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198  structures 957  species 1  interaction 7283  sequences 6  architectures

Family: BMC (PF00936)

Summary: BMC domain

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BMC domain Edit Wikipedia article

BMC
PDB 2a1b EBI.jpg
carboxysome shell protein ccmk2
Identifiers
Symbol BMC
Pfam PF00936
InterPro IPR000249
PROSITE PDOC00876

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]

[edit] References

  1. ^ Kerfeld, C. A.; Sawaya, M. R.; Tanaka, S.; Nguyen, C. V.; Phillips, M.; Beeby, M.; Yeates, T. O. (2005). "Protein Structures Forming the Shell of Primitive Bacterial Organelles". Science 309 (5736): 936–938. doi:10.1126/science.1113397. PMID 16081736. edit
  2. ^ Heldt, D.; Frank, S.; Seyedarabi, A.; Ladikis, D.; Parsons, J. B.; Warren, M. J.; Pickersgill, R. W. (2009). "Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization inClostridium kluyveri". Biochemical Journal 423 (2): 199–207. doi:10.1042/BJ20090780. PMID 19635047. edit
  3. ^ Pang, A.; Warren, M. J.; Pickersgill, R. W. (2011). "Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe–4S cluster-binding site". Acta Crystallographica Section D Biological Crystallography 67 (2): 91–96. doi:10.1107/S0907444910050201. PMID 21245529. edit

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

This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria.

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], 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 CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [PUBMED:15012219, PUBMED:9891798].

Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-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:11844753, PUBMED:10498708] 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 CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation [PUBMED:11844753]. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [PUBMED:11722879].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(128)
Full
(7283)
Representative proteomes NCBI
(3181)
Meta
(404)
RP15
(418)
RP35
(700)
RP55
(840)
RP75
(954)
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Format an alignment

  Seed
(128)
Full
(7283)
Representative proteomes NCBI
(3181)
Meta
(404)
RP15
(418)
RP35
(700)
RP55
(840)
RP75
(954)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(128)
Full
(7283)
Representative proteomes NCBI
(3181)
Meta
(404)
RP15
(418)
RP35
(700)
RP55
(840)
RP75
(954)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Curation and family details

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Seed source: Pfam-B_1071 (release 3.0)
Previous IDs: Bact_microcomp; Bac_microcomp;
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 128
Number in full: 7283
Average length of the domain: 77.20 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 65.78 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.9
Noise cut-off 20.5 20.5
Model length: 75
Family (HMM) version: 14
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Species distribution

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Interactions

There is 1 interaction for this family. More...

BMC

Structures

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 198 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 seqence.

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