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. 2015 Mar 9;290(18):11321–11336. doi: 10.1074/jbc.M114.628149

FIGURE 3.

FIGURE 3.

Detailed features of the Avi-NaalL structure compared with the GCPII structure. Avi-NaalL residues are shown in green, and GCPII residues are shown in gray. Oxygens are colored red, and nitrogens are colored blue. A, calcium ion heptacoordination shell in Avi-NaalL with an electron density map. The calcium ion is coordinated by the Glu-425 and Glu-428 side chain carboxyl groups, the Thr-258 hydroxyl group, the carbonyl oxygens of Leu-261 and Thr-258, and a water molecule. Interactions are depicted as dashed lines with distances shown. The calcium ion is shown as a blue sphere, and water is shown as a red sphere. The 2Fo − Fc map (contoured to 1σ) is shown in blue, whereas the Fo − Fc map (contoured to 3σ) is colored green for positive and red for negative electron density peaks. B, superposition of the zinc ion coordination shells in Avi-NaalL and GCPII (PDB code 2PVW). The coordination shell of the active-site zincs is identical for both proteins, utilizing the side chains of His-368, Asp-378, Glu-417, Asp-445, and His-545 in Avi-NaalL. Additionally, the position of the Glu-416 side chain is identical to the position of the catalytic glutamate (Glu-424) in GCPII. Interactions are depicted as dashed lines with distances shown. C, electron density map around the Avi-NaalL active site. The 2Fo − Fc map (contoured to 1σ) is shown in blue, whereas the Fo − Fc map (contoured to 3σ) is colored green for positive and red for negative electron density peaks. Zinc ions are shown as magenta spheres, and waters are shown as red spheres. D, superposition of amino acids contributing to substrate binding in GCPII with the Avi-NaalL structure. The structure of GCPII E424A mutant (PDB code 3BXM) with bound N-acetyl-l-aspartyl-l-glutamate (NAAG), an endogenous GCPII substrate, is shown. Zinc ions in the GCPII structure are shown as gray spheres, and zinc ions in Avi-NaalL are shown as magenta spheres. Interactions of N-acetyl-l-aspartyl-l-glutamate with GCPII are depicted as dashed lines. E, superposition of the arginine patch in the GCPII (PDB code 3BXM) structure with Avi-NaalL. GCPII water molecule and chloride ion are depicted as gray spheres, and Avi-NaalL waters are shown as green spheres. Interactions of both GCPII and Avi-NaalL are depicted as dashed lines with distances shown.