FIG 5.
Peptide-binding site of HpDppA and comparison to other ABC transporter-associated peptide-binding proteins. (A) Stereoview of the 2mFo-DFc sigma A-weighted electron density for tetrapeptide STSA bound to HpDppA. The map is contoured at 1 σ. (B) A walleye stereodiagram showing the protein side chains that form direct contacts with the bound peptide and hydrogen bonds important for ligand recognition. The ligand is shown with carbon atoms colored green and labeled 1 to 4. (C) Peptide-binding pockets in SBPs from different bacteria, cocrystallized with their native ligands. The protein orientation is similar for all structures, which are sorted according to the size of the cavity, from the largest to the smallest. The protein moieties are shown using a cartoon representation, the bound peptides are drawn using a ball and stick representation, and the ligand-binding cavities are shown using green mesh. LlOppA, oligopeptide-binding protein from L. lactis (PDB ID 3DRF); BsAppA, oligopeptide-binding protein from B. subtilis (PDB ID 1XOC); HpDppA, peptide-binding protein from H. pylori SS1 (this study); TtOppA, peptide-binding protein from T. thermophilus (PDB ID 2D5W); YpOppA, oligopeptide-binding protein from Y. pestis (PDB ID 2Z23); EcDppA, dipeptide-binding protein from E. coli (PDB ID 1DPP). (D) Comparison of the peptide-binding cavity volumes of different bacterial SBPs. The size ranges of their peptide ligands reported in the literature are shown on the top of the bars. a.a., amino acids.