title: Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS.
abstract: 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+is still elusive. Therefore, mechanistic role played by Mg2+in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+have shown entry of Mg2+from bulk solvent into active site. Presence of Mg2+in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a "lid" covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.
authors.affiliation: CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India.
authors.forename: Ranajit Nivrutti
authors.initials: RN
authors.lastname: Shinde
authors.affiliation: CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India.
authors.forename: Subramanian
authors.initials: S
authors.lastname: Karthikeyan
authors.affiliation: CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India.
authors.forename: Balvinder
authors.initials: B
authors.lastname: Singh
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D020134:Catalytic Domain; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D019751:Intramolecular Transferases / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D050505:Mutant Proteins / Q000737:chemistry; D011487:Protein Conformation; D012274:Ribulosephosphates / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D014734:Vibrio cholerae / Q000201:enzymology
chemical_list: D000596:Amino Acids; D050505:Mutant Proteins; D012274:Ribulosephosphates; C031524:ribulose 5-phosphate; D019751:Intramolecular Transferases; C066493:L-3,4-dihydroxy-2-butanone-4-phosphate synthase