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Literature summary for 1.14.13.25 extracted from

  • Jones, J.C.; Banerjee, R.; Shi, K.; Aihara, H.; Lipscomb, J.D.
    Structural Studies of the Methylosinus trichosporium OB3b soluble methane monooxygenase hydroxylase and regulatory component complex reveal a transient substrate tunnel (2020), Biochemistry, 59, 2946-2961 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
diferric and diferrous states of both sMMOH and the sMMOH:MMOB complexes, X-ray diffraction structure determination and analysis at 1.52-2.35 A resolution, the structures are analyzed for O2 access routes enhanced when the complex forms. Evaluation of the structures of oxidized, diferric Mt sMMOH (sMMOHox, PDB:6VK6, 1.52 A), chemically reduced diferrous Mt sMMOH (sMMOHred, PDB:6VK7, 2.12 A), Mt sMMOHox:MMOB (form 1, PDB ID 6VK5, 1.86 A, and form 2, PDB ID 6VK8, 2.03 A), and Mt sMMOHred:MMOB (PDB ID 6VK4, 2.35 A). The two alphabetagamma protomers of sMMOH protein in the crystal are related by 2fold crystallographic symmetry Methylosinus trichosporium

Protein Variants

Protein Variants Comment Organism
additional information kinetic analysis of MMOB mutants, overview Methylosinus trichosporium
V39F site-directed mutagenesis in the MMOB component, the mutant component variant nearly halts the reaction of the reconstituted sMMO system Methylosinus trichosporium
V39R site-directed mutagenesis in the MMOB component, the mutant component variant nearly halts the reaction of the reconstituted sMMO system Methylosinus trichosporium
V41E site-directed mutagenesis in the MMOB component, the mutant component variant nearly halts the reaction of the reconstituted sMMO system Methylosinus trichosporium
V41F site-directed mutagenesis in the MMOB component, the mutant component variant nearly halts the reaction of the reconstituted sMMO system Methylosinus trichosporium
V41R site-directed mutagenesis in the MMOB component, the mutant component variant nearly halts the reaction of the reconstituted sMMO system Methylosinus trichosporium

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
methane + NAD(P)H + H+ + O2 Methylosinus trichosporium
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methanol + NAD(P)+ + H2O
-
?

Organism

Organism UniProt Comment Textmining
Methylosinus trichosporium A0A2D2D5X0 AND A0A2D2D0T8 AND Q53563 AND A0A2D2D0X7
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
methane + NAD(P)H + H+ + O2
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Methylosinus trichosporium methanol + NAD(P)+ + H2O
-
?

Synonyms

Synonyms Comment Organism
sMMO
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Methylosinus trichosporium
soluble methane monooxygenase
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Methylosinus trichosporium

Cofactor

Cofactor Comment Organism Structure
FAD
-
Methylosinus trichosporium
NAD(P)H
-
Methylosinus trichosporium

General Information

General Information Comment Organism
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 Methylosinus trichosporium
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 Methylosinus trichosporium