title: Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids.
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, k(cat)/K(m) = 2 x 10(4) 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 Ca(2+) sequestering and/or in carbon scavenging from alpha-hydroxycarboxylate catabolites during the biochemical transition accompanying petal senescence.
authors.affiliation: Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA.
authors.forename: Zhibing
authors.initials: Z
authors.lastname: Lu
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Feng
authors.forename: Ling
authors.initials: L
authors.lastname: Song
authors.forename: Ying
authors.initials: Y
authors.lastname: Han
authors.forename: Alexander
authors.initials: A
authors.lastname: Kim
authors.forename: Osnat
authors.initials: O
authors.lastname: Herzberg
authors.forename: William R
authors.initials: WR
authors.lastname: Woodson
authors.forename: Brian M
authors.initials: BM
authors.lastname: Martin
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Mariano
authors.forename: Debra
authors.initials: D
authors.lastname: Dunaway-Mariano
mesh_terms: D000595:Amino Acid Sequence; D002264:Carboxylic Acids / Q000378:metabolism*; D002384:Catalysis; D003001:Cloning, Molecular; D029749:Dianthus / Q000201:enzymology*; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D007522:Isocitrate Lyase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D002264:Carboxylic Acids; D010940:Plant Proteins; D007522:Isocitrate Lyase