Fig. 6 | Nature Communications

Fig. 6

From: Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis

Fig. 6

Active site pocket of BacA. a View into the active site from the membrane through the cleft between H4 and H8. The opening from the membrane is marked by a dashed triangle. Access from the periplasm is in the opening marked by the base of the triangle where the helices splay apart. b Surface representation of the view into the active site shown in a. Ser27 in the active site is colored red. c Slice through the view in b to reveal the active site pocket with access to the periplasm. d Electron density in the active site. The Fo–Fc omit density map (green mesh) contoured at 2.5σ shows a lobe of density in the proposed substrate binding pocket. The density sits approximately equidistant from the apposed N-termini of h2 and h7 on the axis of symmetry that passes through the protein in the membrane plane. Attempts made to fit the density with phosphate, pyrophosphate, glycerol, calcium, ammonium, citrate, DDM and water molecules proved unsatisfactory. The distance between E21 and S27 is 3.1 Å (dashed line). e Details of the proposed binding pocket for the pyrophosphate head group of C55PP. The binding pocket includes the guanidinium moieties of Arg174 and Arg261 and the ring of partial positive charges from the amide backbone of loops L1–2 (E21-S27) and L6–7 (L168-R174). Residues in loops are shown as sticks. Polypeptide in the foreground (H3 and H8) and background (H5 and H10), excluding residue R261 in H10, has been removed for clarity. f Alignment of helical axes in helices h2 and h7 on either side of the putative active site. The N-termini of h2 and h7 are ~9 Å apart with helical dipoles opposed. Parts of the protein to the forefront and background have been removed for clarity. The horizontal line marks the location of the approximate C2 axis of pseudosymmetry. The dashed lines align with the helix axis of h2 and h7

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