Figure 4

Location and Effect of CDK8 Substitutions on the Protein Structure

(A) Overall structure of CDK8 (light gray) in complex with cyclin C (dark gray). ATP (blue) was modeled into the CDK8 DMG-in crystal structure (PDB: 4F7S)¹⁸ using aligned CDK9 (PDB 3BLQ).¹⁹ Regions not previously resolved in the crystal structure have been modeled using Molecular Operating Environment (MOE).²⁰

(B) A magnified view of the catalytic region of the CDK8 kinase domain. The Mg²⁺ is shown as a green sphere. Amino acids at which mutations have been identified are colored in orange (except Ser62 in red and Arg178 in yellow), and relevant, potential interaction partners in the input structure are shown as sticks. Ile223 is in close proximity (double-headed arrow) to the Lys153 involved in interaction with ATP-phosphate. Arg178 forms a hydrogen bond with Tyr32 (Gly-rich loop) and interacts ionically with the catalytic Asp151.

(C) A magnified overlay of the wild-type (WT) and mutant molecular-dynamics simulations of CDK8 (light gray) in complex with cyclin C (dark gray) in the presence of ATP (blue spheres). The areas displaying the most pronounced structural differences within the substrate binding site are colored (blue: WT, red: p.Ser62Leu, and yellow: p.Arg178Gln).