Lysidine is an uncommon nucleoside, rarely seen outside of tRNA. It is a derivative of cytidine in which the carbonyl is replaced by the amino acidlysine. The third position in the anti-codon of the Isoleucine-specific tRNA, is typically changed from a cytidine which would pair with guanosine to a lysidine which will base pair with adenosine. Lysidine improves translation fidelity because uridine cannot be used at this position even though it is a conventional partner for adenosine since it will also "wobble base pair" with guanosine.[1][2] Lysidine is denoted as L[3] or k2C[4] (lysine bound to C2 atom of cytidine).
Lysidine base pairs with Adenosine in context of a Cytidine to Guanosine base pair. R = ribose. Arrows indicate hydrogen bonds going from hydrogens to bond acceptor. The notation for lysidine, L, is depicted above.
References
^Nakanishi, Kotaro; Fukai, Shuya; Ikeuchi, Yoshiho; Soma, Akiko; Sekine, Yasuhiko; Suzuki, Tsutomu; Nureki, Osamu (24 May 2005). "Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain". Proceedings of the National Academy of Sciences of the United States of America. 102 (21): 7487–7492. Bibcode:2005PNAS..102.7487N. doi:10.1073/pnas.0501003102. PMC 1140429. PMID 15894617.
^Salowe, Scott P.; Wiltsie, Judyann; Hawkins, Julio C.; Sonatore, Lisa M. (April 2009). "The Catalytic Flexibility of tRNAIle-lysidine Synthetase Can Generate Alternative tRNA Substrates for Isoleucyl-tRNA Synthetase". Journal of Biological Chemistry. 284 (15): 9656–9662. doi:10.1074/jbc.M809013200. PMC 2665086. PMID 19233850.