Fig. 4: The glycine imine-N–O–S-C281 bridge in the Orf1-glycine complex structure.
a An intrinsic electron density (contrasted by 2Fo-Fc map contoured at 1 σ in gray and the Fo-Fc map contoured at 3 σ in green) was unexpectedly found nearby residue C281 at the glycylthricin binding site. b The chemical model that best fits into the electron density region (2Fo-Fc map at 1 σ colored blue) is a glycine imine adduct in a covalent linkage to C281 through a N–O–S bridge. c The C281-iminoglycine adduct is surrounded by residues T298, E312, E313, F316 and E426. The distance between two atoms was labeled with a yellow dashed line. d, e Superposition of two complexes (the C281-adduct and the glycylthricin-containing structures) shows that the distance between the amine group of glycylthricin and α-carbon of the iminoacetate adduct is 3.1 Å within a general H-bond range with a Burgi-Dunitz angle of 99.7° in an approaching trajectory. f Superposition of WT-glycylthricin (green), E312A-glycylthricin (cyan) and C281-iminoglycine adduct (gray) reveals that E312 undergoes a substrate-induced conformational change, in which upon addition the resulting decarboxylation facilitates β-elimination. g Superposition of WT-glycylthricin (green), WT-4-aminobutylthricin (magenta), F316-ST-F (cyan) and C281-iminoglycine adduct (gray) shows considerable displacements of the median γ-aminobutyl and the long β-lysine sidechains away from that of glycylthricin likely as a result of a geographic effect.
