FIGURE 6.
Comparison of the Rv08051–318-fold with GpdQ. A, Rv08051–318 dimer as a ribbon representation (colored as described in the legend to Fig. 1). B, GpdQ (3D03) dimer, ribbon representation. The MPE domains are in light and dark gray, as in Rv0805. The GpdQ cap domain Ser253–Arg274 is colored orange or green. Cobalt ions in the GpdQ active site are in yellow. C, electrostatic surface of Rv08051–318; and D, electrostatic surface of GpdQ dimer (PDB 3D03). Calculations were done using the Poisson-Boltzmann equation (APBS) (33). Cut off −2.5 kT/e was used for negative potential (red) and 2.5 kT/e for positive potential (blue). Active site metals are shown as spheres. Rv0805 and GpdQ are symmetric homodimers related by 180° axis, therefore in the present view, only one active site of the two can be seen. Bis-Tris bound to Rv08051–318 is shown in sticks (carbon, yellow; oxygen, red; nitrogen, blue). E, superposition of Rv08051–318 (gray green) and GpdQ (3d03; chain A) (brown) monomers. Active site metal ions of the two structures superimpose very closely, therefore for clarity, only Fe3+ (cyan) and Mn2+ (magenta) of Rv08051–318 are shown as spheres. Residues in Rv0805 are marked in green, and in brown for GpdQ. The structural alignment in E was done according to Ref. 31.