Figure 1.
Reaction catalyzed by the putative 3-polyprenyl decarboxylases UbiD and UbiX, the decarboxylation of 3-polyprenyl-4-hydroxybenzoate to 2-polyprenylphenol.
In P. aeruginosa ubiquinone, the polyprenyl chain consists of nine isoprene units [2].
Table 1.
Statistics of data collection and refinement for UbiD2 from P. aeruginosa.
Figure 2.
Sequence alignment of UbiD-like proteins.
The top five sequences represent bona fide UbiD type proteins, and the bottom five sequences are from the subclass of PA0254-like enzymes. Conserved residues are white characters in red boxes; similar residues are shown as red characters in blue frames. Secondary structure elements of UbiD from E. coli (PDB code 2IDB) are depicted above the sequence alignment and those of PA0254 from P. aeruginosa at the bottom of the alignment. α and 310 helices are displayed as squiggles, β-strands rendered as arrows, β turns by TT and α turns by TTT. Selected sequences are from top to bottom: bona fide UbiD from E. coli, Yokenella regensburgei, Enterobacter asburiae, Yersinia pestis, P. aeruginosa PAO1 (PA5237) and PA0254-like from Penicillium chrysogenum, Saccharomyces cerevisiae, Streptomyces sp. e14, Yokenella regensburgei and P. aeruginosa PAO1 (PA0254).The metal ligands and the putative active site residues in UbiD2 are marked by green triangles and asterisks, respectively.
Figure 3.
Structure of the P.aeruginosa PA0254 subunit.
A. Stereo view of the structure of the subunit of PA0254 from P. aeruginosa. The three domains are shown in blue (N-terminal domain), green (middle domain) and red (C-terminal domain). The metal site is indicated by a black sphere. N’ and C’ indicate N and C-terminal ends of the polypeptide chain. The helices α11, α12 and α14 involved in dimer formation are indicated. B: Topology diagrams for the three PA0254 domains. The colour-coding is as above.
Figure 4.
Superimposition of the PA0254 subunit from P.aeruginosa (colour-coding as in figure 3) with the corresponding subunit of UbiD from E. coli (PDB code 2IDB, shown in grey) in stereo.
Helices α10 and α11 are labeled, the bound metal ion in PA0254 is depicted as a black sphere.
Figure 5.
Putative active site of PA0254 from P.aeruginosa.
A. View of the metal binding site in PA0254. The unbiased, initial 2Fo-Fc electron density map for PA0254 crystallized in space group P3221, obtained after molecular replacement using the metal-free protein model from the P21 crystal form, is contoured at 1.0 σ. The refined model of the metal site is overlaid. His188 and Glu229 are shown as sticks, the bound metal ion is depicted as a black sphere, red spheres represent water molecules. B. Surface representation of the putative active site cleft at the domain interface in PA0254. Residues are colour-coded according to sequence conservation in the UbiD2 family, from the most conserved residues (purple) to the least conserved residues (cyan). Arg170 and Glu273 are indicated by R and E, respectively. The bound magnesium ion (M) is shown as a green sphere. The figure was prepared with the program Consurf [32].
Figure 6.
Schematic view of the PA0254 dimer.
Chains A and B were colored using the same colour-coding as in figure 3. Helices involved in dimer formation are labeled.