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
- 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.
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