7fi3 | pdb_00007fi3

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

spinqualitylabelsall models 7fi3, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7fi3 is a 8 chain structure with sequence from Thermococcus kodakarensis KOD1 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.3Å Ligands: GOL, MSE, NA, P6G Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 A 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. Structural basis for peptide recognition by archaeal oligopeptide permease A.,Yokoyama H, Kamei N, Konishi K, Hara K, Ishikawa Y, Matsui I, Forterre P, Hashimoto H Proteins. 2022 Jul;90(7):1434-1442. doi: 10.1002/prot.26324. Epub 2022 Mar 5. PMID:35170084 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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