Molecular insights into the multispecific recognition of dipeptides of deep‐sea Gram‐negative bacteria Pseudoalteromonas sp. SM9913

Abstract

Peptide uptake is important for nutrition supply for marine bacteria. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide‐binding protein of dipeptide permease (Dpp), an important bacterial peptide transporter. DppA exclusively controls the substrate specificity of Dpp. Here, the substrate recognition mechanism of deep‐sea pseudoalteromonas sp. SM9913 DppA (PsDppA) was studied. The substrate specificity of PsDppA was analyzed for 25 dipeptides with varying properties. PsDppA showed binding affinities for 8 of the peptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides. PsDppA alternates between an “open” and a “closed” form during substrate binding. Structural analyses of 4 PsDppA‐substrate complexes indicate that dipeptides are bound in the same position and the same orientation in PsDppA. Residues facilitating the interactions with the dipeptides show no clear conformational changes when binding to different ligands. Based on structural and mutational analyses, the multispecific recognition mechanism of PsDppA is explained. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram‐negative bacteria. Our results provide a better understanding of marine bacterial peptide uptake.