Structural basis of molecular recognition of pyridoxal 5′-phosphate in a bacterial periplasmic binding protein

Vitamin B₆ and its vitamers are essential in bacteria. Many are auxotrophic for B₆ vitamers and require salvage pathways and membrane uptake systems. Despite the importance of the uptake systems, very few transporters have been structurally characterized. The structure of the periplasmic binding protein (P5PA) of an ABC uptake transporter from the pathogen Actinobacillus pleuropneumoniae has been recently solved in complex with pyridoxal 5'-phosphate (PLP). Another close homolog from the same organism, AfuA, had been structurally characterized as a complex with glucose-6-phosphate (G6P). To study the molecular recognition of PLP by P5PA, a comparative approach has been applied. The heterologous complexes P5PA-G6P and AfuA-PLP have been generated by docking. Systematic molecular dynamics simulations have been applied to the native and heterologous complexes. Binding energies and molecular interactions have been compared for all the complexes. The results suggest the selective binding of the ligand is achieved by a combination of structural factors specific to each protein, including shape of the binding site, steric hindrance, hydrogen bonding, electrostatic and hydrophobic interactions. No single residue is uniquely responsible for ligand specificity although a few side chains play a significant role. Heterologous ligands are subject to destabilizing interactions that provoke the distortion of the ligand itself and the alteration of the protein dynamics. Residue Q267 appears to provide a significant stabilization contribution in the P5PA-PLP complex but not in AfuA-PLP. Likewise, D207 provides stabilization in the AfuA-G6P complex and not in AfuA-PLP. The indications obtained suggest strategies for the design of specific inhibitors.