Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis

J Biol Chem. 2003 Mar 14;278(11):9481-8. doi: 10.1074/jbc.M209235200. Epub 2002 Dec 17.


Aspartate aminotransferase has been known to undergo a significant conformational change, in which the small domain approaches the large domain, and the residues at the entrance of the active site pack together, on binding of substrates. Accompanying this conformational change is a two-unit increase in the pK(a) of the pyridoxal 5'-phosphate-Lys(258) aldimine, which has been proposed to enhance catalysis. To elucidate how the conformational change is coupled to the shift in the aldimine pK(a) and how these changes are involved in catalysis, we analyzed structurally and kinetically an enzyme in which Val(39) located at both the domain interface and the entrance of the active site was replaced with a bulkier residue, Phe. The V39F mutant enzyme showed a more open conformation, and the aldimine pK(a) was lowered by 0.7 unit compared with the wild-type enzyme. When Asn(194) had been replaced by Ala in advance, the V39F mutation did not decrease the aldimine pK(a), showing that the domain rotation controls the aldimine pK(a) via the Arg(386)-Asn(194)-pyridoxal 5'-phosphate linkage system. The maleate-bound V39F enzyme showed the aldimine pK(a) 0.9 unit lower than that of the maleate-bound wild-type enzyme. However, the positions of maleate, Asn(194), and Arg(386) were superimposable between the mutant and the wild-type enzymes; therefore, the domain rotation was not the cause of the lowered aldimine pK(a) value. The maleate-bound V39F enzyme showed an altered side-chain packing pattern in the 37-39 region, and the lack of repulsion between Gly(38) carbonyl O and Tyr(225) Oeta seemed to be the cause of the reduced pK(a) value. Kinetic analysis suggested that the repulsion increases the free energy level of the Michaelis complex and promotes the catalytic reaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aspartate Aminotransferases / chemistry*
  • Aspartic Acid / chemistry
  • Binding Sites
  • Catalysis
  • Escherichia coli / enzymology
  • Glycine / chemistry
  • Hydrogen-Ion Concentration
  • Kinetics
  • Ligands
  • Lysine / chemistry
  • Malates / chemistry
  • Models, Chemical
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Mutation
  • N-Methylaspartate / pharmacology
  • Oxygen / metabolism
  • Photons
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Spectrophotometry
  • Tyrosine / chemistry
  • Valine / chemistry


  • Ligands
  • Malates
  • Aspartic Acid
  • Tyrosine
  • N-Methylaspartate
  • malic acid
  • Aspartate Aminotransferases
  • Valine
  • Lysine
  • Oxygen
  • Glycine

Associated data

  • PDB/1IX6
  • PDB/1IX7
  • PDB/1IX8