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Updated: Oct 3, 2025
11:27
X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
Published on: May 13, 2020
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Structural basis for peptide recognition by archaeal oligopeptide permease A
Hideshi Yokoyama1, Nanami Kamei2, Keijiro Konishi2
1Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Proteins
|February 16, 2022
Summary
The crystal structure of archaeal Oligopeptide Permease A (OppA) from Thermococcus kodakaraensis was determined. This archaeal OppA binds peptides in a large pocket, suggesting broad substrate specificity similar to Gram-positive bacteria.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Oligopeptide permease A (OppA) is crucial for cellular nutrition and signaling.
- In Thermococcales archaea, OppA is a key protein in membrane vesicles.
- No prior crystal structures of archaeal OppA proteins were available.
Purpose of the Study:
- To determine the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA).
- To elucidate the structural basis for peptide binding in archaeal OppA.
Main Methods:
- X-ray crystallography
- Single-wavelength anomalous dispersion (SAD) method
- Resolution: 2.3 Å
Main Results:
- The crystal structure of TkOppA was determined, revealing three domains similar to bacterial OppA.
- Inserted regions unique to archaeal OppA were identified at the periphery.
- TkOppA binds an endogenous pentapeptide via main-chain hydrogen bonds and hydrophobic interactions.
- The binding pocket is large, accommodating nonapeptides, indicating potential for binding larger peptides.
Conclusions:
- TkOppA exhibits structural homology to bacterial OppA but possesses unique inserted regions.
- The binding characteristics suggest TkOppA has low peptide selectivity with a preference for residues 2 and 3.
- TkOppA's large binding pocket is suitable for accommodating larger peptides, akin to OppAs in Gram-positive bacteria.
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