Crystal Structure of Bacillus anthracis Phosphoglucosamine Mutase, an Enzyme in the Peptidoglycan Biosynthetic Pathway

Abstract

Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme that participates in the cytoplasmic steps of peptidoglycan biosynthesis. As peptidoglycan is essential for bacterial survival and is absent in humans, enzymes in this pathway have been the focus of intensive inhibitor design efforts. Many aspects of the structural biology of the peptidoglycan pathway have been elucidated, with the exception of the PNGM structure. We present here the crystal structure of PNGM from the human pathogen and bioterrorism agent Bacillus anthracis. The structure reveals key residues in the large active site cleft of the enzyme which likely have roles in catalysis and specificity. A large conformational change of the C-terminal domain of PNGM is observed when comparing two independent molecules in the crystal, shedding light on both the apo-and ligand-bound conformers of the enzyme. Crystal packing analyses and dynamic light scattering studies suggest that the enzyme is a dimer in solution. Multiple sequence alignments show that residues in the dimer interface are conserved, suggesting that many PNGM enzymes adopt this oligomeric state. This work lays the foundation for the development of inhibitors for PNGM enzymes from human pathogens.

An Essential Poison: Synthesis and Degradation of Cyclic Di-AMP in Bacillus subtilis

“…This observation is in excellent agreement with previous results (7). Moreover, GlmM exhibited a strong self-interaction, which corresponds to its previously reported formation of homodimers (43). Moreover, we detected a weak but significant interaction between CdaA and GlmM.…”

Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures

“…The active site is located in the large central cleft, found at the confluence of the four domains, and is typically positively charged. 20,21,23 As reflected in their sequence conservation, the arrangement of key active-site loops and catalytic residues is highly similar in all of the known structures (Fig. 1b).…”

“…Another feature commonly observed in the crystal structures is conformational variability of the C-terminus, which moves via a hinge-type rotation relative to the rest of the protein, and is correlated with ligand binding. 16,18,20,21,25,26 Until recently, the quaternary structures of these proteins had been largely unexamined, perhaps because the best characterized enzymes were known to be monomers. However, biochemical characterization of Salmonella typhimurium PGM (StPGM) and Bacillus anthracis PNGM (BaPNGM) demonstrated that these two proteins exist as dimers in solution.…”

“…However, biochemical characterization of Salmonella typhimurium PGM (StPGM) and Bacillus anthracis PNGM (BaPNGM) demonstrated that these two proteins exist as dimers in solution. 20,21,25 The discovery of oligomers within α-D-phosphohexomutase superfamily prompted the current examination of all known structures of these enzymes.…”

“…[16][17][18][19] Over the last two decades, crystal structures have been determined for at least one protein in each subgroup of the α-D-phosphohexomutase superfamily. [20][21][22][23][24] These studies have shown that the enzymes share a conserved four-domain architecture, with a large, centrally located activesite cleft. Another feature commonly observed in the crystal structures is conformational variability of the C-terminus, which moves via a hinge-type rotation relative to the rest of the protein, and is correlated with ligand binding.…”