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 3
Crystal structures of AMP and BocLys-AMP bound to PylRS. (a, b) The F_o - F_c OMIT electron-density maps (contoured at 4 [sigma]

) of the bound AMP (PDB entry 3vqx , molecule A) (a) and BocLys-AMP (PDB entry 3vqx , molecule C) (b) are represented as ball-and-stick models. Transparent ribbon models of the AMP-bound (and BocLys-AMP-bound) forms are visible in the background. (c) Superposition of the structures of the previously determined form 1 (white) and BocLys-AMP-bound (grass green) forms. (d) Superposition of the structures of the Pyl-AMP-bound (white) and BocLys-AMP-bound forms (grass green). (e) The Asn346 side chain hydrogen-bonds to the carbonyl group of the amino-acid substrate and a water-mediated hydrogen bond exists between the [alpha]

-carboxyl group of BocLys (or the [alpha]

-amino group of pyrrolysyl-AMP) and the side-chain amide group of Asn346.