Downloaded from FIGURE 2. Comparison of the PchB structures and the E. coli chorismate mutase structure. a, PchB apo structure. The monomers of the intertwined apo dimer are displayed in red and dark blue, and the N and C termini for each monomer are labeled. The amino acids displayed in yellow ball-and-stick represent the terminal amino acids of the disordered loop between helix 1 and helix 2. The nitrate ion bound in the active site is shown as ball-and-stick with cyan sticks. b, PchB

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... -bound structure. The two distinct dimers of the structure are displayed in orange and royal blue (open monomers) and purple and pink (closed monomers). In the open structure, the amino acids on either side of the disordered loop are displayed in yellow ball-and-stick. The bound pyruvate molecules are shown as ball-and-stick with cyan sticks. c, E. coli chorismate mutase structure (Protein Data Bank accession code 1ECM) (22). The monomers are displayed in green and gold. The oxabicyclic acid transition state analogue is displayed in ball-and-stick with cyan sticks. P. aeruginosa Isochorismate Pyruvate Lyase NOVEMBER 3, 2006 • VOLUME 281 • NUMBER 44 JOURNAL OF BIOLOGICAL CHEMISTRY 33443 by guest on July 21, 2018 http://www.jbc.org/ Downloaded from FIGURE 4. Alignment of the closed pyruvate-bound PchB structure with EcCM. a, structural superposition of PchB (dark purple) and EcCM (green) displayed in the same orientation as in Fig. 2 . The pyruvate molecules bound to PchB are represented in pink ball-and-stick, whereas the TSA bound to EcCM has yellow ball-and-stick. The oxygen atoms in both pyruvate and TSA are red. The N and C termini are labeled, and the red arrows identify the loop between the first and second helices. b, the superposition displayed in panel a, rotated 90°about the vertical axis. c, structure-based sequence alignment of the closed, pyruvate-bound PchB structure with EcCM. The positions of the helices in the PchB structures are shown below, labeled with blue hs. The different shades of blue represent the three different helices. The amino acids not visible in the structures due to disorder are labeled with * and offset lowercase letters. The residues highlighted in green are the hydrophobic amino acids that are found at the monomer:monomer interface. The amino acids highlighted in red are the charged/polar amino acids that interact with the transition state analogue in EcCM and the corresponding amino acids in PchB. P. aeruginosa Isochorismate Pyruvate Lyase NOVEMBER 3, 2006 • VOLUME 281 • NUMBER 44 JOURNAL OF BIOLOGICAL CHEMISTRY 33445 by guest on July 21, 2018 http://www.jbc.org/ Downloaded from FIGURE 6 . Two-dimensional schematic representation of the protein-ligand contacts in the closed, pyruvate-bound structure (a) and the wrong-ligand crystallographic refinement model containing salicylate and pyruvate (b). The amino acid side chains are shown as sticks and labeled with the three-letter amino acid code, amino acid number, and monomer name. The pyruvate and salicylate molecules are depicted as balland-stick and are labeled "Pyr 1," "Pyr 2," and "SalI" with a monomer name of (E). The carbon atoms are black, and the oxygen atoms are white. This figure was generated with LIGPLOT (31). P. aeruginosa Isochorismate Pyruvate Lyase