The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition.
Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.
Cheng
Kin-Yip
KY
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
Noble
Martin E M
ME
Skamnaki
Vicky
V
Brown
Nick R
NR
Lowe
Ed D
ED
Kontogiannis
Luke
L
Shen
Kui
K
Cole
Philip A
PA
Siligardi
Giuliano
G
Johnson
Louise N
LN
D000255:Adenosine Triphosphate / Q000737:chemistry; D020816:Amino Acid Motifs; D020134:Catalytic Domain; D019925:Cyclin A / Q000737:chemistry*; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry*; D006801:Humans; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
D019925:Cyclin A; D010455:Peptides; D000255:Adenosine Triphosphate; D051357:Cyclin-Dependent Kinase 2