Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Department of Microbiology, Monash University, Clayton, Victoria, Australia.
J Bacteriol. 2019 Sep 20;201(20). doi: 10.1128/JB.00400-19. Print 2019 Oct 15.
The gastric pathogen has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by requires an ATP binding cassette (ABC) transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA, which captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, DppA binds, with micromolar affinity, peptides of diverse amino acid sequences ranging between two and eight residues in length. We present analysis of the 1.45-Å-resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the greatest contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides. The World Health Organization listed as a high-priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides, termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for , our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.
胃病原体利用碳水化合物作为碳源的能力有限，而是依赖于外源性氨基酸和肽。某些肽被 吸收需要一个 ATP 结合盒（ABC）转运蛋白注释的二肽渗透酶（Dpp）。转运蛋白的特异性由其同源的底物结合蛋白 DppA 决定，DppA 在周质中捕获配体，并将其递送给渗透酶。在这里，我们表明，与以前表征的 DppA 蛋白不同， DppA 以微摩尔亲和力结合具有 2 到 8 个残基长度的不同氨基酸序列的肽。我们展示了其与四肽 STSA 复合物的 1.45 Å 分辨率晶体结构的分析，该结构为观察到的广泛特异性提供了结构基础。对分子表面的分析揭示了一个足够大的配体结合口袋，可以容纳长达九个残基的肽。该结构表明， DppA 能够通过与肽主链原子形成主要相互作用来识别广泛的肽序列。在来自其他细菌的 DppA 中终止肽结合口袋的环在 蛋白中明显更短，这解释了它能够结合更长的肽的能力。容纳肽配体的两个 N 末端残基的亚基对蛋白质 - 配体结合能的贡献最大，这与二肽结合亲和力接近更长肽的观察结果一致。世界卫生组织将 列为抗生素开发的高优先级病原体。肽转运蛋白在药物设计中的潜力已得到广泛认可。我们发现，肽 ABC 转运蛋白的底物结合蛋白，即二肽渗透酶，是其家族中的一个不寻常成员，因为它直接结合具有 2 到 8 个残基长度的不同氨基酸序列的肽。我们还为观察到的广泛特异性提供了结构基础。由于作为碳源导入肽的能力对 至关重要，我们的发现将为基于膜不可渗透的抗菌剂与肽融合或抑制的药物设计策略提供信息。
