3MJ4

Crystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose

Summary for 3MJ4

• Entry DOI: 10.2210/pdb3mj4/pdb
• Descriptor: UDP-galactopyranose mutase, FLAVIN-ADENINE DINUCLEOTIDE, URIDINE-5'-DIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: udp-galactopyranose mutase, phosphonate analog, inhibitor, binding mode, isomerase
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 10
• Total formula weight: 472082.16

Authors

Karunan Partha, S.,Sadeghi-Khomami, A.,Slowski, K.,Kotake, T.,Thomas, N.R.,Jakeman, D.L.,Sanders, D.A.R. (deposition date: 2010-04-12, release date: 2010-10-20, Last modification date: 2023-09-06)

Primary citation

Partha, S.K.,Sadeghi-Khomami, A.,Slowski, K.,Kotake, T.,Thomas, N.R.,Jakeman, D.L.,Sanders, D.A.
Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase.
J.Mol.Biol., 403:578-590, 2010

PubMed Abstract: UDP (uridine diphosphate) galactopyranose mutase (UGM) is involved in the cell wall biosynthesis of many pathogenic microorganisms. UGM catalyzes the reversible conversion of UDP-α-D-galactopyranose into UDP-α-D-galactofuranose, with the latter being the precursor of galactofuranose (Galf) residues in cell walls. Glycoconjugates of Galf are essential components in the cell wall of various pathogenic bacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis. The absence of Galf in humans and its bacterial requirement make UGM a potential target for developing novel antibacterial agents. In this article, we report the synthesis, inhibitory activity, and X-ray crystallographic studies of UDP-phosphono-galactopyranose, a nonhydrolyzable C-glycosidic phosphonate. This is the first report on the synthesis of a phosphonate analog of UDP-α-D-galactopyranose by a chemoenzymatic phosphoryl coupling method. The phosphonate was evaluated against three bacterial UGMs and showed only moderate inhibition. We determined the crystal structure of the phosphonate analog bound to Deinococcus radiodurans UGM at 2.6 Å resolution. The phosphonate analog is bound in a novel conformation not observed in UGM-substrate complex structures or in other enzyme-sugar nucleotide phosphonate complexes. This complex structure provides a structural basis for the observed micromolar inhibition towards UGM. Steric clashes, loss of electrostatic stabilization between an active-site arginine (Arg305) and the phosphonate analog, and a 180° flip of the hexose moiety account for the differences in the binding orientations of the isosteric phosphonate analog and the physiological substrate. This provides new insight into the ability of a sugar-nucleotide-binding enzyme to orient a substrate analog in an unexpected geometry and should be taken into consideration in designing such enzyme inhibitors.

PubMed: 20850454
DOI: 10.1016/j.jmb.2010.08.053

Experimental method

X-RAY DIFFRACTION (2.65 Å)