The Power of Vanadate in Crystallographic Investigations of Phosphoryl Transfer Enzymes

FEBS Lett. 2004 Nov 19;577(3):315-21. doi: 10.1016/j.febslet.2004.10.022.

Abstract

The formation of transition state mimics of phosphoryl transfer reactions with the metal oxoanion vanadate is a powerful technique in macromolecular crystallography. The tendency of vanadate to form pentacovalent complexes exhibiting trigonal bipyramidal geometry makes this compound a close approximation of the transition state for such reactions. In many cases, vanadate complexes provide the most accurate visualization of the transition state that can be reasonably achieved. A survey of the Protein Data Bank reveals that a relatively small number of structures (39, representing 23 unique proteins) include vanadate, yet these structures represent four of the six E.C. categories of enzymes, and were obtained in crystals with pH values ranging from 5.0 to 7.8. Vanadate has additional advantages over other compounds such as aluminum fluoride, beryllium fluoride and nitrate used for visualization of transition state mimics in that vanadate readily forms covalent bonds with a variety of ligands and has produced a wider variety of transition state mimics. Given the hundreds of crystal structures that have been solved for phosphoryl transfer enzymes, it is surprising that vanadate has not been used more frequently for visualization of transition state analogs. We propose that an opportunity exists for vanadate to become a more commonly utilized component of the macromolecular crystallographer's toolbox.

Publication types

  • Review

MeSH terms

  • Alkaline Phosphatase / chemistry
  • Alkaline Phosphatase / metabolism
  • Amino Acids / chemistry
  • Animals
  • Binding Sites
  • Crystallography, X-Ray*
  • Databases, Protein
  • Dictyostelium / enzymology
  • Enzymes / chemistry
  • Enzymes / metabolism*
  • Escherichia coli / enzymology
  • Humans
  • Hydrogen-Ion Concentration
  • Ligands
  • Molecular Conformation
  • Myosins / chemistry
  • Myosins / metabolism
  • Phosphates / chemistry*
  • Phosphates / metabolism
  • Phosphoric Diester Hydrolases / chemistry
  • Phosphoric Diester Hydrolases / metabolism
  • Protein Binding
  • Protein Structure, Quaternary
  • RNA, Catalytic / chemistry
  • RNA, Catalytic / metabolism
  • Ribonucleotides / metabolism
  • Vanadates / chemistry*
  • Vanadates / metabolism

Substances

  • Amino Acids
  • Enzymes
  • Ligands
  • Phosphates
  • RNA, Catalytic
  • Ribonucleotides
  • hairpin ribozyme
  • Vanadates
  • Alkaline Phosphatase
  • Phosphoric Diester Hydrolases
  • TDP1 protein, human
  • tyrosyl-DNA phosphodiesterase
  • Myosins