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1897  structures 923  species 0  interactions 6224  sequences 6  architectures

Family: BMC (PF00936)

Summary: BMC domain

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BMC domain Edit Wikipedia article

PDB 2a1b EBI.jpg
carboxysome shell protein ccmk2

In molecular biology the Bacterial Microcompartment (BMC) domain is a protein domain found in a variety of shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. These shell proteins form the polyhedral structure of the carboxysome and related structures that plays a metabolic role in bacteria. The BMC domain consists of about 90 amino acid residues, characterized by β-α-β motif connected by a β-hairpin.

The majority of the shell proteins consist of a single BMC domain in each subunit, forming a hexameric structure that assembles to form the flat facets of the polyhedral shell.[1] To date, two shell proteins were found to consist a tandem BMC domains, of which forms a trimeric structure, giving a pseudo-hexameric appearance.[2][3]


  1. ^ Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO (August 2005). "Protein structures forming the shell of primitive bacterial organelles". Science. 309 (5736): 936–8. CiteSeerX doi:10.1126/science.1113397. PMID 16081736.
  2. ^ Heldt D, Frank S, Seyedarabi A, Ladikis D, Parsons JB, Warren MJ, Pickersgill RW (September 2009). "Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri". The Biochemical Journal. 423 (2): 199–207. doi:10.1042/BJ20090780. PMID 19635047.
  3. ^ Pang A, Warren MJ, Pickersgill RW (February 2011). "Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site". Acta Crystallographica D. 67 (Pt 2): 91–6. doi:10.1107/S0907444910050201. PMID 21245529.
This article incorporates text from the public domain Pfam and InterPro: IPR000249

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Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure [1].

Literature references

  1. Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO; , Science 2005;309:936-938.: Protein structures forming the shell of primitive bacterial organelles. PUBMED:16081736 EPMC:16081736

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000249

Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. 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. This domain is found in a variety of polyhedral organelle shell proteins (CcmK), including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologues from other bacteria [ PUBMED:30389783 , PUBMED:25455419 , PUBMED:30901520 ].

Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes [ PUBMED:11722879 ]. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [ PUBMED:14729686 , PUBMED:33116131 ], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO 2 concentrations and are thought to function as part of a CO 2 -concentrating mechanism [ PUBMED:15012219 , PUBMED:9891798 ].

Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B 12 -dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica [ PUBMED:10498708 ]) and ethanolamine utilisation (e.g., in Salmonella typhimurium [ PUBMED:7868611 ]). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [ PUBMED:10498708 , PUBMED:11844753 ] or ethanolamine utilisation eut [ PUBMED:7868611 , PUBMED:10464203 ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO 2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO 2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation [ PUBMED:11844753 ]. It seems probable that enterosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [ PUBMED:11722879 ].

The BMC domain fold consists of three alpha-helices (designated A, B, and C) and four beta-strands ( ). 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 ( ) [ PUBMED:18786396 , PUBMED:20870711 , PUBMED:19328811 ].

Gene Ontology

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Domain organisation

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Seed source: Pfam-B_1071 (release 3.0)
Previous IDs: Bact_microcomp; Bac_microcomp;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 380
Number in full: 6224
Average length of the domain: 75.70 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 64.25 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 74
Family (HMM) version: 22
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the BMC domain has been found. There are 1897 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
P0ABF4 View 3D Structure Click here
P63746 View 3D Structure Click here
P76540 View 3D Structure Click here
P76541 View 3D Structure Click here