Diversity of Function in the Isocitrate Lyase Enzyme Superfamily: TheDianthus caryophyllusPetal Death Protein Cleaves α-Keto and α-Hydroxycarboxylic Acids

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Abstract
The work described in this paper was carried out to define the chemical function a new member of the isocitrate lyase enzyme family derived from the flowering plant Dianthus caryophyllus. This protein (Swiss-Prot entry Q05957) is synthesized in the senescent flower petals and is named the “petal death protein” or “PDP”. On the basis of an analysis of the structural contexts of sequence markers common to the C−C bond lyases of the isocitrate lyase/phosphoenolpyruvate mutase superfamily, a substrate screen that employed a (2R)-malate core structure was designed. Accordingly, stereochemically defined C(2)- and C(3)-substituted malates were synthesized and tested as substrates for PDP-catalyzed cleavage of the C(2)−C(3) bond. The screen identified (2R)-ethyl, (3S)-methylmalate, and oxaloacetate [likely to bind as the hydrate, C(2)(OH)2 gem-diol] as the most active substrates (for each, kcat/Km = 2 × 104 M-1 s-1). In contrast to the stringent substrate specificities previously observed for the Escherichia coli isocitrate and 2-methylisocitrate lyases, the PDP tolerated hydrogen, methyl, and to a much lesser extent acetate substituents at the C(3) position (S configuration only) and hydoxyl, methyl, ethyl, propyl, and to a much lesser extent isobutyl substituents at C(2) (R configuration only). It is hypothesized that PDP functions in oxalate production in Ca2+ sequestering and/or in carbon scavenging from α-hydroxycarboxylate catabolites during the biochemical transition accompanying petal senescence.

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