Exploring Wells-Dawson Clusters Associated With the Small Ribosomal Subunit

Abstract

The polyoxometalate P₂W₁₈ ${\text{O}}_{62}^{6-}$ , the Wells-Dawson cluster, stabilized the ribosome sufficiently for the crystallographers to solve the phase problem and improve the structural resolution. In the following we characterize the interaction of the Wells-Dawson cluster with the ribosome small subunit. There are 14 different P₂W₁₈ ${\text{O}}_{62}^{6-}$ clusters interacting with the ribosome, and the types of interactions range from one simple residue interaction to complex association of multiple sites including backbone interactions with a Wells-Dawson cluster. Although well-documented that bridging oxygen atoms are the main basic sites on other polyoxometalate interaction with most proteins reported, the W=O groups are the main sites of the Wells-Dawson cluster interacting with the ribosome. Furthermore, the peptide chain backbone on the ribosome host constitutes the main sites that associate with the Wells-Dawson cluster. In this work we investigate the potential of one representative pair of closely-located Wells-Dawson clusters being a genuine Double Wells-Dawson cluster. We found that the Double Wells-Dawson structure on the ribosome is geometrically sound and in line with other Double Wells-Dawson clusters previously observed in the solid state and solution. This information suggests that the Double Wells-Dawson structure on the ribosome is real and contribute to characterization of this particular structure of the ribosome.

Keywords: Dawson cluster; H-bonding; double Dawson cluster; polyoxotungstate; protein oxometalate interactions; ribosome.

Figure 1

The structure of the small ribosomal subunit from Thermus thermophilus (T30S) from the (A) front and (B) side, respectively. (C) Symmetry-generated dimeric form of two ribosomal small subunit structure within their crystals showing each of the P₂W₁₈ sites (red). Modified with permission from Bashan and Yonath (2008).

Figure 2

P₂W₁₈, P₂W₁₈${\text{O}}_{62}^{6-}$ in (A) ball-and-stick and (B) polyhedral representations. Labels in (A) show the eight unique types of oxygen atoms and follow a modification to the naming conventions of Keggin clusters (Janik et al., 2003). Darker and lighter polyhedra in (B) represent the cap and belt types of tungsten sites, respectively. The Wells-Dawson structure by Kato et al. (2013) with refcode RIBFUF is the structure with the lowest R₁ value reported (Kato et al., 2013) and is used in this work as a reference Wells-Dawson structure.

Figure 3

Crystals of the small ribosomal subunits (T30S) were soaked for a few minutes in solutions containing small amounts of the Wells-Dawson tungstate complex (P₂W₁₈, PW₁₈ by the authors, WO2 in the PDB). The structure of the complex of the ribosomal subunits with the cluster (PDB Ref code 1I94) is shown. The P₂W₁₈ residues that are described in detail in this manuscript are P₂W₁₈ numbers 1,014 and 1,006 for the discrete clusters and 1,001 and 1,004 for the Double Wells-Dawson cluster (Pioletti et al., 2001).

Figure 4

The structure of POMs number (A) 1,014 (B) 1,006, and (C) 1,576 from 1I94. Numbering as shown in Figure 3 (Pioletti et al., 2001).

Figure 5

Schematic illustration of several hypothetical double Dawson clusters. (A) Double Dawson structures may be connected through a joint oxygen atom on a corner, corner-shared (P₂W₁₈O₆₁)₂O, in a cap-to-cap (top) or belt-to-cap (bottom). (B) Two structural possibilities where the Double Dawson structure are connected through the edge, edge-shared (P₂W₁₈O₆₀)₂O₂, with belt-to-belt (top) and cap-to-cap (bottom). Two full P₂W₁₈ Dawson units can be interacting through (C) H-bonding (2:2 isomer) [from YEFRAF (Liu et al., 2014)] or (D) through some other linker such as 4,4′-bipyridine from Zhao et al. (2008).

Figure 6

The structure of a representative Double Wells-Dawson cluster consisting of clusters 1,001 (Right) and 1,004 (Left) from 1I94.