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PROSITE documentation PDOC51932

Bacterial microcompartment vertex (BMV) 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 (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 PduN.
  • 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.

Last update:

July 2020 / First entry.

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Technical section

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

BMV, PS51932; Bacterial microcompartment vertex (BMV) domain profile  (MATRIX)


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

9AuthorsKeeling T.J. Samborska B. Demers R.W. Kimber M.S.
TitleInteractions and structural variability of beta-carboxysomal shell protein CcmL.
SourcePhotosynth. Res. 121:125-133(2014).
PubMed ID24504539
DOI10.1007/s11120-014-9973-z

10AuthorsSutter M. Wilson S.C. Deutsch S. Kerfeld C.A.
TitleTwo new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species.
SourcePhotosynth. Res. 118:9-16(2013).
PubMed ID23949415
DOI10.1007/s11120-013-9909-z



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