The active site a the mammalian cAMP-dependent protein kinase catalytic subunit (C-sub-unit) has a cluster of nonconserved acidic residues-Glu127, Glul 70, Glu203, Glu230, and Asp241-that are crucial for substrate recognition and binding. Studies have shown that the Glu230 to Gln mutant (E230Q) of the enzyme has physical properties similar to the wild-type enzyme and has decreased affinity for a short peptide substrate, Kemptide. However, recent experiments intended to crystallize tertiary complex of the E230Q mutant with MgATP and protein kinase inhibitor (PKI) could only, obtain crystals of the apo-enzyme of E230Q mutant. To deduce the possible mechanism that prevented tertiary complex formation, we used the relaxed-complex method (Lin, J.-H., et al. J Am Chem Soc 2002, 24, 5632-5633) to study PKI binding to the E230Q mutant C-subunit. In the E230Q mutant, we observed local structural changes of the peptide binding site that correlated closely to the reduced PKI affinity. The structural changes occurred in the F-to-G helix loop and appeared to hinder PKI binding. Reduced electrostatic potential repulsion among Asp241 from the helix loop section and the other acidic residues in the peptide binding site appear to be responsible for the structural change. (c) 2005 Wiley Periodicals, Inc.