Anticodon binding domain DNK

The anticodon binding domain DNK is a compact protein with an OB-fold (Charron et al. 2003). It resides at the C-termini of four Class II AARS: [AsxRS](/class2/asp2/), [AspRS](/class2/asp1/), [AsnRS](/class2/asn/), and [LysRS-II](/class2/lys/), where it recognises the tRNA anticodon loop, approaching the acceptor stem from the major groove side (de Pouplana and Schimmel, 2001). The EMAP domain, which adopts the same fold, is found in AARS from both classes: [MetRS](/class1/met), [TyrRS](/class1/tyr), and the $\beta$-chain of the bacterial-like [PheRS](/class2/phe2) (Wolf et al. 1999). Although they may have different functions, the anticodon binding domain DNK and EMAP are most likely related. In the standard genetic code, these three amino acids have very similar sets of cognate anticodons: GAU/GAC for aspartate, AAU/AAC for asparagine, and AAA/AAG for lysine. It has been suggested that AspRS achieves its discrimination between $\text{tRNA}^\text{Asp}$ and $\text{tRNA}^\text{Asn}$ through a helix in the anticodon binding domain AspRS (Charron et al. 2003). Similarly, the anticodon binding domain of LysRS-II specificially recognises the second and third positions of the anticodon, in order to discriminate against $\text{tRNA}^\text{Asn}$ (Cusack et al. 1996). In MetRS, EMAP promotes dimerisation and also improves tRNA binding affinity (Crepin et al. 2002, Blanquet et al. 1973). It is only present in certain MetRS lineages.

References

Charron, Christophe, et al. "Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain." The EMBO Journal 22.7 (2003): 1632-1643. Cusack, S., A. Yaremchuk, and M. Tukalo. "The crystal structures of T. thermophilus lysyl‐tRNA synthetase complexed with E. coli tRNA (Lys) and a T. thermophilus tRNA (Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl‐adenylate analogue." The EMBO journal 15.22 (1996): 6321-6334. Wolf, Yuri I., et al. "Evolution of aminoacyl-tRNA synthetases—analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events." Genome research 9.8 (1999): 689-710. de Pouplana, Lluı́s Ribas, and Paul Schimmel. "Aminoacyl-tRNA synthetases: potential markers of genetic code development." Trends in biochemical sciences 26.10 (2001): 591-596. Blanquet, Sylvain, Motohiro Iwatsubo, and Jean‐Pierre Waller. "The Mechanism of Action of Methionyl‐tRNA Synthetase from Escherichia coli: 1. Fluorescence Studies on tRNAMet Binding as a Function of Ligands, Ions and pH." European Journal of Biochemistry 36.1 (1973): 213-226. Crepin, Thibaut, et al. "Structure and function of the C-terminal domain of methionyl-tRNA synthetase." Biochemistry 41.43 (2002): 13003-13011.