In a recent directed-evolution study, Escherichia coli D-sialic acid aldolase was converted by introducing eight point mutations into a new enzyme with relaxed specificity, denoted RSaldolase (also known formerly as L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase), which showed a preferred selectivity toward L-KDO. To investigate the underlying molecular basis, we determined the crystal structures of D-sialic acid aldolase and RS-aldolase. All mutations are away from the catalytic center, except for V251I, which is near the opening of the (␣/) 8 -barrel and proximal to the Schiff base-forming Lys-165. The change of specificity from D-sialic acid to RS-aldolase can be attributed mainly to the V251I substitution, which creates a narrower sugar-binding pocket, but without altering the chirality in the reaction center. The crystal structures of D-sialic acid aldolase⅐L-arabinose and RS-aldolase⅐hydroxypyruvate complexes and five mutants (V251I, V251L, V251R, V251W, and V251I/V265I) of the D-sialic acid aldolase were also determined, revealing the location of substrate molecules and how the contour of the active site pocket was shaped. Interestingly, by mutating Val251 alone, the enzyme can accept substrates of varying size in the aldolase reactions and still retain stereoselectivity. The engineered D-sialic acid aldolase may find applications in synthesizing unnatural sugars of C 6 to C 10 for the design of antagonists and inhibitors of glycoenzymes.Carbohydrates on cell surfaces play a pivotal role in the molecular recognition processes in various cellular interactions. Interfering with the recognition processes between pathogens and hosts may present therapeutic strategies for infectious diseases (1, 2). D-Sialic acids are widely found in nature, from bacteria to plants and animal tissues. Cell-surface glycoproteins and glycolipids frequently contain D-sialic acids at the termini of the oligosaccharide chains. The invading bacteria and viruses also target the cell-surface sialic acids of their hosts, which constitutes an important step for infectivity (3). On the other hand, the monosaccharide D-3-deoxy-manno-2-octulosonic acid (D-KDO) 2 has never been identified in vertebrates, but it is an important component in Gram-negative bacteria (4 -6). Because D-KDO is vital to the structural stability of bacterial outer membrane, targeting D-KDO and the related biosynthetic enzymes may be a new strategy for future antibacterial agent discovery.Currently, unnatural enantiomeric compounds become increasingly important in pharmaceutical implementations. Enantiomers (D-form) of natural peptides have been used to target cell-surface D-sugars. These D-peptide cell-surface sugar binders might serve as new drug candidates for infectious disease (7) and as tools for studying the interactions between proteins and carbohydrate. Owing to the resistance to hydrolases and high binding affinity to sugars, the unnatural D-peptides can become potential therapeutic agents. Through mirror-image phage display, natural L-peptides can be...