Shikimate dehydrogenase (SDH) is a reversible enzyme catalyzing the reduction of 3-dehydroshikimate (3DHS) to shikimate (SKM) utilizing NADPH cofactor in the shikimate pathway, a central route for biosynthesis of aromatic amino acids, folates and ubiquinones in microogransims, plants and parasites, which renders the enzymes of this essential pathway as attractive targets for developing antimicrobials, herbicides and antiparasitic agents. In this study, the crystal structure of Mycobacterium tuberculosis SDH (MtSDH) was determined in the apo-form and in complex with a ligand, SKM. The overall structure of MtSDH contains two structural domains with ?/? architecture. The N-terminal substrate binding domain and C-terminal cofactor binding domain are interconnected by two helices forming an active site groove where catalysis occurs. In MtSDH, a series of helices connecting ?10 and ?11 strands replace a long loop found in other known SDH structures and this region may undergo structural changes upon cofactor binding. NADP^(+) was modeled reliably in the cofactor binding site to gain insight into specific interactions. The analysis reveals that NADP(H) binds in anti conformation and in addition to residues in "basic patch", Ser125 within the glycine rich loop may interact with the 2'-phosphate of adenine ribose and form a novel cofactor binding microenvironment in SDH family of enzymes. Biochemically, five inhibitors identified previously from a high-throughput enzyme assay screen were evaluated. The IC_(50) values of these compounds range from 2.8-4.6 uM. Further investigation indicates that these compounds display non-competitive or mixed inhibition mode with both substrate and cofactor. This study is expected to provide better understanding of MtSDH structural features and a framework for rational design of inhibitors based on initially characterized compounds.
