title: Uptake of Organohalide Pollutants, and Release of Partially Dehalogenated Products, by NpRdhA, a 'Base-Off' Cob(II)alamin-Dependent Reductive Dehalogenase from a Deep Sea Bacterium. A Molecular Dynamics Investigation.
abstract: This work shows that, during MD aided by external tiny random forces, 3-bromo-4-hydroxybenzoic acid (LHB), the product of reductive dehalogenation of 3,5-dibromo-4-hydroxybenzoic acid (LBB) by the corrin-based marine enzyme NpRdhA, is expelled along mainly the wide channel that connects the corrin to the external medium. In accordance, unbiased MD showed that LBB migrates relatively rapidly from the external medium to the inside of the channel, finally getting to the corrin active center of NpRdhA. The LBB pose, with bromide head and carboxylate tail nearly equidistant from the corrin Co ion, does not fit the results of previous automatic docking. Either the experimental structure of the NpRdhA-LBB complex, or a quantum-mechanical study of LBB at the corrin active site, are therefore urged.
authors.affiliation: Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, IT-55100 Lucca, (phone/fax: +39-0583-417336). francesco.pietra@accademialucchese.it.
authors.forename: Francesco
authors.initials: F
authors.lastname: Pietra
mesh_terms: D059001:Aquatic Organisms / Q000201:enzymology* / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology* / Q000378:metabolism; D004785:Environmental Pollutants / Q000737:chemistry / Q000378:metabolism*; D006846:Hydrocarbons, Halogenated / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D014805:Vitamin B 12 / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D004785:Environmental Pollutants; D006846:Hydrocarbons, Halogenated; C097751:cob(II)alamin; D014805:Vitamin B 12
keywords: B12-based enzymes; Corrin-based enzymes; Deep-sea bacteria; Molecular dynamics; Reductive dehalogenases