A close-packed planar 4-atom motif serves as a variable-pathway mechanistic switching device in enzymatic catalysis

Bioorg Chem. 2002 Jun;30(3):199-210. doi: 10.1006/bioo.2002.1243.

Abstract

We have found a new kind of structural motif that appears to be highly conserved among the pyridine nucleotide-linked alpha-amino acid dehydrogenases. This feature is comprised of four atoms closely packed in a planar form. Two of the atoms are donated by the enzyme, one is provided by the substrate (or reactive intermediate), a bound water molecule constitutes the fourth. This tetrad, by virtue of its spatial connectivity, constitutes a two-dimensional machine in contrast to the one-dimensional charge-relay system commonly observed at enzyme active sites. As such, this new motif is capable of more complex behavior permitting a wide variety of possible bonding patterns. Modulation of these potentially variable patterns can lead to qualitative differences in mechanism between structurally similar enzymes, and, in the case of a given enzyme, may constitute the core of its catalytic machinery. We offer a conjecture as to how such a structure may participate in enzymatic catalysis.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Catalysis
  • Catalytic Domain*
  • Conserved Sequence
  • D-Amino-Acid Oxidase / chemistry*
  • D-Amino-Acid Oxidase / metabolism*
  • Hydrogen Bonding
  • Kinetics
  • Models, Molecular
  • Protein Conformation
  • Water / chemistry
  • Water / metabolism

Substances

  • Water
  • D-Amino-Acid Oxidase