Extended Data Fig. 6: X-conformations based on R416 and E362 related inter-subdomain salt bridges are structurally extended.
From: Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases
a–d, Homologous A-___domain X-ray structures showing a bent conformation with larger inter-subdomain separation than A-conformation. This conformation is further modelled by MD simulations and shown to feature R416, likely an anchor residue in the AN subdomain. The AN and AC subdomains are coloured in slate and grey, respectively. e–f, Sequence conservation shows that R416 is highly conserved (e) while E362 is marginally conserved (f). Profiles were generated by WebLogo (v2.8.2)71. g–h, Potential salt-bridges were identified between R416 and E444/E441 by smFRET-guided MD simulations for A-domains of aCC1 (g) and aCC2 (h). Inset: close-up of the salt bridge between R416 in the AN subdomain (slate) and E444 (g) or E441 (h) in the AC subdomain (grey), zoomed in from black boxes in the full views in (g) and (h). i–j, Potential salt-bridges were identified between E362 and K434/R439 by smFRET-guided MD simulations for A-domains of aCC1 (i) and aCC2 (j). Inset: close-up of the salt bridge between E362 and K434 or R439. Dark red spheres: N152C-Alexa 647 central atom, yellow spheres: D508C-Alexa 555 central atom (g, i) or S492C-Alexa 555 central atom (h, j). Dyes in (g–j) are shown in sticks.
