Transition-state analysis of AMP deaminase

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Abstract

The transition state of the allosteric AMP deaminase from Saccharomyces cerevisiae has been characterized by 14C and 15N Kmax/Km heavy-atom kinetic isotope effects. The primary 6-14C isotope effect was measured with [6-14C] AMP, and the 6-15N primary isotope effect was measured by isotope ratio mass spectrometry using the natural abundance of 15N in AMP and by using 15N release from ATP as a slow substrate. Isotope effects for AMP as the substrate were measured in the presence and absence of ATP as an allosteric activator and GTP as an allosteric inhibitor. Kinetic isotope effects with [6-14C] AMP were 1.030 ± 0.003, 1.038 ± 0.004, and 1.042 ± 0.003 in the absence of effectors and in the presence of ATP and GTP, respectively. Isotope effects for [6-15N]AMP averaged 1.010 ± 0.002. Allosteric activation increased the 15N isotope effect to 1.016 ± 0.003. A primary 15N kinetic isotope effect with ATP, which has a Vmax/Km 10-6 that for AMP, was 1.013 ± 0.001. The presence of D2O as solvent caused a marginally significant decrease in the [6-15N] AMP kinetic isotope effect from 1.011 ± 0.001 to 1.007 ± 0.002. Previous studies have established that the solvent D2O effect is inverse (0.34) for slow substrates with two or more protons transferred prior to transition state formation and remains inverse (0.79) with AMP as substrate [Merkler, D. J., & Schramm, V. L. (1993) Biochemistry 32, 5792-5799]. Bond vibrational analysis was used to identify transition states for AMP deaminase that are consistent with all kinetic isotope effects. Fully concerted reaction mechanisms can be eliminated, since these would result in normal D2O solvent isotope effects and are inconsistent with 14C and 15N kinetic isotope effects. The transition state most consistent with the data is characterized by an attacking hydroxyl with a bond order near 0.8, a fully bonded NH2, nearly complete conversion to sp3 at C6, and highly asymmetric, nearly complete protonation of N1. This transition state leads to the formation of a short-lived tetrahedral intermediate. Formation of the tetrahedral intermediate is slow, while protonation of NH2 in the intermediate and departure of NH3 occur in rapid steps.

Original languageEnglish (US)
Pages (from-to)12993-13001
Number of pages9
JournalBiochemistry®
Volume32
Issue number48
StatePublished - 1993

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AMP Deaminase
Isotopes
Adenosine Monophosphate
Kinetics
Adenosine Triphosphate
Protonation
Substrates
Guanosine Triphosphate
Biochemistry

ASJC Scopus subject areas

  • Biochemistry

Cite this

Transition-state analysis of AMP deaminase. / Schramm, Vern L.

In: Biochemistry®, Vol. 32, No. 48, 1993, p. 12993-13001.

Research output: Contribution to journalArticle

Schramm, VL 1993, 'Transition-state analysis of AMP deaminase', Biochemistry®, vol. 32, no. 48, pp. 12993-13001.
Schramm, Vern L. / Transition-state analysis of AMP deaminase. In: Biochemistry®. 1993 ; Vol. 32, No. 48. pp. 12993-13001.
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abstract = "The transition state of the allosteric AMP deaminase from Saccharomyces cerevisiae has been characterized by 14C and 15N Kmax/Km heavy-atom kinetic isotope effects. The primary 6-14C isotope effect was measured with [6-14C] AMP, and the 6-15N primary isotope effect was measured by isotope ratio mass spectrometry using the natural abundance of 15N in AMP and by using 15N release from ATP as a slow substrate. Isotope effects for AMP as the substrate were measured in the presence and absence of ATP as an allosteric activator and GTP as an allosteric inhibitor. Kinetic isotope effects with [6-14C] AMP were 1.030 ± 0.003, 1.038 ± 0.004, and 1.042 ± 0.003 in the absence of effectors and in the presence of ATP and GTP, respectively. Isotope effects for [6-15N]AMP averaged 1.010 ± 0.002. Allosteric activation increased the 15N isotope effect to 1.016 ± 0.003. A primary 15N kinetic isotope effect with ATP, which has a Vmax/Km 10-6 that for AMP, was 1.013 ± 0.001. The presence of D2O as solvent caused a marginally significant decrease in the [6-15N] AMP kinetic isotope effect from 1.011 ± 0.001 to 1.007 ± 0.002. Previous studies have established that the solvent D2O effect is inverse (0.34) for slow substrates with two or more protons transferred prior to transition state formation and remains inverse (0.79) with AMP as substrate [Merkler, D. J., & Schramm, V. L. (1993) Biochemistry 32, 5792-5799]. Bond vibrational analysis was used to identify transition states for AMP deaminase that are consistent with all kinetic isotope effects. Fully concerted reaction mechanisms can be eliminated, since these would result in normal D2O solvent isotope effects and are inconsistent with 14C and 15N kinetic isotope effects. The transition state most consistent with the data is characterized by an attacking hydroxyl with a bond order near 0.8, a fully bonded NH2, nearly complete conversion to sp3 at C6, and highly asymmetric, nearly complete protonation of N1. This transition state leads to the formation of a short-lived tetrahedral intermediate. Formation of the tetrahedral intermediate is slow, while protonation of NH2 in the intermediate and departure of NH3 occur in rapid steps.",
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