Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae

Abstract

Background: 3,4-Dihydroxy-2-butanone-4-phosphate synthase (DHBPS) is essential for many pathogens and is absent in humans. Results: We have characterized DHBPS from Vibrio cholerae in the presence of substrate D-ribulose 5-phosphate (Ru5P) and inhibitor 4-phospho-D-erythronohydroxamic acid (4PEH). Conclusion: 4PEH inhibits DHBPS competitively and interacts with enzyme similarly to the substrate. Significance: 4PEH can be used as a lead molecule for designing novel antibiotics.

Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS

“…DHBPS-Ru5P-Zn 2+ structure shows two Zn 2+ along with Ru5P bound in each active site26. These ions occupy M1 and M2 positions forming coordinate bonds with the surrounding water, Ru5P, and DHBPS residues as shown in Supplementary Fig.…”

“…The structures of DHBPS in its apo, Ru5P or Ru5P-ion bound form have been solved for many organisms viz. Escherichia coli 16 , Magnaporthe grisea 1718 , Methanocaldococcus jannaschii 1419 , Yersinia pestis, Candida albicans 2021 , Streptococcus pneumoniae 22 , Mycobacterium tuberculosis 2324 , Salmonella typhimurium 25 , and Vibrio cholerae 26. In these structures, DHBPS mostly exists as homo-dimer (monomer-A and monomer-B), and Ru5P binds in the active site of each monomer.…”

“…An active site cavity is formed mostly by loops of one monomer with a side being lined by loops of another monomer. Accordingly, in Vibrio cholera DHBPS, monomer-A active site is surrounded by loop-1 (34–41), loop-2 (82–98), and loop-3 (175–185) of the monomer-A, and loop-4 (103′–111′) and loop-5 (132′–138′) of the monomer-B26. A similar arrangement of loops is found in the active site of monomer-B, as shown in Supplementary Fig.…”

“…DHBPS-Ru5P structures have been solved for C. albicans 2021 , S. typhimurium 25, and V. cholerae 26 whereas DHBPS-Ru5P-ion complexes are solved for M. jannaschii 14 and V. cholerae 26 in the presence of inactive ions such as Zn 2+ and Ca 2+ . Numerous structural studies have speculated that inactive ions occupy the same position as that of active Mg 2+ , and mimics native like binding14182526. Failure of inactive ions to initiate the reaction, even if these bind at the same position, forming the same number of co-ordinate bonds, having similar charge and ionic radii to that of Mg 2+ , is attributed to their lower Lewis acid strength14.…”

“…Earlier, our group has solved the structures of Vibrio cholerae DHBPS in complex with Ru5P as well as in complex with Ru5P and Zn 2+  26. DHBPS-Ru5P-Zn 2+ structure shows two Zn 2+ along with Ru5P bound in each active site26.…”