Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C

Abstract

Lattice-translocation or crystal order-disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of \overline 3 symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions.

Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell

“…Aside from this missing density, we judged the structure interpretation to be reliable. The absence of non-origin peaks in a native Patterson map ruled out the possibility that the crystals were affected by a translocation disorder, as had been observed in previous BMC protein crystals (35). 94.6% of the residues were in the most favored region of a Ramachandran plot, with the remaining 5.4% of residues in the additional allowed regions.…”

The PduL Phosphotransacylase Is Used To Recycle Coenzyme A within the Pdu Microcompartment

“…The function of the Pdu MCP requires that the enzymes encapsulated within be provided with a steady supply of their required substrates and cofactors. On the basis of crystallographic studies, it was proposed that the central pores seen in BMC-domain shell proteins provide specific conduits for metabolites (31)(32)(33)(34)(35)46), and recent studies showed that the PduA shell protein forms a selective pore tailored to allow the influx of 1,2-PD while restricting the efflux of propionaldehyde (47). Moreover, recent studies showed that enzymatic cofactors can be regenerated internally within MCPs to maintain steady cofactor supplies.…”

“…The main building blocks of MCP shells are a family of small proteins that have bacterial microcompartment (BMC) domains (29)(30)(31). Many hexameric BMC-domain proteins contain small central pores that are proposed to mediate the movement of substrates and products into and out of MCPs (31)(32)(33). In addition, a family of trimeric tandem-BMC-domain shell proteins (EutL, CsoS1D, and CcmP) has been crystallized in pore-open and poreclosed conformations, suggesting a gated pore (34)(35)(36)(37).…”

Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO 2 Fixation in Cyanobacteria and Some Proteobacteria

“…The proposed mechanism for selective permeability of the shell relates to the presence of a conserved charged pore at the 6-fold axis of symmetry in the CsoS1x oligomers studied to date (113,118,119), which may be sufficient to allow preferential transit of charged molecules. Kinney et al (113) suggested that the positively charged pores may promote passage or binding of negatively charged molecules, such as bicarbonate, while remaining indifferent to uncharged molecules, such as O 2 or CO 2 .…”

“…Briefly, crystal structures of the CsoS1A, CsoS1C, and CsoS1D proteins have been elucidated, showing that these pro- teins contain the characteristic bacterial microcompartment (BMC) domain and form flattened, regularly hexagonal hexamers (CsoS1A and -C) or trimers (CsoS1D) (118)(119)(120), as BMC proteins from ethanolamine (EUT) and propanediol (PDU) microcompartments do (113). An important observation is that each hexamer type has a central pore of a size and charge distribution that may allow entry of specific substrates (HCO 3 Ϫ , RuBP, and Mg 2ϩ ) or exit of products such as PGA, while retarding entry of O 2 and leakage of CO 2 (113,118,119). These BMC oligomers form sheets in crystallographic studies, which strongly suggests that the sheet structure represents the behavior of CsoS1 proteins in vivo.…”