10ES

Chloroplast Glutamyl Peptidase WT in open-open conformation

Summary for 10ES

• Entry DOI: 10.2210/pdb10es/pdb
• EMDB information: 75117
• Descriptor: Isoform 2 of Probable glutamyl endopeptidase, chloroplastic (1 entity in total)
• Functional Keywords: s9 protease, enzyme, serine protease, alpha-beta-alpha sandwich fold, beta-propeller, plant protein
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 2
• Total formula weight: 200717.22

Authors

Ehrlich, J.J.,Routray, P.,van Wijk, K.J.,Kawate, T. (deposition date: 2026-01-15, release date: 2026-05-27)

Primary citation

Ehrlich, J.J.,Routray, P.,Enns, L.,van Wijk, K.J.,Kawate, T.
Structural basis for dimerization, catalytic regulation, and substrate selectivity of the chloroplast S9D CGEP protease in Arabidopsis thaliana.
Protein Sci., 35:e70624-e70624, 2026

PubMed Abstract: S9 proteases are widely distributed across the tree-of-life and play essential roles in protein processing. However, the structural and mechanistic basis for protease activity in the S9D subfamily, restricted to photosynthetic eukaryotes (e.g., plants), cyanobacteria, proteobacteria and flavobacteria, is unknown. Here, we report the first high-resolution cryo-EM structures of an S9D protease, chloroplast glutamyl endopeptidase (CGEP) from the model plant Arabidopsis thaliana. CGEP adopts a dimeric architecture stabilized by two distinct interfaces: hydrophobic interactions between catalytic domains and an interdomain β-sheet linking the cap and catalytic domains. These interactions create a scaffold that supports a hinge loop, which acts as a steric gate to restrict substrate access and confine catalytic activity to the closed conformation. Unlike S9A-B-C proteases, CGEP maintains an intact catalytic triad in both open and closed states, relying on hinge-loop gating rather than catalytic disruption for regulation. Structural analysis and mutagenesis reveal that the hinge loop forms a conserved pocket favoring glutamate side chains, explaining CGEP's strong glutamate preference at cleavage sites. Together, these findings uncover a unique regulatory paradigm for S9D proteases and provide a structural framework for understanding substrate selectivity and dimerization.

PubMed: 42144868
DOI: 10.1002/pro.70624

Experimental method

ELECTRON MICROSCOPY (3 Å)