Structural and biochemical characterization of compounds inhibiting Mycobacterium tuberculosis pantothenate kinase

J Biol Chem. 2013 Jun 21;288(25):18260-70. doi: 10.1074/jbc.M113.476473. Epub 2013 May 9.


Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms.

Keywords: CoaA; Coenzyme A; Crystal Structure; Drug Design; Enzyme Inhibitors; Mycobacterium tuberculosis; Pantothenate Kinase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Biocatalysis / drug effects
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Mycobacterium tuberculosis / enzymology*
  • Pantothenic Acid / analogs & derivatives
  • Pantothenic Acid / metabolism
  • Phosphotransferases (Alcohol Group Acceptor) / chemistry*
  • Phosphotransferases (Alcohol Group Acceptor) / genetics
  • Phosphotransferases (Alcohol Group Acceptor) / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Bacterial Proteins
  • Enzyme Inhibitors
  • Pantothenic Acid
  • phosphopantothenic acid
  • Adenosine Triphosphate
  • Phosphotransferases (Alcohol Group Acceptor)
  • pantothenate kinase

Associated data

  • PDB/4BFS
  • PDB/4BFT
  • PDB/4BFU
  • PDB/4BFV
  • PDB/4BFW
  • PDB/4BFX
  • PDB/4BFY
  • PDB/4BFZ