The pore-forming shell protein, EutL, of 219 aas, of the bacterial ethanolamine-utilizing (ethanolamine ammonialyase )microcompartment (BMC) (Takenoya et al. 2010). The crystal structure has been described (Sagermann et al. 2009). It allows E. coli to use thanolamine as the sole source for carbon and nitrogen. The crystal structure of this shell protein at 2.2-Å resolution was determined. It is the largest representative of this BMC's shell proteins. In the crystal, EutL forms a trimer that exhibits a hexagonally shaped tile structure. The tiles arrange into a tightly packed 2D array that resembles the proteinaceous membrane of the intact BMC. In contrast to other BMC shell proteins, which have only 1 pore per tile, EutL exhibits 3 pores per tile, thereby significantly increasing the overall porosity of this protein membrane. Each of the individual pores is lined with negatively charged residues and aromatic residues that are proposed to facilitate passive transport of specific solutes. The characteristic shape of the hexagonal tile, which is also found in the microcompartments of carbon-fixating bacteria, may present an inherent and fundamental building unit that may provide a general explanation for the formation of differently sized microcompartments (Sagermann et al. 2009).  Ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening (Thompson et al. 2015). Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, revealed that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism proposed is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function (Thompson et al. 2015).

EutL of E. coli

PduB shell protein of 270 aas of a propanediol utilization polyhedral body

PduB of Salmonella paratyphi C

Trimeric bacterial microcompartment shell protein of 230 aas.  The protein hydropathy plot shows 5 peaks moderate hydrophobicity that may be TMSs.  Two bacterial microcompartment shell proteins [EtuA (ethanol utilization shell protein A) and EtuB] are encoded in the genome clustered with the genes for ethanol utilization. The function of the bacterial microcompartment is to facilitate fermentation by sequestering the enzymes, substrates and intermediates. Recent structural studies of bacterial microcompartment proteins have revealed both hexamers and pentamers that assemble to generate the pseudo-icosahedral bacterial microcompartment shell. Some of these shell proteins have pores on their symmetry axes. Heldt et al. 2009 reported the structure of the trimeric bacterial microcompartment protein EtuB, which has a tandem structural repeat within the subunit and pseudo-hexagonal symmetry. The pores in the EtuB trimer are within the subunits rather than between symmetry related subunits. The evolutionary advantage of this is that it releases the pore from the rotational symmetry constraint allowing more precise control of the fluxes of asymmetric molecules, such as ethanol, across the pore. EtuA was modeled suggesting that the two proteins have the potential to interact to generate the casing for a metabolosome (Heldt et al. 2009).

EutB of Clostridium kluyveri

Uncharacterized DUF692 domain-containing protein of 286 aas with a moderately hydrophobic profile, and with possibly 4 moderately hydrophobic peaks in the C-terminal half of the protein.  It is not known if this is a shell protein, but it appears to be destantly related to some of them (e.g., the protein listed under TC# 1.S.2.1.1).

UP of Nocardia grenadensis

PduU shell protein of 116 aas.  The hydropathy plot indicates two moderately hydrophobic peaks that may not be sufficiently hydrophobic to pass through the membrane.  The Pdu microcompartment is a proteinaceous, subcellular structure that serves as an organelle for the metabolism of 1,2-propanediol in Salmonella enterica (Crowley et al. 2008). It encapsulates several related enzymes within a shell composed of a few thousand protein subunits. Structural studies on the carboxysome, a related microcompartment involved in CO₂ fixation, have concluded that the major shell proteins from that microcompartment form hexamers that pack into layers comprising the facets of the shell. The crystal structure of PduU was determined. Though PduU is a hexamer like other characterized shell proteins, it has undergone a circular permutation leading to dramatic differences in the hexamer pore. In view of the hypothesis that microcompartment metabolites diffuse across the outer shell through these pores, the unique structure of PduU suggests the possibility of a special functional role (Crowley et al. 2008).

PduU of Salmonella enterica (typhimurium)

The BMC-H or CutR: BMC shell protein of 116 aas. Sutter et al. 2019 have engineered a synthetic protein that consists of a tandem duplication of BMC-H connected by a short linker. The synthetic protein forms cyclic trimers that self-assemble to form a smaller (25 nm) icosahedral shell with gaps at the pentamer positions. When coexpressed in vivo with the pentamer fused to an affinity tag, complete icosahedral shells could be purified (Sutter et al. 2019). It is a minor shell protein of the choline degradation-specific bacterial microcompartment (BMC). Proteins such as this one with circularly permuted BMC domains may play a key role in conferring heterogeneity and flexibility in this BMC.

CutR of Streptococcus intermedius SK54