FIGURE 2.

General architecture of KgpB. A, ribbon-type plot of Kgp(CD+IgSF) showing the regular secondary structure elements (CD, α-helices as orange ribbons, β-strand as yellow arrows, and coils in tan; IgSF, β-strand as blue arrows labeled β16–β21 and coils in lilac). The N and C termini and the four structural cations (calciums Ca⁹⁹⁹ and Ca⁹⁹⁸ in red and sodiums Na⁹⁹⁷ and Na⁹⁹⁶ in blue) are depicted. The (putative) catalytic triad, Cys⁴⁷⁷ (covalently modified at Sγ with an l-lysinylmethyl group; carbons in lilac), His⁴⁴⁴, and Asp³⁸⁸, is further shown as sticks. Black arrows point to the solvent channel (see Fig. 3D). B, picture of a tooth with its parts labeled. C, (2mF_obs − DF_calc)-type Fourier map of the region around the catalytic cysteine Cys⁴⁷⁷ obtained with diffraction data to 1.75-Å resolution and contoured at 1σ above threshold. D, structure of Kgp(CD+IgSF) in cross-eye stereo in standard orientation (28, 79), which corresponds to a horizontal 90° rotation of the view in A, i.e. viewing the CD cusp region. Regular secondary structure elements of the CD (helices α1–α14 and strands β1–β15) are labeled. The NSD is on top, and the CSD is at the bottom (see also Fig. 5D). E, close-up of D in stereo centered on the non-primed side of the active site. Residues framing the specificity pocket S₁ and pocket S₂ are labeled. Small green spheres represent solvent molecules.