The swimming behavior of Escherichia coli at any moment is dictated by the intracellular concentration of the phosphorylated form of the chemotaxis response regulator CheY, which binds to the base of the flagellar motor. CheY is phosphorylated on Asp57 by the sensor kinase CheA and dephosphorylated by CheZ. Previous work (Silversmith et al., J. Biol. Chem. 276:18478, 2001) demonstrated that replacement of CheY Asn59 with arginine resulted in extreme resistance to dephosphorylation by CheZ despite proficient binding to CheZ. Here we present the X-ray crystal structure of CheYN59R in a complex with Mn(2+) and the stable phosphoryl analogue BeF(3)(-). The overall folding and active site architecture are nearly identical to those of the analogous complex containing wild-type CheY. The notable exception is the introduction of a salt bridge between Arg59 (on the beta3alpha3 loop) and Glu89 (on the beta4alpha4 loop). Modeling this structure into the (CheY-BeF(3)(-)-Mg(2+))(2)CheZ(2) structure demonstrated that the conformation of Arg59 should not obstruct entry of the CheZ catalytic residue Gln147 into the active site of CheY, eliminating steric interference as a mechanism for CheZ resistance. However, both CheYE89A and CheYE89Q, like CheYN59R, conferred clockwise flagellar rotation phenotypes in strains which lacked wild-type CheY and displayed considerable (approximately 40-fold) resistance to dephosphorylation by CheZ. CheYE89A and CheYE89Q had autophosphorylation and autodephosphorylation properties similar to those of wild-type CheY and could bind to CheZ with wild-type affinity. Therefore, removal of Glu89 resulted specifically in CheZ resistance, suggesting that CheY Glu89 plays a role in CheZ-mediated dephosphorylation. The CheZ resistance of CheYN59R can thus be largely explained by the formation of the salt bridge between Arg59 and Glu89, which prevents Glu89 from executing its role in catalysis.