University of SaskatchewanHARVEST
  • Login
  • Submit Your Work
  • About
    • About HARVEST
    • Guidelines
    • Browse
      • All of HARVEST
      • Communities & Collections
      • By Issue Date
      • Authors
      • Titles
      • Subjects
      • This Collection
      • By Issue Date
      • Authors
      • Titles
      • Subjects
    • My Account
      • Login
      JavaScript is disabled for your browser. Some features of this site may not work without it.
      View Item 
      • HARVEST
      • Electronic Theses and Dissertations
      • Graduate Theses and Dissertations
      • View Item
      • HARVEST
      • Electronic Theses and Dissertations
      • Graduate Theses and Dissertations
      • View Item

      Structural and inhibition studies on UDP-galactopyranose mutase

      Thumbnail
      View/Open
      SarathyKarunanParthaPhDThesisNovember2010.pdf (13.48Mb)
      Date
      2010-10
      Author
      Karunan Partha, Sarathy
      Type
      Thesis
      Degree Level
      Doctoral
      Metadata
      Show full item record
      Abstract
      UDP-galactopyranose mutase (UGM) is a flavoenzyme which catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDPGalf). UDP-Galf is the active precursor of Galf residues. Glycoconjugates of Galf residues are found in the cell wall of bacteria and on the cell surface of higher eukaryotes. Galf residues have not been found in humans and the fact that they are essential for the growth of pathogenic bacteria makes UGM a potential antibacterial target. In the present study, crystal structures of UGM from Deinocococcus radiodurans (drUGM) in complex with substrate (UDP-Galp) were determined. UDP-Galp is buried in the active site and bound in a U-shaped conformation. The binding mode and active site interactions of UDP-Galp are consistent with the previous biochemical and mechanistic studies. The mobile loops in the substrate complex structures exist in a closed conformation and Arg198 on one of the mobile loops stabilizes the phosphate groups of the substrate. The anomeric carbon of galactose is 2.8 Å from the N5 of FAD (in the reduced complex) favorable to form FAD-galactosyl adduct. In addition to substrate complex structures, the crystal structures of drUGM in complex with UDP, UMP, and UDP-Glc have been determined. The mobile loops in all these complexes exist in a closed conformation. Inhibitors for UGM were identified by ligand-based and structure-based methods. The phosphonate analog of UDP-Galp (GCP) showed only weak inhibition against various bacterial UGMs. The structure of drUGM in complex with GCP provided a basis for its inhibitory activity. Poor stabilization of the phosphate groups by conserved arginines (Arg198 and Arg305) and altered sugar binding mode account for its activity. Novel indole-based (LQ1, LQ6 and LQ10) inhibitors of UGM were identified through structure-based virtual screening (SBVS) of a chemical library. Inhibition studies also allowed the identification of an active site aspartic acid that plays role in inhibitor binding. The structural studies on drUGM provided a basis for understanding substrate binding to UGM. In vitro enzyme inhibition studies allowed the identification of novel indole-based inhibitors. The structural and inhibition studies reported here enhance the understanding of UGM-ligand interactions and will assist in the development of more potent inhibitors of UGM.
      Degree
      Doctor of Philosophy (Ph.D.)
      Department
      Chemistry
      Program
      Chemistry
      Supervisor
      Sanders, David
      Committee
      Pedras; Reid; Mosimann, Steven; Grochulski; Baranski
      Copyright Date
      October 2010
      URI
      http://hdl.handle.net/10388/etd-01122011-111624
      Subject
      substrate complexes and inhibitiors
      crystallography
      UDP-galactopyranose mutase
      cell wall
      galactofuranose
      Collections
      • Graduate Theses and Dissertations
      University of Saskatchewan

      University Library

      © University of Saskatchewan
      Contact Us | Disclaimer | Privacy