PROSITE documentation PDOC00876

Bacterial microcompartment (BMC) domain signature and profile and BMC circularly permuted 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, 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 (see <PDOC00876>) (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].

The BMC domain fold consists of three α helices (designated A, B, and C) and four β strands (designated β1, β2, β3, and β4) (see <PDB:3NGK>). Some instances of the BMC shell protein reveal a circular permutation in which a highly similar tertiary structure is built from secondary structure elements occurring in a different order. The secondary structure elements contributed by the C-terminal region of the typical BMC fold are instead contributed by the N-terminal region of the BMC circularly permuted domain (see <PDB:3CGI>) [1,9,10].

Some proteins containing a BMC or a circularly permuted BMC domain are listed below:

• Escherichia coli and Salmonella typhimurium EutM (or CchA), involved in the degradation of ethanolamine. Contains one BMC domain.
• Escherichia coli and Salmonella typhimurium EutK (or YffI), involved in the degradation of ethanolamine. It has an extra protein domain (EutK-Ctail) of about 60 amino acids (see <PDOC51933>) following the conserved BMC domain.
• Escherichia coli and Salmonella typhimurium ethanolamine utilization protein EutL. Contains two circularly permuted BMC domains.
• Escherichia coli and Salmonella typhimurium ethanolamine utilization protein EutS. Contains one circularly permuted BMC domain.
• Salmonella typhimurium PduA, involved in 1,2-propanediol metabolism. Contains one BMC domain.
• Salmonella typhimurium propanediol utilization protein PduB. Contains two circularly permuted BMC domains.
• Salmonella typhimurium propanediol utilization protein PduU. Contains one circularly permuted BMC domain.
• Synechococcus CcmK, involved in the formation of the carboxysome which is a polyhedral inclusion where RuBisCO is sequestered. Contains one BMC domain.
• Synechococcus CcmO, involved in the formation of the carboxysome which is a polyhedral inclusion where RuBisCO is sequestered. Contains two BMC domains.
• Halothiobacillus neapolitanus carboxysome shell proteins csoS1A, csoS1B and csoS1C, involved in the formation of the carboxysome which is a polyhedral inclusion where RuBisCO is sequestered. Contain one BMC domain.

As a signature pattern, we selected a conserved region in the N-terminal section of the BMC domain. We also developed two profiles covering respectively the entire BMC and circularly permuted BMC domains.