Atomic-Level Models of the Bacterial Carboxysome Shell

Abstract

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.

Insights from multiple structures of the shell proteins from the β‐carboxysome

“…The C-terminus has been noted to be the region of largest coordinate differences between CcmK paralogs, CcmK2 and CcmK4, elucidated earlier. 6 The coordinates of CcmK1 were employed in an earlier study aimed at modeling the assembly of the intact carboxysome, 8 …”

“…The hexameric structures of the CcmK proteins have been elucidated, but which side faces toward the carboxysome interior-and would therefore be most likely to be involved in protein-protein interactions-is uncertain. 7,8 Here we present a series of crystal structures of the CcmK1 and CcmK2 proteins in full length forms and as C-terminal truncations. Comparisons illustrate the structural features that are most conserved, while highlighting potentially relevant structural variations and providing further insights into molecular transport across pores through the hexagonally packed protein layers.…”

“…25 Crystal structures of minor carboxysome shell proteins CcmL and CsoS4A, unrelated to the BMC family, were recently elucidated and found to be pentameric. 8 The findings from those structural studies led to a rough atomic model of the carboxysome shell in which the pentameric proteins introduce curvature by forming the vertices of the icosahedral microcompartment shell, while the flat facets of the microcompartment are comprised of a large number of hexameric (BMC-type) shell proteins packed into a layer [ Fig. 1(D)].…”

The Structure of CcmP, a Tandem Bacterial Microcompartment Domain Protein from the β-Carboxysome, Forms a Subcompartment Within a Microcompartment

“…Both ␣-and ␤-types of carboxysome shells contain a minor component, CsoS4 or CcmL, respectively, that belongs to the EutN domain family (pfam03319); CsoS4 and CcmL form pentamers proposed to serve as the vertices of the icosahedron (1,3).…”

Addressing microbial organelles: A short peptide directs enzymes to the interior

“…The shells of BMCs that have been purified and studied directly were shown to be composed of several thousand copies of orthologous polypeptides with conserved domains (Pfam 00936); recent crystallographic studies revealed that individual monomers of the predominant BMC shell proteins are arranged into thin hexamers that strongly interact in an "edgeon" fashion to form the flat facets of the polyhedral compartments (6)(7)(8). Another, albeit minor, shell constituent (Pfam 03319) that appears to occur in all BMCs forms the pentamers thought to occupy the vertices of the polyhedral structures (9). One of the great mysteries surrounding BMCs is the mechanism by which their shells, all of which apparently are built from proteins that belong to the same two structural families, function in widely diverse metabolic pathways and package a large variety of different and seemingly structurally unrelated enzymes.…”