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Structures of bacterial kynurenine formamidase reveal a crowded binuclear-zinc catalytic site primed to generate a potent nucleophile.

DOI: 10.1042/BJ20140511 DOI Help
PMID: 24942958 PMID Help

Authors: Laura Diaz Saez (University of Dundee, U.K.) , Kannan Srikannathasan (University of Dundee, U.K.) , Martin Zoltner (University of Dundee, U.K.) , William Hunter (University of Dundee, U.K.)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Biochemical Journal , VOL 462 , PAGES 581–589

State: Published (Approved)
Published: June 2014

Open Access Open Access

Abstract: Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalyzed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. Here, 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 coordination 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.

Journal Keywords: Bacillus; Biocatalysis; Burkholderia; Catalytic; Crystallography; X-Ray; Kinetics; Protein; Pseudomonas; Zinc

Subject Areas: Chemistry

Instruments: I03-Macromolecular Crystallography

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