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Figure 4
Conserved binding mode of the signal-peptide C regions. (a), (b) and (c) show the peptide-binding cleft in surface representation with the peptides Pep1, Pep2 and Pep3 shown in stick mode in their 2Fo − Fc electron density contoured at 1.0σ. Peptide C-region residues are labelled P1–P6. (a) The structure of Pep1 shows an absence of electron density for the mature peptide region (P1′–P3′), which has been cleaved by SpsB. The catalytic Ser is rotated away from the carboxylate group of the cleaved peptide. There is no interpretable electron density for the peptide between P7 and the MBP linkage. (b) As for Pep1, the Pep2 peptide structure shows no electron density for the mature peptide region and rotation of the catalytic Ser away from the carboxylate group of the cleaved peptide. The entire cleaved peptide from P1 to the MBP linkage is well ordered. (c) The Pep3 inhibitor (yellow) bound in the peptide-binding cleft. A proline at position P1′ prevents cleavage. (d) Overlay of Pep1 (cyan), Pep2 (blue) and Pep3 (yellow) signal peptides shows that all peptide and SpsB residues (β-strands 1 and 4) share virtually identical main-chain atom positions, with only the Pep3 P1 residue being significantly displaced. The peptides (P1–P5) are shown in stick form and the SpsB residues as lines. All side chains have been removed, except for the Ala residues at P1 and P3 and Pro at P5.

IUCrJ
Volume 3| Part 1| January 2016| Pages 10-19
ISSN: 2052-2525
doi:10.1107/S2052252515019971