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Figure 2
The promirolysin structure. (a) A ribbon-type plot in cross-eyed stereo of native promirolysin in standard orientation (Gomis-Rüth, Botelho et al., 2012BB31). The PS is in pink with the helices in magenta (α1p and α2p; for numbering, see Fig. 1[link]). The CD is in pale blue, with the helices (α1–α6) in cyan and the β-strands (β1–β8) in blue. The four zinc-binding residues from the PS and the CD are shown for their side chains and labelled, as are the alanine-replacing catalytic Glu225, the first residue of mature mirolysin upon activation (Arg55), the Met-turn methionine (Met284) and Asp231, which replaces the canonical glycine of the zinc-binding motif. The catalytic zinc and the structural calcium cations are shown as magenta and blue spheres, respectively, the latter are labelled with their residue number, as are the N- and C-terminus. A green arrow pinpoints the final activation cleavage site (Ser54–Arg55). (b) Close-up in stereo of (a) after a horizontal 45° rotation downward depicting only segment Trp236–Tyr258, calcium ions Ca997 and Ca998 (blue spheres), and the liganding solvent molecules (red spheres). Calcium-coordinating atoms are connected by green lines, the solvents bridging the cations are linked with magenta lines. Residues involved in cation binding are labelled with their residue numbers. (c) Close-up in stereo of (a) after a 25° rotation to the left showing the active-site cleft of promirolysin, with the CD in cyan/blue (labels in blue) and the PS in pink/magenta (labels in magenta). PS segment Arg21–Asn28 is shown as a stick model for its main chain; selected side chains are further displayed (pink carbons), as are relevant side chains of the CD (pale blue carbons). The CD zinc ligands are not labelled for clarity [see (a)]. (d) Close-up in stereo of (a) after a horizontal 30° rotation downward and a 50° rotation to the right. A green arrow pinpoints the final activation cleavage site (Ser54–Arg55).

IUCrJ
Volume 7| Part 1| January 2020| Pages 18-29
ISSN: 2052-2525
https://doi.org/10.1107/S2052252519013848