1.S.1. The Bacterial Microcompartment Shell/Pore-forming Protein-1 (BMC-SP1) Family 

Bacterial micro/nano-compartments are protein-based 'organelles' or 'machines' that function in the catalysis of specific reactions or reaction pathways, where the essential enzymes are surrounded by a proteineaceious shell, some of the proteins of which contain pores for the diffusion of certain metabolites but not others (Saier 2013).The shell protein and their pores have been fairly extensively characterized (Cheng et al. 2008). For example, the PduU shell protein from the 1,2-propanediol-metabolizing organelle in Salmonella typhimurium is a hexameric structure of a 99 aas protein containing a well defiined pore (Crowley et al. 2008) while the EutL shell protein of the ethanolamine ammonia lyase microcompartment in E. coli is a much larger protein of 219 aas that forms a trimer with a hexagonally shpaped tile structure (Sagermann et al. 2009) and the EutB shell protein in the ethanol utilizing microcompartment of Chlostridium kluyveri is also trimeric (Heldt et al. 2009).  There appear to be many such substrate-specific organelles in prokaryotes, and many of these have homologous pore-forming shell proteins.  The crystal structures of several of these are known and are described under the specific protein entries.



This family belongs to the .

 

References:

Cheng, S., Y. Liu, C.S. Crowley, T.O. Yeates, and T.A. Bobik. (2008). Bacterial microcompartments: their properties and paradoxes. Bioessays 30: 1084-1095.

Crowley, C.S., M.R. Sawaya, T.A. Bobik, and T.O. Yeates. (2008). Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure 16: 1324-1332.

Heldt, D., S. Frank, A. Seyedarabi, D. Ladikis, J.B. Parsons, M.J. Warren, and R.W. Pickersgill. (2009). Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri. Biochem. J. 423: 199-207.

Park, J., S. Chun, T.A. Bobik, K.N. Houk, and T.O. Yeates. (2017). Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell. J Phys Chem B 121: 8149-8154.

Sagermann, M., A. Ohtaki, and K. Nikolakakis. (2009). Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc. Natl. Acad. Sci. USA 106: 8883-8887.

Saier, M.H., Jr. (2013). Microcompartments and protein machines in prokaryotes. J. Mol. Microbiol. Biotechnol. 23: 243-269.

Takenoya, M., K. Nikolakakis, and M. Sagermann. (2010). Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli. J. Bacteriol. 192: 6056-6063.

Examples:

TC#NameOrganismal TypeExample
1.S.1.1.1

The PduA shell protein of 99 aas which forms a hexameric array with a porein the array for diffusion of 1,2-propanediol but not propionaldehyde (Park et al. 2017).  A serine that protrudes into the poreat the point of construction to form a hydrogen bond with propionaldehyde prevent it's free diffusion. 

PduA of Salmonella typhimurium

 
1.S.1.1.2

EutM pore-forming shell protein of the ethanolamine metabolizing Eut microcompartment (Takenoya et al. 2010).

EutM of E. coli

 
1.S.1.1.3

Uncharacterized carboxysome shell protein of 103 aas.

UP of Nostoc sphaeroides

 
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.

BMC protein of Thermovenabulum gondwanense

 
1.S.1.1.5

BMC domain-containing protein of 96 aas

BMC protein of Amycolatopsis jejuensis

 
1.S.1.1.6

Carbon dioxide-concentrating mechanism protein, CcmK, of 103 aas.

CcmK of Leptolyngbya foveolarum (microbial mat metagenome)