular tunnel that mediates the transit of O2 from the solvent. This bottleneck is relieved by conformational changes in both MMOB and sMMOHred when the sMMOHred:MMOB complex forms. A second cause of the low reactivity of O2 with sMMOHred is the position of the Glu209 ligand to the diiron cluster, which blocks the approach to the open iron coordination site. An angle change of this residue in the sMMOHred:MMOB complex exposes the site for O2 binding. The formation of intermediate P* is followed by a spontaneous formation of a peroxo-intermediate P, and finally, O-O bond cleavage to yield the reactive dinuclear Fe4+ intermediate Q. Q can react directly with methane to form methanol with the incorporation of one atom of oxygen sourced from O2. Intermediate Q is generated and stabilized by precisely coordinated sMMO protein component interactions. Regulation of electron transfer in the sMMO system, mechanism, modeling, detailed overview. MMOR causes both the N-terminal tail and the core region of MMOB to dissociate from sMMOH	764181	
1.14.13.25	physiological function	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. 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. Although chemically reduced sMMOH can carry out the oxygenation chemistry alone, the reaction only proceeds at a physiologically relevant rate when sMMOH is complexed with MMOB. Many regulatory functions of MMOB have been discovered but its most important effects are to decrease the redox potential of the diiron cluster by 132 mV, accelerate O2 binding by 1000fold, increase the turnover number 150fold, and tune sMMOH to selectively bind and oxygenate methane over other more easily oxidized hydrocarbons	764976	
1.14.13.25	physiological function	soluble methane monooxygenase in methanotrophs converts methane to methanol under ambient conditions. The maximum catalytic activity of hydroxylase (MMOH) is achieved through the interplay of its regulatory protein (MMOB) and reductase. An additional auxiliary protein, MMOD, functions as an inhibitor for MMOH by competing with MMOB for MMOH association as well as by disrupting the active geometric form of the di-iron center. The expression level of MMOD is relatively low and it binds tightly with MMOH near the di-iron center. ApoMMOH (iron removed) in the presence of MMOD or MMOB demonstrates that both MMOD and MMOB block iron loading toward apoMMOH instead of promoting it. Both iron atoms show full occupancy at the di-iron center during structure refinement, indicating that there is no loss of iron upon MMOD association. One potential function is that MMOD acts as a protein chaperone to assist the protein folding of MMOH by protecting MMOH until MMOHbeta-NT latches on as the final step of the protein folding process, potential function of MMOD as a protein chaperone	-, 765765	
1.14.13.25	physiological function	soluble methane monooxygenase is a bacterial enzyme that converts methane to methanol at a carboxylate-bridged diiron center with exquisite control. The enzyme is also capable of hydroxylating and epoxidizing a broad range of hydrocarbon substrates in addition to methane	711260	
1.14.13.25	physiological function	the enzyme is strongly regulated by the availability of copper. Methanobactin produced by Methylosinus trichosporium OB3b plays a key role in controlling expression of MMO genes in this strain	744100	
1.14.13.25	physiological function	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	764175