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. 2020 Mar 17;9:e51420. doi: 10.7554/eLife.51420

Figure 2. Structure of C. difficile HypD with Hyp bound.

(A) Dimeric structure of HypD (green) with the glycyl radical domain that houses the Gly loop in yellow and the Cys loop in purple. Gly765, Cys434, and Hyp are shown in spheres. (B) 2Fo-Fc maps (contoured at 1.0σ, gray) indicate electron density for Hyp. Hyp is positioned above the Gly loop (yellow) and Cys loop (purple) with residues from the strands of the β-barrel (green) forming the sides of the active site. A water molecule is shown as red sphere. (C) C5 of HypD (starred) is the closest atom to the catalytic Cys (Cys434), which is found in the active site within van der Waals distance of Gly765, the site of the glycyl radical. See Figure 8A for additional distances between Hyp and Cys434.

Figure 2—source data 1. Cartesian coordinates for zwitterionic Hyp in Cγ-exo pucker calculated from DFT.
Coordinates of zwitterionic Hyp structure used to fit into the HypD crystal structure.
Figure 2—source data 2. Cartesian coordinates for zwitterionic Hyp in Cγ-endo pucker calculated from DFT.
Coordinates of zwitterionic Hyp structure used to fit into the HypD crystal structure.

Figure 2.

Figure 2—figure supplement 1. A 2.05 Å resolution structure of HypD with glycerol bound in the active site.

Figure 2—figure supplement 1.

(A) 2Fo-Fc maps (contoured at 1.0σ, gray) indicate electron density for glycerol. (B) Distances between glycerol hydroxyl groups and nearby residues are indicated. Water molecules are not shown.
Figure 2—figure supplement 2. HypD conformers generated by DFT calculations.

Figure 2—figure supplement 2.

Structures of zwitterionic Hyp obtained for Cγ-endo and Cγ-exo puckered states. Cartesian coordinates are provided in source data.
Figure 2—figure supplement 3. Comparison of electron density maps for Cγ-exo Hyp versus Cγ-endo Hyp modeled into HypD active site.

Figure 2—figure supplement 3.

2Fo-Fc maps (contoured at 1.0σ, gray) indicate electron density for substrate in both (A) Cγ-exo Hyp and (B) Cγ-endo Hyp pucker states. Conformers were restrained to the calculated optimal conformation of each pucker. 2Fo-Fc maps show cleaner electron density for Hyp modeled in the Cγ-exo conformation. Fo-Fc maps (contoured at 3.0σ, positive difference density in green, negative difference density in red), for (C) Cγ-exo Hyp and (D) Cγ-endo Hyp further supports the modeling of Hyp in the Cγ-exo pucker. Positive difference density in Fo-Fc maps indicates that atoms should be modeled into the structure at that location; negative difference density indicates that atoms have been modelled into the structure at this location that are inconsistent with the diffraction data.