Pyridoxal 5'-phosphate (PLP) and pyridoxal 5'-diphosphate (PLDP) were used to identify lysyl residues at the phosphate-binding locus in the lysS-encoded and the lysU-encoded lysyl-tRNA synthetases (LysRSs and LysRSu, respectively) from Escherichia coli. Incubation of LysRSs with either reagent, followed by borohydride reduction, resulted in a time-dependent covalent incorporation of the reagent, accompanied with the loss of both tRNA(Lys) aminoacylation and lysine-dependent ATP-PPi exchange activities. By contrast, LysRSu activity was insensitive to prolonged incubation with either reagent, possibly reflecting a difference at the phosphate-binding locus in the two enzyme species. MgATP protected LysRSs against inactivation by PLP or PLDP. Complete inactivation of LysRSs corresponded to the incorporation of 2.6 +/- 0.1 mol of PLP or PLDP per mol of dimeric enzyme. Either reagent was found to label the same set of eight lysyl residues (Lys-25, Lys-82, Lys-114, Lys-132, Lys-156, Lys-185, Lys-364, and Lys-505) as adenosine di- or triphosphopyridoxal (see the preceding paper in this issue). These lysyl residues might represent the subsite for the phosphate moiety of ATP in LysRSs. None of the identified lysyl residues is located within the three sequence motifs considered as characteristic of the class 2 aminoacyl-tRNA synthetases. The present results are discussed on the basis of the crystalline structure of the closely related aspartyl-tRNA synthetase from Saccharomyces cerevisiae.