Lysyl-tRNA synthetase

Fig. 1. Structure of the OB-fold domain. The anticodon-binding domain of the E. coli lysyl-tRNA synthetase (pdb code lkrs) is shown as a prototype of single-stranded nucleic acid-binding OB-folds. The model was drawn using the Molscript v2.1 program...

Cusack, S., Yaremchuk, A., and Tukalo, M. (1996). 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. EM BO J. 15, 6321—6334. 

Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, and Soil D. A emyarchaeal lysyl-tRNA synthetase resemblance to class I synthetases. Science 1997 278 1119-1122. 

Polycarpo C, Ambrogelly A, Ruan B, Tumbula-Hansen D, Ataide SF, Ishitani R, Yokoyama S, Nureki O, Ibba M, Soil D. Activation of the pyrrolysine suppressor tRNA reqtrires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol Cell, 2003 12 287-294. 

This is a lysyl tRNA synthetase enzyme in the first instance that should have the expected capacity to couple the naturally available amino acid L-lysine to appropriate cognate tRNAs bearing anti-codon sequences complementary to lysine codons (see Section 1.6.1). However in the presence of zinc ions, Zn +, the function of this enzyme becomes altered to catalyse the biosynthesis of diadenosine-5, (Ap4A) followed by... 

Figure 8.19 H-NMR assay. Lysyl tRNA synthetase (LysU) assay system. Conversion of ATP into Ap A is observed by W-NMR spectroscopy when reaction is run in a 5mm NMR tube. signals of adenine ring are shifted upfield with conversion of ATP (6h 8.55 [H-2] and 8.29 [W-8] p.p.m.) to Ap4A ( h 8.40 [H-2] and 8.18 [W-8] p.p.m.). Rates of conversion are followed by changes in appropriate W-NMR signal peak areas as a function of time (illustration adapted from Theoclitou et al., 1996, Fig. 2).

S. Onesti, A. D. Miller and P. Brick, The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure, 1995, 3,163-176 (pdb llyl). 

G. Desogus, F. Todone, P. Brick and S. Onesti, Active site of lysyl-tRNA synthetase structural studies of the adenylation reaction. Biochemistry, 2000, 39, 8418-8425 (pdbs lelt, le22 le24). 

N. Boonyalai, S. Thipayang, M. Wright, 1. R. Gould and A. D. Miller, Investigating the binding of GTP to lysyl-tRNA synthetase enzyme (LysU) in vitro and in silico, 2008, in preparation. 

S. J. Hughes, J. A. Tanner, A. D. Hindley, A. D. Miller and I. R. Gould, Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment, BMC Structural Biology, 2003, 3, 5. 

Figure 15.6. Complementary phylogenetic patterns. (A) The two classes of lysyl-tRNA synthetases. Note that both COGs include T. pallidum] it encodes an unusual class II enzyme that might not be involved in translation. (B) Two classes of fructose-1,6-bisphosphate aldolase. Note that E. coll and A. aeolicus encode both types of aldolases.

Yanagisawa T, Sumida T, Ishii R, Ttikemoto C, Yokoyama S (2010) A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol 17 1136-1143... 

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