7FI3

Archaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with an endogenous pentapeptide

7FI3 の概要

• エントリーDOI: 10.2210/pdb7fi3/pdb
• 分子名称: ABC-type dipeptide/oligopeptide transport system, endogenous pentapeptide, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: oligopeptide permease, peptide binding protein
• 由来する生物種: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)); 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 341088.18

構造登録者

Yokoyama, H.,Kamei, N.,Konishi, K.,Hara, K.,Hashimoto, H. (登録日: 2021-07-30, 公開日: 2022-04-13, 最終更新日: 2024-10-16)

主引用文献

Yokoyama, H.,Kamei, N.,Konishi, K.,Hara, K.,Ishikawa, Y.,Matsui, I.,Forterre, P.,Hashimoto, H.
Structural basis for peptide recognition by archaeal oligopeptide permease A.
Proteins, 90:1434-1442, 2022

PubMed Abstract: Oligopeptide permease A (OppA) plays an important role in the nutrition of cells and various signaling processes. In archaea, OppA is a major protein present in membrane vesicles of Thermococcales. Because there being no crystal structures of archaeal OppAs determined to date, we report the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA) at 2.3 Å resolution by the single-wavelength anomalous dispersion method. TkOppA consists of three domains similarly to bacterial OppAs, and the inserted regions not present in bacterial OppAs are at the periphery of the core region. An endogenous pentapeptide was bound in the pocket of domains I and III of TkOppA by hydrogen bonds of main-chain atoms of the peptide and hydrophobic interactions. No hydrogen bonds of side-chain atoms of the peptide were observed; thus, TkOppA may have low peptide selectivity but some preference for residues 2 and 3. TkOppA has a relatively large pocket and can bind a nonapeptide; therefore, it is suitable for the binding of large peptides similarly to OppAs of Gram-positive bacteria.

PubMed: 35170084
DOI: 10.1002/prot.26324

実験手法

X-RAY DIFFRACTION (2.3 Å)