Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes

Biochemistry. 2000 Sep 5;39(35):10702-10. doi: 10.1021/bi9927080.


The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.

Publication types

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

MeSH terms

  • Animals
  • Apoenzymes / chemistry
  • Apoenzymes / metabolism
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Computer Simulation
  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Glyceraldehyde 3-Phosphate / chemistry
  • Glyceraldehyde 3-Phosphate / metabolism
  • Glyceraldehyde-3-Phosphate Dehydrogenases / chemistry*
  • Glyceraldehyde-3-Phosphate Dehydrogenases / metabolism
  • Holoenzymes / chemistry
  • Holoenzymes / metabolism
  • Humans
  • Models, Molecular
  • NAD / chemistry*
  • NAD / metabolism
  • Nephropidae
  • Protein Conformation
  • Structure-Activity Relationship
  • Substrate Specificity


  • Apoenzymes
  • Bacterial Proteins
  • Holoenzymes
  • NAD
  • Glyceraldehyde 3-Phosphate
  • Glyceraldehyde-3-Phosphate Dehydrogenases

Associated data

  • PDB/1DC3
  • PDB/1DC4
  • PDB/1DC5
  • PDB/1DC6