Evolution of a transition state

Role of lys100 in the active site of isocitrate dehydrogenase

Stephen P. Miller, Susana Gonçalves, Pedro M. Matias, Antony M. Dean

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β-decarboxylation at the (2R)-malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH, the negatively charged C4-carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize - and perhaps even protonate - an oxyanion formed on the nicotinamide 3-carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH might catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K+ and NH4+ represents a throwback to the primordial state of the first promiscuous substrate family member. Same but different: In isocitrate dehydrogenase, the substrate C4-carboxylate abuts the positively charged nicotin- amide of the coenzyme. Lys100 stabilizes the oxyanion formed on the nicotin- amide 3-carboxamide so that hydride transfer can occur without neutralizing the positive charge on the nicotinamide. This transition state differs in related dehydrogenases without this lysine.

Original languageEnglish
Pages (from-to)1145-1153
Number of pages9
JournalChembiochem
Volume15
Issue number8
DOIs
Publication statusPublished - 26 May 2014

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Keywords

  • catalysis
  • evolution
  • hydride transfer
  • isocitrate dehydrogenases

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