A Study of the Structure/Function Relationship of NicF in the Bordetella bronchiseptica Nicotinic Acid Degradation Pathway

Roger D. Klein


Six genes responsible for the aerobic catabolism of nicotinic acid have been recently identified in bacterial systems (Jiminez et. al., 2008). We examine this pathway in the pathogenic genus Bordetella, in which the buildup of nicotinic acid has been shown to affect the expression of transcription factors regulating the virulence factors during infection in humans and other mammals. The fifth enzyme in this pathway, NicF, catalyzes the hydrolytic deamination of maleamic acid to maleic acid. Based on a crystal structure obtained using X-ray diffraction, we propose a complete catalytic mechanism based on the chemical identity and arrangement of residues in the active site. This mechanism occurs in two major steps, the first of which is the formation of a covalently bound tetrahedral intermediate following the attack of Cys150 on the alpha carbon. Following the release of ammonia, a second tetrahedral intermediate forms upon the attack of a hydroxide ion on the carbon, resulting in subsequent substrate release. Asp29 is thought to play an important role as both a general acid and general base in the abstraction and subsequent donation of a proton from cysteine to ammonia. To further probe structure and potential conformational changes during catalysis, a series of conditions based around Hampton Research's Crystal Screen® were explored in an attempt to co-crystallize NicF with its product, maleic acid. Unfortunately, these screens proved unsuccessful in obtaining a product-bound form of NicF. Attempts were also made to reproduce the conditions used to obtain crystals of the apoenzyme for use in soaking studies. However, even under the identical buffer and protein conditions, diffraction-quality crystals did not form. It was determined that Buffer 15 (0.2 M Ammonium sulfate + 0.1 M sodium cacodylate trihydrate 6.5 + 30 percent w/v Polyethylene glycol 8,000) yielded the most promising results, and that variants of the buffer should be tested under tightly controlled temperature and humidity conditions for further studies. The KD of the product, maleic acid, was also determined using isothermal titration calorimetry (ITC) to be 3.8 ± 0.4 mM, a value 40-fold higher than the KD of the substrate, maleamic acid.