Mutational analysis of Mycobacterium tuberculosis lysine ɛ-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes

Biochem Biophys Res Commun. 2015 Jul;463(1-2):154-60. doi: 10.1016/j.bbrc.2015.05.055. Epub 2015 May 20.


Lysine ɛ-aminotransferase (LAT) converts lysine to α-aminoadipate-δ-semialdehyde in a PLP-mediated reaction. We mutated active-site T330, N328 and E243, and structurally rationalized their properties. T330A and T330S mutants cannot bind PLP and are inactive. N328A although inactive, binds to PLP. E243A retains activity, but binds α-ketoglutarate in a different conformation. We had earlier identified 2-aminomethyl piperidine derivative as a LAT inhibitor. The co-crystal structure reveals that it mimics binding of C5 substrates and exhibits two binding modes. E243, that shields R422 in the apo enzyme, exhibits conformational changes to permit the binding of the inhibitor in one of the binding modes. Structure-based analysis of bound water in the active site suggests optimization strategies for synthesis of improved inhibitors.

Keywords: 2-Aminomethyl piperidine derivative; Crystal structure; Glu243 switch; Lysine ε-aminotransferase; Mycobacterium tuberculosis; α-ketoglutarate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics*
  • Catalytic Domain / genetics
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Ketoglutaric Acids / metabolism
  • L-Lysine 6-Transaminase / antagonists & inhibitors
  • L-Lysine 6-Transaminase / chemistry*
  • L-Lysine 6-Transaminase / genetics*
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Mycobacterium tuberculosis / enzymology*
  • Mycobacterium tuberculosis / genetics*
  • Piperidines / chemistry
  • Piperidines / pharmacology
  • Protein Conformation
  • Pyridoxal Phosphate / metabolism
  • Static Electricity


  • Bacterial Proteins
  • Enzyme Inhibitors
  • Ketoglutaric Acids
  • Piperidines
  • Pyridoxal Phosphate
  • L-Lysine 6-Transaminase