Figure 5

Structural comparisons of the Ami1_Mab, Ami1_Mtb, and Ami1_Msm. (A) Overall crystal structure of Ami1_Mab (left)_, Ami1_Msm (middle) and Ami1_Mtb (PDB id: 4LQ6) (right). Each structure is shown as a cartoon representation and is colored differently and according to its secondary structures. α, β, and η indicate alpha-helices, beta-strands, and 3₁₀ helices, respectively. The catalytic zinc ion (Zn²⁺) appears as a wheat-colored sphere. (B) Fo-Fc simulated-annealed OMIT map. The electron density map as seen in the Ami1_Mab:dipeptide co-crystal structure and surrounding l-Ala-d-IsoGln (yellow sticks) is displayed as a grey mesh and contoured at 3 σ level. (C) Close up of the active site of Ami1_Mab as seen in the Ami1_Mab: dipeptide co-crystal structure. l-Ala-d-IsoGln (yellow sticks) tightly interacts by H-bonding and salt-bridge as illustrated by the dashed lines. Water molecules appear as green spheres. (D) The figure shows the molecular interactions seen in the co-crystal structure of Ami1_Mtb bound to dipeptide (PDB id: 4M6G). (E) Active site of the Ami1_Msm.