Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b

Natesan Elango, Ramaswamy Radhakrishnan, Wayne A. Froland, Bradley J. Wallar, Cathleen A. Earhart, John D. Lipscomb, Douglas H. Ohlendorf

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Abstract

Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the O2-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory 'B' component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo-bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type II, which differ markedly in cellular and metabolic characteristics, are known to produce the sMMO. The structure of MMOH from the Type X methanotroph Methylococcus capsulatus Bath (MMO Bath) has been reported recently. Two different structures were found for the essential diiron cluster, depending upon the temperature at which the diffraction data were collected. In order to extend the structural studies to the Type II methanotrophs and to determine whether one of the two known MMOH structures is generally applicable to the MMOH family, we have determined the crystal structure of the MMOH from Type 11 Methylosinus trichosporium OB3b (MMO OB3b) in two crystal forms to 2.0 Å and 2.7 Å resolution, respectively, both determined at 18 °C. The crystal forms differ in that MMOB was present during crystallization of the second form. Both crystal forms, however, yielded very similar results for the structure of the MMOH. Most of the major structural features of the MMOH Bath were also maintained with high fidelity. The two irons of the active site cluster of MMOH OB3b are bridged by two OH (or one OH and one H20), as well as both carboxylate oxygens of Glu α144. This bis-(max)-hydroxo-bridged 'diamond core' structure, with a short Fe-Fe distance of 2.99 Å, is unique for the resting state of proteins containing analogous diiron clusters, and is very similar to the structure reported for the cluster from flash frozen (-160 °C) crystals of MMOH Bath, suggesting a common active site structure for the soluble MMOHs. The high-resolution structure of MMOH OB3b indicates 26 consecutive amino acid sequence differences in the β chain when compared to the previously reported sequence inferred from the cloned gene. Fifteen additional sequence differences distributed randomly over the three chains were also observed, including Dα209E, a ligand of one of the irons.

Original languageEnglish (US)
Pages (from-to)556-568
Number of pages13
JournalProtein Science
Volume6
Issue number3
DOIs
StatePublished - Mar 1997

Bibliographical note

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

  • X-ray crystallography
  • dinuclear iron cluster
  • methane oxidation
  • methanotroph
  • oxygen activation

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