D
IPR044872

CcmK/CsoS1, bacterial microcompartment domain

InterPro entry
Short nameCcmK/CsoS1_BMC
Overlapping
homologous
superfamilies
 
domain relationships

Description

Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. They are found across 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
[4, 3, 2]
.

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 centre of symmetry that enable metabolite transport across the shell
[1, 11, 4, 3, 2, 10, 12, 9]
.

The BMC domain fold consists of three α-helices (designated A, B, and C) and four β-strands (designated β1, β2, β3, and β4). 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
[1, 8, 7]
.

This entry represents the BMC domain found in CsoS1/CcmK and related proteins. CsoS1 and CcmK are the shell proteins of the carboxysome, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, ccbL-ccbS) is sequestered
[5, 6]
.

References

1.Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Crowley CS, Sawaya MR, Bobik TA, Yeates TO. Structure 16, 1324-32, (2008). View articlePMID: 18786396

2.Bacterial microcompartments and the modular construction of microbial metabolism. Kerfeld CA, Erbilgin O. Trends Microbiol 23, 22-34, (2015). PMID: 25455419

3.Diverse bacterial microcompartment organelles. Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Microbiol Mol Biol Rev 78, 438-68, (2014). PMID: 25184561

4.The shells of BMC-type microcompartment organelles in bacteria. Yeates TO, Jorda J, Bobik TA. J Mol Microbiol Biotechnol 23, 290-9, (2013). PMID: 23920492

5.Engineering bacterial microcompartment shells: chimeric shell proteins and chimeric carboxysome shells. Cai F, Sutter M, Bernstein SL, Kinney JN, Kerfeld CA. ACS Synth Biol 4, 444-53, (2015). PMID: 25117559

6.A challenging interpretation of a hexagonally layered protein structure. Thompson MC, Yeates TO. Acta Crystallogr D Biol Crystallogr 70, 203-8, (2014). PMID: 24419393

7.Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA. J. Mol. Biol. (2009). PMID: 19328811

8.Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. J. Biol. Chem. 285, 37838-46, (2010). View articlePMID: 20870711

9.Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Wheatley NM, Gidaniyan SD, Liu Y, Cascio D, Yeates TO. Protein Sci. 22, 660-5, (2013). View articlePMID: 23456886

10.Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells. Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. Plant Physiol 179, 156-167, (2019). PMID: 30389783

11.Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies. Sutter M, McGuire S, Ferlez B, Kerfeld CA. ACS Synth Biol 8, 668-674, (2019). PMID: 30901520

12.β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. Sommer M, Cai F, Melnicki M, Kerfeld CA. J Exp Bot 68, 3841-3855, (2017). PMID: 28419380

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