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Figure 5
Proton-transfer inhibition in a monomer of AxqNOR Glu494Ala. (a) The location of Glu494 (magenta sticks) in wild-type AxqNOR (teal cartoon; PDB entry 6qq5) relative to the dimer-stabilizing TMII. (b) 4.5 Å resolution AxqNOR Glu494Ala peak 2 cryo-EM-derived density map (khaki) with wild-type AxqNOR (teal cartoon) rigidly docked into the map, showing displacement of TMI and TMII. (c) Alignment of wild-type AxqNOR (teal cylinders) and the AxqNOR Glu494Ala peak 2 structure (orange cylinders), with an overall r.m.s.d. of 1.06 Å, with the helices showing the greatest displacement, TMI, TMII, TMIX and TMX, labelled with roman numerals. (d) Disruption of the putative proton-transfer channel by movement of TMX of the AxqNOR Glu494Ala peak 2 structure (orange) across the cavity (∼8 Å from Ile564Cα), with the Glu569–Ser523 interaction in the wild-type structure (teal) likely to be perturbed as a result. Asn600 shows a conserved conformation, despite being hydrogen-bonded to Glu494 in the wild-type structure. (e) Binuclear centre of the AxqNOR Glu494Ala monomer (orange cartoon, grey cryo-EM density map contoured at 3σ) compared with wild-type AxqNOR (teal cartoon), with no density for His486 (omitted from the AxqNOR Glu494Ala peak 2 model) and unclear density for the nonheme metal. The His537 and His538 conformations are significantly altered in the absence of the nonheme metal and could contribute to downstream structural movements.

IUCrJ
Volume 7| Part 3| May 2020| Pages 404-415
ISSN: 2052-2525
https://doi.org/10.1107/S2052252520003656