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 ?M. 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.
- Sacchettini, James Professor