A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site

Yanagisawa, T.; Sumida, T.; Ishii, R.; Yokoyama, S.

doi:10.1107/S0907444912039881

Figure 6
Snapshots of the Asn346 side chain during aminoacyl-tRNA synthesis. Schematic representation of the conformational changes of the Asn346 side chain according to the status of the tRNA-aminoacylation reaction. In the ATP-binding step (the AMPPNP-bound forms; PDB entries 2q7e , 3vqv and 3vqw ), the Asn346 side chain fluctuates by approximately 60°. In the initial state of amino-acid binding or pre-aminoacyl-AMP synthesis (form 2; PDB entry 3vqy ), the Asn346 side chain points toward the [alpha]

-phosphate of AMPPNP and does not interact with the N-carbonyl group of the amino-acid substrate. On the other hand, in the fixed state of amino-acid binding [CpocLys-ATP-bound form (PDB entry 2q7g ), Pyl-AMPPNP-bound form (PDB entry 2zce ) and form 1 (PDB entry 2zin )], the Asn346 side chain interacts specifically with the N-carbonyl group of the bound amino-acid substrate. The specific interactions between the Asn346 side chain and the N-carbonyl group of the amino-acid substrate remain unchanged during aminoacyl-AMP synthesis [Pyl-AMP-bound form (PDB entry 2zim ) and BocLys-AMP-bound form (PDB entry 3vqx )]. The orientation of the Asn346 side chain shifts by a maximum of 85-90° around the C atom, compared with that in the post-aminoacyl-AMP synthesis state and the fixed state of amino-acid binding, after the aminoacyl-tRNA synthesis (AMP-bound form; PDB entry 3vqx ) and following AMP release (ligand-free form; PDB entry 2e3c ). The conformations of motif 2, the ordering loops and the [beta]

8 hairpin along with the aminoacylation reaction are also shown.