Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine (By similarity). diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) Binds 2 magnesium ions per subunit. One of the ions does not make direct protein contacts. The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. In the N-terminal section; belongs to the tRNA(Ile)-lysidine synthase family. In the C-terminal section; belongs to the purine/pyrimidine phosphoribosyltransferase family.