title: Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme.
abstract: The three-component naphthalene dioxygenase (NDO) enzyme system carries out the first step in the aerobic degradation of naphthalene by Pseudomonas sp. strain NCIB 9816-4. The three-dimensional structure of NDO revealed that several of the amino acids at the active site of the oxygenase are hydrophobic, which is consistent with the enzyme's preference for aromatic hydrocarbon substrates. Although NDO catalyzes cis-dihydroxylation of a wide range of substrates, it is highly regio- and enantioselective. Site-directed mutagenesis was used to determine the contributions of several active-site residues to these aspects of catalysis. Amino acid substitutions at Asn-201, Phe-202, Val-260, Trp-316, Thr-351, Trp-358, and Met-366 had little or no effect on product formation with naphthalene or biphenyl as substrates and had slight but significant effects on product formation from phenanthrene. Amino acid substitutions at Phe-352 resulted in the formation of cis-naphthalene dihydrodiol with altered stereochemistry [92 to 96% (+)-1R,2S], compared to the enantiomerically pure [>99% (+)-1R,2S] product formed by the wild-type enzyme. Substitutions at position 352 changed the site of oxidation of biphenyl and phenanthrene. Substitution of alanine for Asp-362, a ligand to the active-site iron, resulted in a completely inactive enzyme.
authors.affiliation: Department of Microbiology and Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA. rebecca-parales@uiowa.edu
authors.forename: R E
authors.initials: RE
authors.lastname: Parales
authors.forename: K
authors.initials: K
authors.lastname: Lee
authors.forename: S M
authors.initials: SM
authors.lastname: Resnick
authors.forename: H
authors.initials: H
authors.lastname: Jiang
authors.forename: D J
authors.initials: DJ
authors.lastname: Lessner
authors.forename: D T
authors.initials: DT
authors.lastname: Gibson
mesh_terms: D019943:Amino Acid Substitution; D001665:Binding Sites; D001673:Biodegradation, Environmental; D001713:Biphenyl Compounds / Q000378:metabolism; D003470:Culture Media; D049308:Dioxygenases; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D007203:Indigo Carmine; D007211:Indoles / Q000378:metabolism; D008958:Models, Molecular; D009097:Multienzyme Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016297:Mutagenesis, Site-Directed; D009281:Naphthalenes / Q000378:metabolism*; D010105:Oxygenases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010616:Phenanthrenes / Q000378:metabolism; D010957:Plasmids / Q000235:genetics; D013379:Substrate Specificity
chemical_list: D001713:Biphenyl Compounds; D003470:Culture Media; D049308:Dioxygenases; D007203:Indigo Carmine; D007211:Indoles; D009097:Multienzyme Complexes; D009281:Naphthalenes; D010105:Oxygenases; D010616:Phenanthrenes; C031721:naphthalene; C010574:biphenyl; C031181:phenanthrene; C038703:naphthalene dioxygenase