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, 82 (9), 2263-7

Structural Conservation of the B Subunit in the Ammonia Monooxygenase/Particulate Methane Monooxygenase Superfamily

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Structural Conservation of the B Subunit in the Ammonia Monooxygenase/Particulate Methane Monooxygenase Superfamily

Thomas J Lawton et al. Proteins.

Abstract

The ammonia monooxygenase (AMO)/particulate methane monooxygenase (pMMO) superfamily is a diverse group of membrane-bound enzymes of which only pMMO has been characterized on the molecular level. The pMMO active site is believed to reside in the soluble N-terminal region of the pmoB subunit. To understand the degree of structural conservation within this superfamily, the crystal structure of the corresponding domain of an archaeal amoB subunit from Nitrosocaldus yellowstonii has been determined to 1.8 Å resolution. The structure reveals a remarkable conservation of overall fold and copper binding site location as well as several notable differences that may have implications for function and stability.

Keywords: AMO; amoB; copper; crystal structure; cupredoxin; hydrocarbon monooxygenase; methanotroph; pMMO.

Figures

Figure 1
Figure 1
Members of the AMO/pMMO superfamily. A: Phylogenetic tree. β-AOB, ammonia oxidizing β-proteobacteria; γ-AOB, ammonia oxidizing γ-proteobacteria; γ-MOB, methane oxidizing γ-proteobacteria; γ-bacteria, non methanotrophic γ-proteobacteria. B: Multiple sequence alignment of representative B subunits from each phylogenetic cluster. C: Gene cluster arrangement typically found in AOA and bacteria. The gene shown in grey is a conserved hypothetical protein of unknown function. The break between amoA and amoC indicates these genes are not always clustered in AOA.
Figure 2
Figure 2
Structure of N-terminal cupredoxin domain of N. yellowstonii amoB subunit (Ny_amoB). Center: Overall structure (pink with copper ions as gray spheres) with analogous domain of M. capsulatus (Bath) pmoB (magenta with copper ions as dark blue spheres) superimposed. Upper-left: Zoomed-in view of insertion region with residues 55–88 shown in gray and residues at interface with core domain shown as sticks. Upper-right: Zoomed-in view of copper binding sites in M. capsulatus (Bath) pmoB and Ny_amoB.

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