Structure and quantum chemical analysis of NAD + ‐dependent isocitrate dehydrogenase: Hydride transfer and co‐factor specificity

The crystal structure of Acidithiobacillus thiooxidans isocitrate dehydrogenase complexed with NAD + and citrate has been solved to a resolution of 1.9 Å. The protein fold of this NAD + ‐dependent enzyme shares a high similarity with those of NADP + ‐dependent bacterial ICDHs. The NAD + and the citrate are clearly identified in the active site cleft with a well‐defined electron density. Asp‐357 is the direct cofactor‐specificity determinant that interacts with 2′‐OH and 3′‐OH of the adenosine ribose. The adenosine ribose takes a C2′‐endo puckering conformation as previously reported for an NAD + ‐specific isopropylmalate dehydrogenase. The nicotinamide moiety of NAD + has the amide NH 2 group oriented in cis conformation with respect to the C4 carbon of the nicotinamide ring, slanted toward the bound citrate molecule with a dihedral angle of −21°. The semi‐empirical molecular orbital calculation suggests that the pro‐R hydrogen atom at C4 of NADH would bear the largest negative charge when the amide NH 2 group is in such conformation, suggesting that the amide group has a catalytically significant role in stabilizing the transition state as NADH is being formed during the hydride transfer catalysis. Proteins 2008. © 2007 Wiley‐Liss, Inc.