view article
Figure 5
Fo − Fo difference maps reveal local conformational shifts connecting the active site, interdomain inter­face, and dimer inter­face. Center: overview of the isomorphous Fo − Fo difference electron-density map at ±3σ (green–red mesh) for the 240 K data set (cyan) minus the 100 K data set (dark blue) (see Fig. S10 for Fo − Fo maps for all tem­per­atures). Ligands from cocrystal structures are shown at the active site (dashed oval) (pale orange, 6lu7), interdomain inter­face (purple, 5ree; yellow, 5rec), and dimer inter­face (orange, 7lfp; pink, 5rf0). (a) Glu290 switches from one side-chain rotamer at 100 K to two alternate rotamers at 240 K. Glu290 is spatially adjacent to Cys128, which switches from two alternate rotamers at 100 and 240 K to a single rotamer at 277 K and above in our multiconformer models; the alternate rotamer occupancy is lower at 240 K, consistent with its positive Fo − Fo peak (see Fig. S12). These residues are near two ligands from separate crystallographic screens (7lfp and 5rf0), as well as many ordered PEG mol­ecules from the crystallization cocktails of various structures (7kvr, 7kvl, 7kfi, and 7lfe). (b) An ∼45°-rotated view relative to part (a) shows that these two ligands bind at the dimer inter­face of the biological monomer, constituted in the crystal from a symmetry-related protomer (gray surface). This inter­face also includes the Asp197 region (right). (c) Thr198 switches from two alternate side-chain rotamers at 100 K to a single rotamer at 240 K, while Glu240 – located across the interdomain inter­face – changes side-chain rotamer (curved arrows), with additional effects on the adjacent backbone of Pro241. In the other direction from Asp197 (down in this view), other residues in the P5 substrate-binding pocket loop (Fig. 3[link]) undergo conformational adjustments en route to the active site. Meanwhile, an inter­acting water mol­ecule at 100 K (blue sphere) becomes displaced at 240 K, and is correspondingly absent in that model.

IUCrJ
Volume 9| Part 5| September 2022| Pages 682-694
ISSN: 2052-2525
https://doi.org/10.1107/S2052252522007497