Figure 2

The DHO Active Sites. (A) The active sites of DHO from E. coli (pdb:1j79A; cyan carbon atoms), A. aeolicus (pdb:1xrfA; magenta carbon atoms), and the A. aeolicus native complex of DHO and ATC (pdb:3d6nA; yellow carbon atoms). Zinc atoms are shown as grey spheres. Significant water molecules (“J”) and ligand atoms (“X”) are also differentiated by the carbon color. The water molecules are labeled by their role in the active site (Figure 2C) because the numbers assigned to water molecules in the same site vary among the numerous DHO structures. Here, Jα5β5 is HOH1407 in 1j79.pdb; Jα5 is HOH2 in 1xrf.pdb; Xα5 is the OG1 atom from the citrate ligand in 3d6n.pdb; and Jβ is HOH577 in 3d6n.pdb; (B) Superposition of the active sites of A. aeolicus DHO from the native complex (3d6n.pdb); yellow carbon atoms) and the mutant complex (4bjh.pdb; green carbon atoms). Zinc atoms are shown as grey spheres. Significant water molecules (“J”) and ligand atoms (“X”) are differentiated by the carbon color. Jα5 is HOH2018/A in 4bjh.pdb; Xα5 is the OG1 atom from the citrate ligand in 3d6n.pdb; and Jβ is HOH577 in the wild-type 3d6n.pdb and HOH2080/A in 4bjh.pdb. (C) A schematic diagram of the first and second binding shells for two zinc atoms in the active sites of type-I and type-II DHO enzymes. The first shell ligands are shown as labeled residues for A. aeolicus DHO. The second shell ligands are shown as labeled circles. The analogous first shell residues for S. aureus, B. anthracis, and T. thermophilus DHO and the second shell ligands for all four species are listed in the supplement (Additional file 1: Table S1) together with values for the distances marked by dashed lines in the diagram.