Figure 3.

Structure of LdcB

(A–C) Cartoon representations of (A) SpLdcB, (B) BsLdcB, and (C) BaLdcB; α helices (red) and β strands (yellow) are numbered. The loops between secondary structure elements are colored silver. The bound zinc ion is shown as a gray sphere.

(D–F) The active sites of (D) SpLdcB, (E) BsLdcB, and (F) BaLdcB. A zinc ion is coordinated in a tetrahedral manner in the structures by two invariant histidines and a well-conserved aspartate. Residual electron density in SpLdcB, shown in (D), corresponds to D-alanine in the S₁′ subsite, and an unknown compound in S₁, adjacent to the zinc ion. Electron density corresponding to a phosphate ion, a component of the crystallization medium, in the S₁ subsite of BsLdcB shown in (E) is a mimic of the tetrahedral transition state. A second feature in the S₁′ subsite is unmodeled. The residual difference density features are shown contoured at a level of 3σ and hydrogen bonds are drawn as dashed black lines.