| TCID | Name | Domain | Kingdom/Phylum | Protein(s) |
|---|---|---|---|---|
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1.S.1.1.1 | The PduA shell protein of 99 aas which forms a hexameric array with a pore in the array for diffusion of 1,2-propanediol but not propionaldehyde (Park et al. 2017). A serine that protrudes into the pore at the point of construction to form a hydrogen bond with propionaldehyde prevent it's free diffusion. Substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments confers a selective advantage for the host organism. The pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic propionaldehyde generated within the microcompartment (Park et al. 2017). PduA forms a selectively permeable pore tailored for the influx of 1,2-propanediol while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism (Chowdhury et al. 2015). The hexamer-hexamer interactions seen in PduA crystals persist in the cytoplasmic structures and reveal the profound influence of the two key amino acids, Lys-26 and Arg-79, on tiling, not only in the crystal lattice but also in the bacterial cytoplasm (Pang et al. 2014). There are several shell proteins, PduA and PduT being two of them, and their crystal structures have been determined (Crowley et al. 2010). PduA forms a symmetric homohexamer whose central pore appears tailored for facilitating transport of the 1,2-propanediol substrate. PduT is a novel, tandem domain shell protein that assembles as a pseudohexameric homotrimer. Its structure reveals an unexpected site for binding an [Fe-S] cluster at the center of the PduT pore (Crowley et al. 2010). The location of a metal redox cofactor in the pore of a shell protein suggests a novel mechanism for either transferring redox equivalents across the shell or for regenerating luminal [Fe-S] clusters.It is a minor shell protein of the Salmonella enterica microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation. The isolated BMC shell component protein ratio for J:A:B':B:K:T:U is approximately 15:10:7:6:1:1:2 (Crowley et al. 2010). PduJ is 89% identical to PduA; PduB is protein 1.S.2.1.2; PduU is protein 1.S.2.3.1 in TCDB. | Bacteria |
Pseudomonadota | PduA of Salmonella typhimurium |
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1.S.1.1.2 | EutM pore-forming shell protein of 96 aas with most of the protein except the C-terminus showing substantial hydrophobicity. It is in the ethanolamine metabolizing Eut microcompartment (Takenoya et al. 2010). Compartmentalization prevents escape of volatile or toxic intermediates, prevents off-pathway reactions, and creates private cofactor pools. Encapsulation in synthetic microcompartment organelles enhances the function of heterologous pathways. To this end, Slininger Lee et al. 2017 explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. The ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. The hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations affect growth on 1,2-propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the use of two strategies to engineer microcompartments to control metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores (Slininger Lee et al. 2017). This is a BMC-H protein. | Bacteria |
Pseudomonadota | EutM of E. coli |
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1.S.1.1.3 | Uncharacterized carboxysome shell protein of 103 aas. The carboxysome shell is permeable to protons (Menon et al. 2010). | Bacteria |
Cyanobacteriota | UP of Nostoc sphaeroides |
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1.S.1.1.4 | BMC domain-containing protein of 185 aas. It has an internally duplicated domain of about 80 aas, corresponding to and homologous to the smaller (~90 residue) members of this family. | Bacteria |
Bacillota | BMC protein of Thermovenabulum gondwanense |
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1.S.1.1.5 | BMC domain-containing protein of 96 aas | Bacteria |
Actinomycetota | BMC protein of Amycolatopsis jejuensis |
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1.S.1.1.6 | Carbon dioxide-concentrating mechanism protein, CcmK, of 103 aas. | Bacteria |
Cyanobacteriota | CcmK of Leptolyngbya foveolarum (microbial mat metagenome) |
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1.S.1.1.7 | ComK1 of 111 aas, possibly with one N-terminal TMS. It is one of four Carboxysome shell proteins called ComK1 - 4, all of which are homologous to each other (Kerfeld et al. 2005). The structures of other proteins in the carboxysome have been solved structurally. These include CsoSCA (formerly CsoS3), a bacterial carbonic anhydrase localized in the shell of the carboxysome, where it converts HCO3- to CO2 for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) (Sawaya et al. 2006). The carboxysome contains a viral capsid-like protein shell (see above) (Yeates et al. 2007) and a RuBisCO chaperone protein, RbcX (Tanaka et al. 2007). Atomic-level models of the bacterial carboxysome shell have been proposed (Tanaka et al. 2008). Molecular simulations have unraveled the molecular principles that mediate selective permeability of carboxysome shell proteins (Faulkner et al. 2020). | Bacteria |
Cyanobacteriota | CcmK1 of Synechocystis sp. PCC6803 |
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1.S.1.1.8 | CcmK3 shell protein of 102 aas. Heterohexamers formed by CcmK3 and CcmK4 increase the complexity of beta carboxysome shells (Sommer et al. 2019). | Bacteria |
Cyanobacteriota | CcmK3 of Synechococcus elongatus PCC7942 |
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1.S.1.1.9 | Carboxysome shell protein, CcmK4, of 113 aas. It is a minor shell protein component of the carboxysome, a polyhedral inclusion where RuBisCO is sequestered. The central pore probably regulates metabolite flux, as might the gaps between assembled homohexamers (Kerfeld et al. 2005). Homohexamers make sheets that probably form the facets of the polyhedral carboxysome (Dryden et al. 2009). This subunit probably makes both homohexamers and heterohexamers with CcmK3 (Sommer et al. 2019). Trettel et al. 2024 have summarized the properties of carboxysomes including the pore-forming shell protein subunits, ComK4, and considered how that can be useful for biotechnological purposes. They have also compared the shell proteins of carboxysomes with those of other metabolic compartments. Their models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion (Trettel et al. 2024). | Bacteria |
Cyanobacteriota | CcmK4 of Synechococcus elongatus PCC7942 |
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1.S.1.1.10 | ComK2 shell protein of 184 aas with 4 regions of mild hydrophobicity. It is a BMC-T protein (Faulkner et al. 2020). | CcmK2 of Salmonella enterica subsp. enterica serovar Newport | ||
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1.S.1.1.11 | Cut BMC shell protein, CmcB, of 94 aas (Ochoa et al. 2023). This shell protein plays a major role in choline transport across the shell of the choline utilization microcompartment of Escherichia coli 536 (Ochoa et al. 2023). | CmcB of E. coli | ||
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1.S.1.1.13 | Shell protein of 213 aas, an internal duplication of single domain proteins such as listed under TC#s 1.S.1.1.1 and 1.S.1.1.2, It shows 62 - 65 % identity with the latter two proteins. | Bacteria |
Myxococcota | Duplicated shell protein of Haliangium ochraceum |
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1.S.1.1.14 | Duplicated BMC domain-containing shell protein of 208 aas. | Bacteria |
Planctomycetota | Shell protein of Planctomycetaceae bacterium |