Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Proc Natl Acad Sci U S A. 2021 Apr 20;118(16):e2025658118. doi: 10.1073/pnas.2025658118.


Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.

Keywords: Mycobacterium smegmatis; cryo-electron microscopy; dye-decolorizing peroxidase; encapsulin nanocompartment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Bacterial Proteins / ultrastructure*
  • Cryoelectron Microscopy / methods
  • Mycobacterium smegmatis / metabolism
  • Mycobacterium smegmatis / pathogenicity
  • Mycobacterium smegmatis / ultrastructure*
  • Organelles / metabolism
  • Organelles / physiology
  • Peroxidases / metabolism
  • Peroxidases / ultrastructure*


  • Bacterial Proteins
  • Peroxidases