title: Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile.
abstract: Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalysed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. In the present study, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment, and, unlike most Zn2+-dependent enzymes, there is little scope to increase co-ordination number during catalysis. We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism.
authors.affiliation: *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
authors.forename: Laura
authors.initials: L
authors.lastname: Díaz-Sáez
authors.affiliation: *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
authors.forename: Velupillai
authors.initials: V
authors.lastname: Srikannathasan
authors.affiliation: *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
authors.forename: Martin
authors.initials: M
authors.lastname: Zoltner
authors.affiliation: *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
authors.forename: William N
authors.initials: WN
authors.lastname: Hunter
mesh_terms: D005558:Arylformamidase / Q000737:chemistry* / Q000378:metabolism; D001408:Bacillus anthracis / Q000201:enzymology; D055162:Biocatalysis; D057508:Burkholderia cenocepacia / Q000201:enzymology; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D007700:Kinetics; D011487:Protein Conformation; D011550:Pseudomonas aeruginosa / Q000201:enzymology; D015032:Zinc / Q000378:metabolism*
chemical_list: D005558:Arylformamidase; D015032:Zinc