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Figure 4
Active-site configuration and proton-transfer channel in the dimeric cryo-EM structure of NmqNOR. (a) Active site of the `native' NmqNOR cryo-EM structure with the corresponding density, showing FeB (brown sphere) to be ligated by four ligands (Glu494, His490, His541 and His542), with Glu494 contoured at 4σ and the histidines at 8σ. The Glu494–FeB bond is shown as a red dashed line (2.4 Å) and the trihistidyl–FeB coordination is shown as black dashed lines. (b) Comparison between the active-site structures of PacNOR (transparent pink sticks), AxqNOR V495A (transparent magenta sticks) and NmqNOR (cyan sticks), clearly showing that the terminal glutamate of PacNOR and NmqNOR (Glu494) ligates FeB (black and red dashed lines, respectively). Glu494 may display flexibility as part of its function in proton transfer, as the equivalent glutamate in AxqNOR ligates a water (orange sphere) in lieu of FeB. (c) Top: active site of PacNOR (PDB entry 3o0r; Hino et al., 2010BB15), with Glu211 (equivalent to Glu494 in NmqNOR) ligating FeB (purple sphere) in a bidentate fashion, as shown by the black dashed lines (distances are also shown). Bottom: active site of AxqNOR V495A (PDB entry 6qq6) showing Glu490 (equivalent to Glu494 in NmqNOR) ligating a water molecule (Wat; orange sphere), with FeB (yellow sphere) having trihistidyl coordination. (d) Putative proton-transfer channel in NmqNOR, with residues shown as cyan sticks and contoured at 6σ (except for Glu259 and Glu573, which are both contoured at 4σ). Asn604 and Glu498 are hydrogen-bonded (black dashed line) in the cryo-EM structure; FeB and calcium ions are shown as brown and green spheres, respectively.

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