1.S.6. The Bacterial/Archaeal Nanocompartment Encapsulin Shell Protein1 (BANC-SP1) Family
The two main classes of microbial protein compartments are bacterial microcompartments (BMCs) and encapsulin nanocompartments (ENCs). Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein (Giessen 2022). Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed by Giessen 2022.
Sutter et al. 2008 showed, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution revealed that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.
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Encapsulin of 259 aas and probably no TMSs, but 4 evenly spaced short regions of moderate hydrophobicity. The protein has been described by Sutter et al. 2008. Williams et al. 2018 redesigned the pore-forming loop region in encapsulin from Thermotoga maritima, and successfully enlarged the pore diameter up to an estimated 11 Å and increased mass transport rates by 7-fold. A 2.87 Å resolution cryo-EM structure has been determined (Xiong et al. 2020). It has the viral capsid protein-HK97-fold.
Encapsulin of Thermotoga maritima
Encapsulin shell protein, Enc or Cfp29, of 265 aas.
Enc of Mycobacterium tuberculosis
The encapsulin shell protein of 280 aas with four equidistant peaks of moderate hydrophobicity. This encapsulin nanocompartment protein is formed by 60 subunits; monomers form pentamers which assemble to form shells. There are 12 pores where the pentamers meet as well as 3-fold axis channels and dimer channels; none are larger than 3-4 Angstroms in diameter. The N-terminus of the protein is inside the shell, the C-terminus is outside (He et al. 2016). The shell component is for a type 1 encapsulin nanocompartment. It assembles into proteinaceous icosahedral shells 24 nm in diameter in the presence and absence of its ferritin cargo protein. The center of cargo-loaded nanocompartments is loaded with iron. The empty encapsulin nanocompartment sequesters about 2200 Fe ions while the cargo-loaded nanocompartment can maximally sequester about 4150 Fe ions. It does not have detectable ferroxidase activity (He et al. 2016).
Encapsulin of Rhodospirillum rubrum