The structures of NADP+ and magnesium isocitrate bound to the NADP(+)-dependent isocitrate dehydrogenase of Escherichia coli have been determined and refined at 2.5-A resolution. NADP+ is bound by the large domain of isocitrate dehydrogenase, a structure that has little similarity to the supersecondary structure of the nucleotide-binding domain of the lactate dehydrogenase-like family of nucleotide-binding proteins ...
The structures of NADP+ and magnesium isocitrate bound to the NADP(+)-dependent isocitrate dehydrogenase of Escherichia coli have been determined and refined at 2.5-A resolution. NADP+ is bound by the large domain of isocitrate dehydrogenase, a structure that has little similarity to the supersecondary structure of the nucleotide-binding domain of the lactate dehydrogenase-like family of nucleotide-binding proteins. The coenzyme-binding site confirms the fundamentally different evolution of the isocitrate dehydrogenase-like and the lactate dehydrogenase-like classes of nucleotide-binding proteins. In the magnesium-isocitrate complex, magnesium is coordinated to the alpha-carboxylate and alpha-hydroxyl oxygen of isocitrate in a manner suitable for stabilization of a negative charge on the hydroxyl oxygen during both the dehydrogenation and decarboxylation steps of the conversion of isocitrate to alpha-ketoglutarate. The metal ion is also coordinated by aspartate side chains 283' (of the second subunit of the dimer) and 307 and two water molecules in a roughly octahedral arrangement. On the basis of the geometry of the active site, the base functioning in the dehydrogenation step is most likely aspartate 283'. E. coli isocitrate dehydrogenase transfers a hydride stereospecifically to the A-side of NADP+, and models for a reactive ternary complex consistent with this stereospecificity are discussed.
Related Citations:
Regulation of an Enzyme by Phosphorylation at the Active Site Hurley, J.H., Dean, A.M., Sohl, J.L., Koshlandjunior, D.E., Stroud, R.M. (1990) Science 249: 1012
Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-Range Conformational Change in the Free Enzyme Hurley, J.H., Dean, A.M., Thorsness, P.E., Koshlandjunior, D.E., Stroud, R.M. (1990) J Biol Chem 265: 3599
Regulation of an Enzyme by Phosphorylation at the Active Site Hurley, J.H., Dean, A.M., Sohl, J.L., Koshlandjunior, D.E., Stroud, R.M. (1990) Science 249: 1012
Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase Hurley, J.H., Thorsness, P.E., Ramalingam, V., Helmers, N.H., Koshlandjunior, D.E., Stroud, R.M. (1989) Proc Natl Acad Sci U S A 86: 8635
Organizational Affiliation:
Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.
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