PROSITE documentation PDOC51932

Bacterial microcompartment vertex (BMV) domain profile

Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. They are found across the Kingdom Bacteria where they play functionally diverse roles including CO(2) fixation and the catabolism of a range of organic compounds. They function as organelles by sequestering particular metabolic processes within the cell. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products (including toxic or volatile intermediates) into and out of the lumen. Although functionally distinct BMCs vary in their encapsulated enzymes, all are defined by homologous shell proteins. The shells of BMCs are made primarily of a family of proteins whose structural core is the BMC domain (see <PDOC00876>), and variations upon this core provide functional diversity. There are three classes of constituent proteins that form a shell with icosahedral symmetry: hexamer-forming proteins containing a single BMC domain (BMC-H); trimer/ pseudohexamer-forming proteins consisting of a fusion of two BMC domains (BMC-T), and pentamer-forming proteins containing a bacterial microcompartment vertex (or BMV) domain (BMC-P). The BMC-H and BMC-T proteins form the facets, and the BMC-P proteins form the vertices of the icosahedron. These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell [1,2,3,4,5,6,7,8,9,10].

The family of pentameric vertex proteins appears distinct in sequence and structure from the hexameric/pseudohexameric BMC family of proteins. The BMV domain has an OB (oligonucleotide/oligosaccharide binding) fold structure with a five-stranded curved β sheet forming a closed β-barrel with a short helix located between strands four and five on the inside of the pentamer. The five-stranded, predominantly antiparallel β-barrel has 1,-2,3,-5,4 topology (see <PDB:4I7A>) [8,9,10].

Some proteins containing a BMV domain are listed below:

• Escherichia coli and Salmonella typhimurium ethanolamine utilization protein EutN, a pentameric shell protein from the microcompartment.
• Salmonella typhimurium propanediol utilization microcompartment protein PduN.
• Rhodospirillum rubrum GrpN protein, from a glycyl radical enzyme-containing propanediol utilizing microcompartment.
• Synechococcus carbon dioxide concentrating mechanism protein CcmL, involved in the formation of the carboxysome which is a polyhedral inclusion where RuBisCO is sequestered.

The profile we developed covers the entire BMV domain.