Improved homology model of cyclohexanone monooxygenase from Acinetobacter calcoaceticus based on multiple templates.

Eduardo Bermúdez, Oscar N Ventura, Leif A Eriksson, Patricia Saenz-Méndez

Journal: Computational biology and chemistry 2015;49():14-22

PMID: 24530814

Full Text on Elsevier Science View on PubMed

Abstract

A new homology model of cyclohexanone monooxygenase (CHMO) from Acinetobacter calcoaceticus is derived based on multiple templates, and in particular the crystal structure of CHMO from Rhodococcus sp. The derived model was fully evaluated, showing that the quality of the new structure was improved over previous models. Critically, the nicotinamide cofactor is included in the model for the first time. Analysis of several molecular dynamics snapshots of intermediates in the enzymatic mechanism led to a description of key residues for cofactor binding and intermediate stabilization during the reaction, in particular Arg327 and the well known conserved motif (FxGxxxHxxxW) in Baeyer-Villiger monooxygenases, in excellent agreement with known experimental and computational data.

Address: Computational Chemistry and Biology Group, Facultad de Química, UdelaR, Isidoro de María 1620, Montevideo 11800, Uruguay.; Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96 Göteborg, Sweden. Electronic address: [email protected].; Computational Chemistry and Biology Group, Facultad de Química, UdelaR, Isidoro de María 1620, Montevideo 11800, Uruguay; Departamento de Química Orgánica, Facultad de Química, UdelaR, General Flores 2124, Montevideo 11800, Uruguay. Electronic address: [email protected].

DOI: 10.1016/j.compbiolchem.2014.01.012

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MeSH Terms: Acinetobacter calcoaceticus, Biocatalysis, Cyclohexanones, Models, Molecular, Molecular Structure, Oxygenases, Rhodococcus