1kmw

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

MODEL STRUCTURE OF THE CATALYTIC SUBUNIT-REGULATORY SUBUNIT DIMERIC COMPLEX OF THE C-AMP-DEPENDENT PROTEIN KINASE

spinqualitylabelsall models 1kmw Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, PDBsum, ProSAT Publication Abstract from PubMed Previous neutron scattering studies elaborated the topographical relationship of the regulatory (R(IIalpha)) and catalytic (C(alpha)) subunits of the cAMP-dependent protein kinase. We present here the results of a set of computations that lead to an atomic model of the cAMP-dependent protein kinase heterodimer, Delta(1-91)R(IIalpha)-C(alpha). The first step in the modeling utilized the crystal structures for the porcine C(alpha) and bovine Delta(1-90)R(Ialpha) or rat Delta(1-111)R(IIbeta), to homology-model structures of the species and isoforms that had been used in the neutron scattering experiments (bovine C(alpha) subunit and murine Delta(1-91)R(IIalpha) subunit, respectively). A docking procedure, constrained by the dimensions and positions of the ellipsoids in the neutron-derived R-C model as well as mutagenesis data, was used to develop "best fit" models for the heterodimer. Simulated annealing, molecular dynamics, and energy minimization were then used to refine the side chain packing at the heterodimer interface. For comparison, the calculations were done using the homology models derived from both the R(Ialpha) and R(IIbeta) crystal structures. Both resultant models had many similarities. Each predicted similar interfaces. The R(Ialpha)-based model has 25% more hydrogen bonds than that based on R(IIbeta), with seven of these potential bonds in common. The distribution of hydrophobic, polar, and charged residues at the interface was similar for both models, with a distribution more characteristic of the exposed surface residues than those in the protein interior. The calculated interface area in each is relatively small (<2000 A(2)). The R(Ialpha)-based model, however, has a significantly better fit with the scattering data and is therefore the one of distinctly higher probability. With its small interface area that has a high proportion of charged and polar residues, the complex appears poised for dissociation, and each subunit existing as a stable entity. This result is consistent with the known physiological events required for cAMP-dependent activation of the kinase. A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase.,Tung CS, Walsh DA, Trewhella J J Biol Chem. 2002 Apr 5;277(14):12423-31. Epub 2002 Jan 17. PMID:11799117 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Proteopedia Page Contributors and Editors (what is this?)

OCA