Studies of the Enzymic Mechanism of Candida tenuis Xylose Reductase (AKR 2B5): X-ray Structure and Catalytic Reaction Profile for the H113A Mutant

Regina Kratzer, Kathryn L. Kavanagh, David K. Wilson, Bernd Nidetzky

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Abstract

Xylose reductase from the yeast Candida tenuis (CtXR) is a family 2 member of the aldoketo reductase (AKR) superfamily of proteins and enzymes. Active site His-113 is conserved among AKRs, but a unified mechanism of how it affects catalytic activity is outstanding. We have replaced His-113 by alanine using site-directed mutagenesis, determined a 2.2 Å structure of H113A mutant bound to NADP+, and compared catalytic reaction profiles of NADH-dependent reduction of different aldehydes catalyzed by the wild type and the mutant. Deuterium kinetic isotope effects (KIEs) on kcat and kcat/ Km xylose show that, relative to the wild type, the hydride transfer rate constant (k7 ≈ 0.16 s-1) has decreased about 1000-fold in H113A whereas xylose binding was not strongly affected. No solvent isotope effect was seen on kcat and k cat/Km xylose for H113A, suggesting that proton transfer has not become rate-limiting as a result of the mutation. The pH profiles of log(kcat/Km xylose) for the wild type and H113A decreased above apparent pKa values of 8.85 and 7.63, respectively. The ΔpKa of -1.2 pH units likely reflects a proximally disruptive character of the mutation, affecting the position of Asp-50. A steady-state kinetic analysis for H113A-catalyzed reduction of a homologous series of meta-substituted benzaldehyde derivatives was carried out, and quantitative structure-reactivity correlations were used to factor the observed kinetic substituent effect on kcat and kcat/Km aldehyde into an electronic effect and bonding effects (which are lacking in the wild type). Using the Hammett σ scale, electronic parameter coefficients (ρ) of +0.64 (kcat) and +0.78 (k cat/Km aldehyde) were calculated and clearly differ from ρ(kcat/Kaldehyde) and ρ(kcat) values of +1.67 and approximately 0.0, respectively, for the wild-type enzyme. Hydride transfer rate constants of H113A, calculated from kinetic parameters and KIE data, display a substituent dependence not seen in the corresponding wild-type enzyme rate constants. An enzymic mechanism is proposed in which His-113, through a hydrogen bond from Nε2 to aldehyde O1, assists in catalysis by optimizing the C=O bond charge separation and orbital alignment in the ternary complex.

Original languageEnglish (US)
Pages (from-to)4944-4954
Number of pages11
JournalBiochemistry
Volume43
Issue number17
DOIs
StatePublished - May 4 2004

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Aldehyde Reductase
Candida
Xylose
Aldehydes
Oxidoreductases
X-Rays
Isotopes
X rays
Rate constants
Kinetics
Hydrides
Enzymes
Electronic scales
Cats
Mutagenesis
Proton transfer
Deuterium
Data Display
NADP
Mutation

ASJC Scopus subject areas

  • Biochemistry

Cite this

Studies of the Enzymic Mechanism of Candida tenuis Xylose Reductase (AKR 2B5) : X-ray Structure and Catalytic Reaction Profile for the H113A Mutant. / Kratzer, Regina; Kavanagh, Kathryn L.; Wilson, David K.; Nidetzky, Bernd.

In: Biochemistry, Vol. 43, No. 17, 04.05.2004, p. 4944-4954.

Research output: Contribution to journalArticle

Kratzer, Regina ; Kavanagh, Kathryn L. ; Wilson, David K. ; Nidetzky, Bernd. / Studies of the Enzymic Mechanism of Candida tenuis Xylose Reductase (AKR 2B5) : X-ray Structure and Catalytic Reaction Profile for the H113A Mutant. In: Biochemistry. 2004 ; Vol. 43, No. 17. pp. 4944-4954.
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abstract = "Xylose reductase from the yeast Candida tenuis (CtXR) is a family 2 member of the aldoketo reductase (AKR) superfamily of proteins and enzymes. Active site His-113 is conserved among AKRs, but a unified mechanism of how it affects catalytic activity is outstanding. We have replaced His-113 by alanine using site-directed mutagenesis, determined a 2.2 {\AA} structure of H113A mutant bound to NADP+, and compared catalytic reaction profiles of NADH-dependent reduction of different aldehydes catalyzed by the wild type and the mutant. Deuterium kinetic isotope effects (KIEs) on kcat and kcat/ Km xylose show that, relative to the wild type, the hydride transfer rate constant (k7 ≈ 0.16 s-1) has decreased about 1000-fold in H113A whereas xylose binding was not strongly affected. No solvent isotope effect was seen on kcat and k cat/Km xylose for H113A, suggesting that proton transfer has not become rate-limiting as a result of the mutation. The pH profiles of log(kcat/Km xylose) for the wild type and H113A decreased above apparent pKa values of 8.85 and 7.63, respectively. The ΔpKa of -1.2 pH units likely reflects a proximally disruptive character of the mutation, affecting the position of Asp-50. A steady-state kinetic analysis for H113A-catalyzed reduction of a homologous series of meta-substituted benzaldehyde derivatives was carried out, and quantitative structure-reactivity correlations were used to factor the observed kinetic substituent effect on kcat and kcat/Km aldehyde into an electronic effect and bonding effects (which are lacking in the wild type). Using the Hammett σ scale, electronic parameter coefficients (ρ) of +0.64 (kcat) and +0.78 (k cat/Km aldehyde) were calculated and clearly differ from ρ(kcat/Kaldehyde) and ρ(kcat) values of +1.67 and approximately 0.0, respectively, for the wild-type enzyme. Hydride transfer rate constants of H113A, calculated from kinetic parameters and KIE data, display a substituent dependence not seen in the corresponding wild-type enzyme rate constants. An enzymic mechanism is proposed in which His-113, through a hydrogen bond from Nε2 to aldehyde O1, assists in catalysis by optimizing the C=O bond charge separation and orbital alignment in the ternary complex.",
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