Structural basis for peroxidase encapsulation in a protein nanocompartment

Abstract

Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogenKlebsiella pneumoniae. By combining cryo-electron microscopy with TP mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.

Structural and biochemical characterization of an encapsulin-associated rhodanese fromAcinetobacter baumannii

“…Encapsulin nanocompartments are self-assembling compartmentalization systems widespread in prokaryotes where cargo enzymes are specifically encapsulated inside 18 to 42 nm icosahedral protein shells 15,[16][17][18] . Encapsulins have been shown to be involved in iron storage [19][20][21] , peroxide detoxification 22,23 , and sulfur metabolism 24 . In the A. baumannii system, a cysteine desulfurase enzyme was identified as the cargo enzyme and was shown to be able to sequester and store substantial amounts of elemental sulfur inside the encapsulin shell.…”

Structural and biochemical characterization of an encapsulin‐associated rhodanese from Acinetobacter baumannii

“…Encapsulin nanocompartments are self‐assembling compartmentalization systems widespread in prokaryotes where cargo enzymes are specifically encapsulated inside 18–42 nm icosahedral protein shells (Giessen, 2022 ; Giessen & Silver, 2017 ; Jones, Benisch, & Giessen, 2023 ; Nichols et al, 2017 ). Encapsulins have been shown to be involved in iron storage (Eren et al, 2022 ; Giessen et al, 2019 ; Sutter et al, 2008 ), peroxide detoxification (Jones, Andreas, & Giessen, 2023 ; Lien et al, 2021 ), and sulfur metabolism (Nichols et al, 2021 ). In the A. baumannii system, a cysteine desulfurase (CD) enzyme was identified as the cargo enzyme and was shown to be able to sequester and store substantial amounts of elemental sulfur inside the encapsulin shell.…”