title: Briefly bound to activate: transient binding of a second catalytic magnesium activates the structure and dynamics of CDK2 kinase for catalysis.
abstract: 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.
authors.affiliation: Department of Biological Chemistry and the Bioinformatics Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Zhao Qin
authors.initials: ZQ
authors.lastname: Bao
authors.forename: Douglas M
authors.initials: DM
authors.lastname: Jacobsen
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Young
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain; D003001:Cloning, Molecular; D003460:Crystallization; D018360:Crystallography, X-Ray; D019925:Cyclin A / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004789:Enzyme Activation; D004926:Escherichia coli; D005459:Fluorides / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D017616:Magnesium Compounds / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010710:Phosphates / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D019925:Cyclin A; D017616:Magnesium Compounds; D010710:Phosphates; D011994:Recombinant Proteins; C031288:magnesium fluoride; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; C495894:CDK2 protein, human; D051357:Cyclin-Dependent Kinase 2; D005459:Fluorides