Fig. 5. ApdA/ApdP stabilize the pre-attack state at the PTC.

a View of the PTC of a pre-attack state (PDB ID 1VY4)²⁶, showing a fMet-NH-tRNA (gold/blue) at the P-site and a phenylyl-NH-tRNA (purple/green) at the A-site. The distance (3.0 Å) between the attacking amine of the A-tRNA and the carbonyl-carbon of the P-tRNA is arrowed. b Same view as (a), but for the ApdP-SRC with ApdP-tRNA (red/dark blue) in the P-site and Pro-tRNA (cyan/green) in the A-site. c Overlay of (a, b) (aligned on the basis of the 23S rRNA) highlighting the difference in the distance between the attacking nitrogen groups of A-site aminoacyl moiety and the carbonyl carbons at the P-site. d View of the PTC of a pre-attack state (PDB ID 8CVK)²⁷, showing a tripeptidyl-NH-tRNA (gold/blue) at the P-site and a phenyl-NH-tRNA (purple/green) at the A-site. The distance (3.0 Å) between the attacking nitrogen of the A-tRNA and the carbonyl-carbon of the P-tRNA is arrowed. e Same view as (d), but for the ApdP-SRC with ApdP-tRNA (red/dark blue) in the P-site and Pro-tRNA (cyan/green) in the A-site. f Overlay of (d, e) (aligned on the basis of the 23S rRNA) highlighting the difference in the distance between the attacking nitrogen groups at the A-site and the carbonyl carbons at the P-site. g Schematic view of the PTC of a pre-attack from (d), but with hydrogen atoms (white) modeled in silico for the α-amino group of the Phe moiety in the A-site. The yellow spheres indicate the lone pair electrons that make the nucleophilic attack (arrowed) on the carbonyl-carbon of the fMet moiety on the P-site tRNA. h Same schematic as (b), but with the hydrogen atom (white) modeled in silico towards the 2’OH of A76 of the P-site tRNA, which would allow a nucleophilic attack (arrowed) on the carbonyl-carbon of the Pro133 moiety attached to the P-site tRNA. i Same schematic as (h) but with the hydrogen atom (white) modeled toward the carbonyl of Ala132, a conformation that would prohibit any nucleophilic attack.