The molecular structure of Rv2074, a probable pyridoxine 5′-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 Å resolution

The crystal structure of a conserved hypothetical protein corresponding to open reading frame Rv2074 from Mycobacterium tuberculosis (Mtb) has been solved by the two-wavelength anomalous dispersion method. Refinement of the molecular structure at 1.6 Å resolution resulted in an R_work of 0.178 and an R_free of 0.204. The crystal asymmetric unit contains an Rv2074 monomer; however, the crystallographic twofold symmetry operation of space group P4₃2₁2 generates dimeric Rv2074. Each monomer folds into a six-stranded antiparallel β-barrel flanked by two α-helices. The three-dimensional structure of Rv2074 is very similar to that of Mtb Rv1155, a probable pyridoxine 5′-­phosphate oxidase (PNPOx), which corroborates well with the relatively high sequence similarity (52%) between the two. A structural comparison between Rv2074 and Rv1155 revealed that the core structure (a six-stranded β-barrel) is also well conserved; the major differences between the two lie in the N- and C-­termini and in the small helical domain. Two citric acid molecules were observed in the active site of Rv2074, the crystals of which were grown in 0.2 M sodium citrate buffer pH 5.0. The citric acid molecules are bound to Rv2074 by hydrogen-bonding interactions with Thr55, Gln60 and Lys61. One of the two citric acid molecules occupies the same spatial position that corresponds to the position of the phosphate and ribose sugar moieties of the flavin mononucleotide (FMN) in the Mtb Rv1155–FMN, Escherichia coli PNPOx–FMN and human PNPOx–FMN complex structures. Owing to its extensive structural similarity with Mtb Rv1155 and to the E. coli and human PNPOx enzymes, Rv2074 may be involved in the final step in the biosynthesis of pyridoxal 5′-phosphate (PLP; a vitamin B₆).