The crystal structure and biochemical properties of DHBPS from Streptococcus pneumoniae, a potential anti-infective target for Gram-positive bacteria

The enzymes involved in riboflavin biosynthesis are considered to be potential anti-bacterial drug targets because these proteins are essential in bacterial pathogens but are absent in humans. 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) is one of the key enzymes in the biosynthesis of riboflavin. DHBPS catalyzes the conversion of ribulose-5-phosphate (Ru5P) to 3,4-Dihydroxy-2-butanone-4-phosphate (DHBP) and formate. The purified SpDHBPS enzyme, in the presence of Mg2+ ion, catalyzed the conversion of Ru5P to DHBP at a rate of 109 nmol min−1 mg−1 with an apparent Km value of 181 μM at 37 °C. Surprisingly, our experiments first revealed that DHBPS showed activity in the presence of the trivalent metal ion, Fe3+. Furthermore, we determined the crystal structure of DHBPS from Gram-positive bacteria, Streptococcus pneumoniae, with 2.0 Å resolution. The overall architecture of SpDHBPS was similar to its homologs, which comprise one β-sheet (five-stranded) and eight α-helices, adopting a three-layered α-β-α sandwich fold. Similar to the homologs, gel-filtration experiments verified that the enzyme was arranged as a dimer. Although the overall fold of DHBPS was similar, the significant structural differences between the species at the active site region may be utilized to develop antibacterial agents that are species-specific.