title: Evolution of a transition state: role of Lys100 in the active site of isocitrate dehydrogenase.
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.
authors.affiliation: Biotechnology Institute, The University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108 (USA).
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Miller
authors.forename: Susana
authors.initials: S
authors.lastname: Gonçalves
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Matias
authors.forename: Antony M
authors.initials: AM
authors.lastname: Dean
mesh_terms: D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D007521:Isocitrate Dehydrogenase / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D007700:Kinetics; D008239:Lysine / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D015394:Molecular Structure
chemical_list: D007521:Isocitrate Dehydrogenase; D008239:Lysine
keywords: catalysis; evolution; hydride transfer; isocitrate dehydrogenases