Lipopolysaccharide biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multi-drug resistant bacteria. A key player in lipopolysaccharide synthesis is the enzyme D-arabinose 5-phosphate isomerase, which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the lipopolysaccharide inner core. D-arabinose 5-phosphate isomerase is composed of two main domains: an N-terminal sugar isomerase domain, and a pair of cystathionine-ß-synthase domains of unknown function. As the three-dimensional structure of an enzyme is a pre-requisite for the rational development of novel inhibitors, we present here the crystal structure of the sugar isomerase domain of a catalytic mutant (K59A) of E. coli D-arabinose 5-phosphate isomerase, KdsD(K59A), at 2.6Å resolution. Our structural analyses and comparisons made with other sugar isomerase domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. Based on such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two-domain isomerases.
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