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. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family.