Briefly bound to activate: transient binding of a second catalytic magnesium activates the structure and dynamics of CDK2 kinase for catalysis

Structure. 2011 May 11;19(5):675-90. doi: 10.1016/j.str.2011.02.016.


We have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF(3)(-). Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg(2+) ion in the active site. Coupled with a strong [Mg(2+)] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg(2+) ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg(2+) concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg(2+) ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated γ-phosphate from solvent.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Diphosphate / metabolism*
  • Adenosine Triphosphate / metabolism
  • Biocatalysis
  • Catalytic Domain
  • Cloning, Molecular
  • Crystallization
  • Crystallography, X-Ray
  • Cyclin A / chemistry*
  • Cyclin A / genetics
  • Cyclin A / metabolism
  • Cyclin-Dependent Kinase 2 / chemistry*
  • Cyclin-Dependent Kinase 2 / genetics
  • Cyclin-Dependent Kinase 2 / metabolism
  • Enzyme Activation
  • Escherichia coli
  • Fluorides / metabolism*
  • Humans
  • Kinetics
  • Magnesium Compounds / metabolism*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Phosphates / metabolism
  • Protein Binding
  • Protein Conformation
  • Recombinant Proteins / chemistry*
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Substrate Specificity


  • Cyclin A
  • Magnesium Compounds
  • Phosphates
  • Recombinant Proteins
  • magnesium fluoride
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • CDK2 protein, human
  • Cyclin-Dependent Kinase 2
  • Fluorides

Associated data

  • PDB/3QHR
  • PDB/3QHW