Functions of the D-ribosyl moiety and the lower axial ligand of the nucleotide loop of coenzyme B(12) in diol dehydratase and ethanolamine ammonia-lyase reactions

J Biochem. 2002 Dec;132(6):935-43. doi: 10.1093/oxfordjournals.jbchem.a003307.

Abstract

The roles of the D-ribosyl moiety and the bulky axial ligand of the nucleotide loop of adenosylcobalamin in coenzymic function have been investigated using two series of coenzyme analogs bearing various artificial bases. The 2-methylbenzimidazolyl trimethylene analog that exists exclusively in the base-off form was a totally inactive coenzyme for diol dehydratase and served as a competitive inhibitor. The benzimidazolyl trimethylene analog and the benzimidazolylcobamide coenzyme were highly active for diol dehydratase and ethanolamine ammonia-lyase. The imidazolylcobamide coenzyme was 59 and 9% as active as the normal coenzyme for diol dehydratase and ethanolamine ammonia-lyase, respectively. The latter analog served as an effective suicide coenzyme for both enzymes, although the partition ratio (k(cat)/k(inact)) of 630 for ethanolamine ammonia-lyase is much lower than that for diol dehydratase. Suicide inactivation was accompanied by the accumulation of a cob(II)amide species, indicating irreversible cleavage of the coenzyme Co-C bond during the inactivation. It was thus concluded that the bulkiness of a Co-coordinating base of the nucleotide loop is essential for both the initial activity and continuous catalytic turnovers. Since the k(cat)/k(inact) value for the imidazolylcobamide in diol dehydratase was 27-times higher than that for the imidazolyl trimethylene analog, it is clear that the ribosyl moiety protects the reaction intermediates from suicide inactivation. Stopped-flow measurements indicated that the rate of Co-C bond homolysis is essentially unaffected by the bulkiness of the Co-coordinating base for diol dehydratase. Thus, it seems unlikely that the Co-C bond is labilized through a ground state mechanochemical triggering mechanism in diol dehydratase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoenzymes / chemistry
  • Apoenzymes / metabolism
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Cobamides / chemistry*
  • Cobamides / metabolism
  • Ethanolamine Ammonia-Lyase / chemistry
  • Ethanolamine Ammonia-Lyase / metabolism*
  • Ligands*
  • Molecular Structure
  • Nucleic Acid Conformation*
  • Propanediol Dehydratase / chemistry
  • Propanediol Dehydratase / metabolism*
  • Spectrum Analysis

Substances

  • Apoenzymes
  • Bacterial Proteins
  • Cobamides
  • Ligands
  • Propanediol Dehydratase
  • Ethanolamine Ammonia-Lyase
  • cobamamide