Comparative modeling studies of the calmodulin‐like domain of calcium‐dependent protein kinase from soybean

Calmodulin‐like domain protein kinases (CDPKs) represent a new class of calcium‐dependent protein‐phosphorylating enzymes that are not activated by calmodulin or phospholipid compounds. They have been found exclusively in plant and protozoal tissues. CDPKs are typified by four distinct domains: an N‐terminal leader sequence, a protein kinase (PK) domain, a calmodulin‐like domain (CLD), and a junction domain (JD) between the PK domain and CLD. Structural characterization of the CLD of CDPKα from soybean was undertaken based on the amino acid sequence homology of CLD to the structurally well‐characterized calmodulin (CaM) family of structures. Tertiary models of apo‐CLD, Ca2+–CLD complex, and intermolecularly bound Ca2+–CLD–JD complexes were obtained via automated and non‐automated homology building methods. The resulting structures were compared and validated based on energy differences, phi‐psi angle distribution, solvent accessibility, and hydrophobic potential. Circular dichroism, one‐dimensional, and two‐dimensional nuclear magnetic resonance spectroscopy studies of the CLD and peptides encompassing the JD provide experimental support to the models. The results suggest that there is a possible interaction between the CLD and JD domain similar to that of the CaM/calmodulin‐dependent protein kinase II system. At low Ca2+ levels, the JD may act as an autoinhibitory domain for kinase activity, and during calcium activation an intramolecular CLD–JD complex may form, relieving inhibition of the PK domain. Interactions between the JD and the C terminus of the CLD appear to be particularly important. The outcome of this study supports an intramolecular binding model for calcium activation of CDPK, although not exclusively. Proteins 2000;39:343–357. © 2000 Wiley‐Liss, Inc.