High-resolution NMR structure of a Zn2+-containing form of the bacteriophage T5 l-alanyl-d-glutamate peptidase

Abstract

This paper represents the spatial solution structure of the Zn²⁺-containing form of the bacteriophage T5 L-alanyl-D-glutamate peptidase (EndoT5-Zn²⁺). The core of this α + β protein is formed by three α-helices (residues 7–15, 20–30, and 87–104) and a β-sheet containing three β-strands (residues 35–39, 71–76, and 133–135). The protein has two short loops (residues 16–19 and 31–34), a medium-length loop (residues 77–86) containing a short β-hairpin (residues 77–82), and two long loops (residues 40–70 and 105–132). The long loops include a stable 3₁₀-helix (residues 66–68) and labile α-helices 46–53 and 113–117. Catalytic Zn²⁺-binding site is represented by three amino acid residues, His₆₆, Asp₇₃, and His₁₃₃. The cation-binding His residues are located near the foundations of the long loops, whereas Asp₇₃ is positioned in the middle of the core β-sheet. The catalytic center localization contributes to the stabilization of the entire molecule, with Zn²⁺-binding playing a key role in the folding of this protein.