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

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 ( Ps DppA) was studied. The substrate specificity of Ps DppA was analyzed for 25 dipeptides with varying properties. Ps DppA showed binding affinities for 8 of the peptides. To explain the multispecific substrate recognition mechanism of Ps DppA, we solved the crystal structures of unliganded Ps DppA and of Ps DppA in complex with 4 different types of dipeptides. Ps DppA alternates between an “open” and a “closed” form during substrate binding. Structural analyses of 4 Ps DppA‐substrate complexes indicate that dipeptides are bound in the same position and the same orientation in Ps DppA. 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 Ps DppA is explained. Additionally, sequence alignment suggests that the substrate recognition mechanism of Ps DppA may be common in Gram‐negative bacteria. Our results provide a better understanding of marine bacterial peptide uptake.