as problem to be solved. We determined a crystal structure of a complex of ArgRS from Pyrococcus horikoshii, tRNA Arg CCU and ATP analog with Rfactor = 0.215 (Rfree = 0.259) at 2.0 resolution and could give one solution for this problem using newly obtained structural information about position of ATP. The experimental results show that the ArgRS protein lacking the additional N-terminal domain characteristic for ArgRS possesses sufficient catalytic activity in the aminoacylation reaction for tRNA. Modeling of relative positions of amino acid, Ade76 of tRNA and ATP on ArgRS was made to find the suitable position to tRNA-assisted formation mechanism of Arg-AMP. It was found that formation of hydrogen bond between 2'OH of Ade76 of tRNA and O2 of carboxy group -C-O2H=O1 of arginine can be achieved in one conformation by rotation around C -C of carboxy group. In ATP-PPi exchange reaction at low pH, reversible conversion between C=O1 and C-O1-P is controlled by the formation of this hydrogen bond. On the other hand, at pH8.0, experimental results in the deacylation reaction of Arg-tRNA is also understood by mechanism that NH + of guanidium group -N + H=C-(NH2)2 of Arg-tRNA donates a proton to C=O2 of ester bond of Arg-tRNA, resulting in carbonium C + -O2H. We discuss in detail these mechanisms.
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Ruf et al. (2008) studied this question.