Ligand-binding and segmental motion of the 29 kD enzyme DDAH
Beatriz S. Magalhães; Richard Harris; Paul C. Driscoll.
Department of Biochemistry and Molecular Biology, University College London, U.K.
Introduction. The enzyme dimethylarginine dimethylaminohydrolase (DDAH) is responsible for the metabolism of free asymmetric methylarginine residues (AMAs) to citrulline and mono- or di-methylamines. In mammals, the asymmetric methylarginines Nh,Nh-dimethylarginine (ADMA) and Nh-methylarginine (L-NMMA) are endogenous inhibitors of all nitric oxide synthase (NOS) isoforms. By controlling local levels of AMAs, DDAH activity is implicated in the regulation of nitric oxide (NO) production, which gives rise to interest in the therapeutic potential of this enzyme in vascular disease. To date, it has not proved possible to obtain a 3D structure of any mammalian isoforms of DDAH, however, the crystal structure of the bacterial Pseudomonas aeruginosa DDAH (PaDDAH) homologue has been solved. The enzyme is a 58 kD homodimer and adopts a β/α-propeller fold. This work describes the application of NMR methodology to study the backbone dynamics of the engineered monomeric variant of PaDDAH and interactions with ligands and inhibitors, as this protein provides an attractive template to further investigate the structure-function characteristics of DDAH isoforms and β/α-propeller enzymes in general. Methodology. A suite of triple resonance experiments allowed the complete assignment of the backbone resonances. 15N R1, R2 relaxation rates and {1H}-15N heteronuclear NOE parameters were determined at three different magnetic field strengths. The titration of substrate and ligand molecules to the enzyme was followed with a series of 15N HSQC experiments which enabled the mapping of the binding site and the determination of the dissociation constants (Kd) of the different complexes. Results and Discussion. 15N backbone relaxation studies of the mutant protein, analysed in the model-free formalism, revealed that the loop that closes down on the active site displays low values of the generalised N-H bond order parameter (S2) consistent with a high degree of mobility on the pico- to nano-second timescale. Furthermore, the interaction of PaDDAH with a variety of small molecule ligands has revealed that these molecules give rise to specific broadening of a subset of N-H cross peaks, including those of residues around the active site and in the loop that closes the ligand binding pocket. The results are interpreted to imply that in the bound state the dynamic profile of the backbone of the PaDDAH enzyme is altered, with ordering of the loop but retaining a component of conformational exchange that gives rise to residual line broadening, even in the saturated state. A similar result is obtained with a ligand covalently bound to Cys249 of the catalytic triad.
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