Fig. 5: Structure of MaFRSA bound to m-CF3-2-BMA and AMP-PNP reveals basis for distinct reactivity at pro-R and pro-S substrate carboxylates. | Nature Chemistry

Fig. 5: Structure of MaFRSA bound to m-CF3-2-BMA and AMP-PNP reveals basis for distinct reactivity at pro-R and pro-S substrate carboxylates.

From: Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo

Fig. 5

a, Structure of the MaFRSA dimer containing two non-identical chains in the asymmetric unit. b, Alignment of the active sites of chains A (light purple) and B (dark purple) reveals m-CF3-2-BMA (grey) bound in two alternative conformations. c, In chain A, m-CF3-2-BMA is coordinated by an extensive hydrogen bond network (orange dashes) that positions the pro-R carboxylate oxygen for nucleophilic attack (blue dashes). Interatomic distances (in Å) are shown alongside the dashed lines. d, In chain B, m-CF3-2-BMA is coordinated by similar hydrogen bonds, but in this case the pro-S carboxylate is rotated away from AMP-PNP with a loss of the hydrogen bond to Arg150 (red dashes) and a longer distance between the pro-S carboxylate nucleophile and the α-phosphate of AMP-PNP. e, Alignment of active site A with WT MmPylRS bound to Pyl and AMP-PNP (PDB: 2ZCE, blue)37 illustrates the difference between the water-mediated hydrogen bonds (orange dashes) to the α-amine of Pyl in PylRS compared with the direct carboxy-to-backbone hydrogen bonding of m-CF3-2-BMA bound to MaFRSA. f, Comparison of active site B with MmBtaRS (N346G, C348Q) bound to Bta (PDB: 4ZIB, red)62 reveals similar binding modes with hydrogen bonds (orange dashes) between the substrate carboxylate and backbone amide of the enzyme when Asn166/Asn346 (Ma/Mm numbering) is mutated.

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