Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase

Biochemistry. 2007 May 8;46(18):5391-7. doi: 10.1021/bi700061t. Epub 2007 Apr 14.


Human NAD-dependent isocitrate dehydrogenase (IDH) is allosterically activated by ADP by lowering the Km for isocitrate. The enzyme has three subunit types with distinguishable sequences present in the approximate ratio 2alpha:1beta:1gamma and, per tetramer, binds 2 mol of each ligand. To evaluate whether the subunits also have distinct functions, we replaced equivalent aspartates, one subunit at a time, by asparagines; each expressed, purified enzyme was composed of one mutant and two wild-type subunits. The aspartates were chosen because beta-Asp192 and gamma-Asp190 had previously been affinity labeled by a reactive ADP analogue and alpha-Asp181 is equivalent based on sequence alignments. The alpha-D181N IDH mutant exhibits a 2000-fold decrease in Vmax, with increases of 15-fold in the Kms for Mn(II) and NAD and a much smaller change in the Km for isocitrate. In contrast, the Vmax values of the beta-D192N and gamma-D190N IDHs are only reduced 4-5-fold as compared to wild-type enzyme. The Km for NAD of the beta-D192N enzyme is 9 times that of the normal enzyme with little or no effect on the affinity for Mn(II) or isocitrate, while the Kms for coenzyme and for Mn(II) of the gamma-D190N enzyme are 19 and 72 times, respectively, that of the normal enzyme with a much smaller effect on the Km for isocitrate. Finally, all three mutant enzymes fail to respond to ADP by lowering the Km for isocitrate, although they do bind ADP. Thus, these aspartates are close to but not in the ADP site and are required for communication between the ADP and isocitrate sites. These results demonstrate that alpha-Asp181 is the only one of these aspartates essential for catalysis. Beta-Asp192 is a determinant of the enzyme's affinity for NAD, as is gamma-Asp190, while gamma-Asp190 also influences the enzyme's affinity for metal ion. We conclude that the NAD and ADP sites are shared between alpha- and beta- and alpha- and gamma-subunits, and the Mn(II) site is shared between alpha- and gamma-subunits, while the alpha-subunit is essential for catalysis. Although alpha-Asp181, beta-Asp192, and gamma-Asp190 may have derived from a common progenitor, these aspartates of the three subunits have evolved distinct functions.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Diphosphate / chemistry
  • Adenosine Diphosphate / metabolism
  • Asparagine / genetics
  • Aspartic Acid / chemistry*
  • Aspartic Acid / genetics
  • Catalytic Domain / genetics
  • Humans
  • Isocitrate Dehydrogenase / chemistry*
  • Isocitrate Dehydrogenase / genetics
  • Isocitrate Dehydrogenase / physiology
  • Mutagenesis, Site-Directed
  • NAD / chemistry*
  • NAD / genetics
  • Protein Subunits / chemistry*
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • Structure-Activity Relationship
  • Substrate Specificity / genetics


  • Protein Subunits
  • NAD
  • Aspartic Acid
  • Adenosine Diphosphate
  • Asparagine
  • Isocitrate Dehydrogenase
  • isocitrate dehydrogenase (NADP+)