8B1B

DtpB-Nb132-AL

8B1B の概要

• エントリーDOI: 10.2210/pdb8b1b/pdb
• 分子名称: Dipeptide and tripeptide permease B, DECANE, HEXANE, ... (12 entities in total)
• 機能のキーワード: mfs, proton coupled oligopeptide transporter, membrane protein
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 70340.13

構造登録者

Killer, M.,Finocchio, G.,Lei, J.,Jungnickel, K.,Kotov, V.,Steinke, J.,Bartels, K.,Strauss, J.,Dupeux, F.,Humm, A.S.,Cornaciu, I.,Marquez, J.,Pardon, E.,Steyeart, J.,Loew, C. (登録日: 2022-09-09, 公開日: 2023-08-09)

主引用文献

Kotov, V.,Killer, M.,Jungnickel, K.E.J.,Lei, J.,Finocchio, G.,Steinke, J.,Bartels, K.,Strauss, J.,Dupeux, F.,Humm, A.S.,Cornaciu, I.,Marquez, J.A.,Pardon, E.,Steyaert, J.,Low, C.
Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition.
Cell Rep, 42:112831-112831, 2023

PubMed Abstract: Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.

PubMed: 37467108
DOI: 10.1016/j.celrep.2023.112831

実験手法

X-RAY DIFFRACTION (2.8 Å)