Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction

J Biol Chem. 2003 Oct 17;278(42):41069-76. doi: 10.1074/jbc.M305865200. Epub 2003 Jul 26.

Abstract

The pyridoxal 5'-phosphate-dependent enzymes have been evolved to catalyze diverse substrates and to cause the reaction to vary. 1-Aminocyclopropane-1-carboxylate deaminase catalyzes the cyclopropane ring-opening reaction followed by deamination specifically. Since it was discovered in 1978, the enzyme has been widely investigated from the mechanistic and physiological viewpoints because the substrate is a precursor of the plant hormone ethylene and the enzymatic reaction includes a cyclopropane ring-opening. We have previously reported the crystal structure of the native enzyme. Here we report the crystal structures of the two reaction intermediates created by the mutagenesis complexed with the substrate. The substrate was validated in the active site of two forms: 1). covalent-bonded external aldimine with the coenzyme in the K51T form and 2). the non-covalent interaction around the coenzyme in the Y295F form. The orientations of the substrate in both structures were quite different form each other. In concert with other site-specific mutation experiments, this experiment revealed the ingenious and unique strategies that are used to achieve the specific activity. The substrate incorporated into the active site is reactivated by a two-phenol charge relay system to lead to the formation of a Schiff base with the coenzyme. The catalytic Lys51 residue may play a novel role to abstract the methylene proton from the substrate in cooperation with other factors, the carboxylate group of the substrate and the electron-adjusting apparatuses of the coenzyme.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Carbon-Carbon Lyases / chemistry*
  • Carbon-Carbon Lyases / genetics
  • Catalysis
  • Crystallography, X-Ray
  • Cyclopropanes / chemistry*
  • Electrons
  • Escherichia coli / metabolism
  • Lysine / chemistry
  • Models, Chemical
  • Models, Molecular
  • Mutagenesis
  • Mutation
  • Protein Binding
  • Salmonella typhimurium / metabolism

Substances

  • Cyclopropanes
  • cyclopropane
  • 1-aminocyclopropane-1-carboxylate deaminase
  • Carbon-Carbon Lyases
  • Lysine

Associated data

  • PDB/1F2D
  • PDB/1J0C
  • PDB/1J0D
  • PDB/1J0E