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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: May 11, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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Published on: May 13, 2020

A self-compartmentalizing hexamer serine protease from Pyrococcus horikoshii: substrate selection achieved through

Dóra K Menyhárd1, Anna Kiss-Szemán, Éva Tichy-Rács

  • 1Protein Modeling Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary.

The Journal of Biological Chemistry
|May 2, 2013
PubMed
Summary

This study reveals the unique double-gated entry mechanism of the Pyrococcus horikoshii oligopeptidase (PhAAP), explaining substrate size limitation. Different oligopeptidases employ distinct strategies for substrate selection and assembly.

Keywords:
Acylaminoacyl PeptidaseAggregationAmylogenic β-StrandPeptide InteractionsProtein Self-assemblySelf-compartmentalizationSerine ProteaseSubstrate Size SelectionX-ray Crystallography

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Last Updated: May 11, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Oligopeptidases restrict substrate size, but the underlying mechanism remains unclear.
  • Understanding these limitations is crucial for enzyme function and drug development.

Purpose of the Study:

  • To elucidate the structural basis for substrate size selectivity in oligopeptidases.
  • To investigate the unique substrate access mechanism of a hexameric serine protease, PhAAP.

Main Methods:

  • X-ray crystallography to determine the structure of Pyrococcus horikoshii oligopeptidase (PhAAP).
  • Structural analysis to identify substrate entry pathways and gating mechanisms.
  • Comparative analysis of oligopeptidase structures to understand evolutionary strategies.

Main Results:

  • The hexameric PhAAP possesses a self-compartmentalized internal space with a double-gated entry system.
  • Substrates access monomer active sites through a surface pore and a secondary, smaller opening at the domain interface.
  • A catalytic residue is positioned near an amylogenic β-edge, requiring specific protection strategies.

Conclusions:

  • PhAAP employs a unique, multi-step gating system for substrate selection, enforcing size limitations.
  • Oligopeptidase family members exhibit diverse self-assembly and substrate selection mechanisms.
  • Structural insights into PhAAP provide a model for understanding oligopeptidase substrate specificity.