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PROSITE documentation PDOC00876

Bacterial microcompartment (BMC) domain signature and profile and BMC circularly permuted domain profile





Description

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.

Last update:

July 2020 / Text revised; profiles added.

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Technical section

PROSITE methods (with tools and information) covered by this documentation:

BMC_2, PS51930; Bacterial microcompartment (BMC) domain profile  (MATRIX)

BMC_CP, PS51931; Bacterial microcompartment (BMC) circularly permuted domain profile  (MATRIX)

BMC_1, PS01139; Bacterial microcompartment (BMC) domain signature  (PATTERN)


References

1AuthorsCrowley C.S. Sawaya M.R. Bobik T.A. Yeates T.O.
TitleStructure of the PduU shell protein from the Pdu microcompartment of Salmonella.
SourceStructure 16:1324-1332(2008).
PubMed ID18786396
DOI10.1016/j.str.2008.05.013

2AuthorsSutter M. McGuire S. Ferlez B. Kerfeld C.A.
TitleStructural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies.
SourceACS. Synth. Biol. 8:668-674(2019).
PubMed ID30901520
DOI10.1021/acssynbio.9b00011

3AuthorsYeates T.O. Jorda J. Bobik T.A.
TitleThe shells of BMC-type microcompartment organelles in bacteria.
SourceJ. Mol. Microbiol. Biotechnol. 23:290-299(2013).
PubMed ID23920492
DOI10.1159/000351347

4AuthorsChowdhury C. Sinha S. Chun S. Yeates T.O. Bobik T.A.
TitleDiverse bacterial microcompartment organelles.
SourceMicrobiol. Mol. Biol. Rev. 78:438-468(2014).
PubMed ID25184561
DOI10.1128/MMBR.00009-14

5AuthorsKerfeld C.A. Erbilgin O.
TitleBacterial microcompartments and the modular construction of microbial metabolism.
SourceTrends. Microbiol. 23:22-34(2015).
PubMed ID25455419
DOI10.1016/j.tim.2014.10.003

6AuthorsSommer M. Sutter M. Gupta S. Kirst H. Turmo A. Lechno-Yossef S. Burton R.L. Saechao C. Sloan N.B. Cheng X. Chan L.-J.G. Petzold C.J. Fuentes-Cabrera M. Ralston C.Y. Kerfeld C.A.
TitleHeterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.
SourcePlant. Physiol. 179:156-167(2019).
PubMed ID30389783
DOI10.1104/pp.18.01190

7AuthorsSommer M. Cai F. Melnicki M. Kerfeld C.A.
Titlebeta-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints.
SourceJ. Exp. Bot. 68:3841-3855(2017).
PubMed ID28419380
DOI10.1093/jxb/erx115

8AuthorsWheatley N.M. Gidaniyan S.D. Liu Y. Cascio D. Yeates T.O.
TitleBacterial microcompartment shells of diverse functional types possess pentameric vertex proteins.
SourceProtein. Sci. 22:660-665(2013).
PubMed ID23456886
DOI10.1002/pro.2246

9AuthorsCrowley C.S. Cascio D. Sawaya M.R. Kopstein J.S. Bobik T.A. Yeates T.O.
TitleStructural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell.
SourceJ. Biol. Chem. 285:37838-37846(2010).
PubMed ID20870711
DOI10.1074/jbc.M110.160580

10AuthorsKlein M.G. Zwart P. Bagby S.C. Cai F. Chisholm S.W. Heinhorst S. Cannon G.C. Kerfeld C.A.
TitleIdentification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport.
SourceJ. Mol. Biol. 392:319-333(2009).
PubMed ID19328811
DOI10.1016/j.jmb.2009.03.056



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