Structures of Mycobacterium tuberculosis pyridoxine 5′-phosphate oxidase and its complexes with flavin mononucleotide and pyridoxal 5′-phosphate

The X-ray crystal structure of a conserved hypothetical protein of molecular weight 16.3 kDa from Mycobacterium tuberculosis corresponding to open reading frame (ORF) Rv1155 has been solved by the multiwavelength anomalous dispersion method and refined at 1.8 Å resolution. The crystal structure revealed that Rv1155 is a dimer in the crystal and that each monomer folds into a large and a small domain; the large domain is a six-stranded antiparallel β-barrel flanked by two small α-helices and the small domain is a helix–loop–helix motif. The dimer interface is formed by residues protruding primarily from five of the six β-strands in each subunit. Based on structural similarity and on ligand binding, it has been established that Rv1155 is a pyridoxine 5′-phosphate oxidase, the Escherichia coli and human counterparts of which catalyse the terminal step in the biosynthesis of pyridoxal 5′-phosphate (PLP), a cofactor used by many enzymes involved in amino-acid metabolism. The structures of flavin mononucleotide (FMN) and pyridoxal 5′-phosphate (PLP) bound separately to Rv1155 have been determined at 2.2 and 1.7 Å resolution, respectively. Only one monomer binds non-covalently to one FMN molecule or to one PLP molecule. Arg55 and Lys57 are the key residues making hydrogen bonds and ionic inter­actions with the phosphate and ribose groups of the FMN molecule, whereas Arg55 and Arg129 provide hydrogen bonds and ionic interactions with the phosphate group of the PLP. Structural comparisons of Rv1155 from M. tuberculosis with its E. coli and human counterparts demonstrate that the core structure is highly conserved and the FMN-binding site is similarly disposed in each of the structures.