PyPrx6 active site depicting the sulfinic acid and the binding orientations of glycerol. (A) Fc-Fo omit map (1.62 σ) of the active site from the 4 chains within the asymmetric unit of PyPrx6 (PDB: 3TB2) showing the density assigned to both the sulfinic acid of CP and the glycerol bound in the active site. Glycerol and sulfinic acid are labelled as GOL and CSD, respectively. Note that the carbons are yellow, sulfur is green, oxygen is red, and nitrogen is blue. (B) A comparison of the binding orientations of each of the glycerol molecules of PyPrx6 relative to H2O2 derived from an alignment with the ApTrx-H2O2 structure (PDB: 3A2V) with our PyPrx6 structure. The H2O2 is shown as the red oxygen atoms with positions OA and OB labelled, while the 4 glycerol molecules in the PyPrx6 structure are shown with different coloured backbones and red oxygen atoms. Note that in each case, the terminal oxygen of the glycerol molecule aligns with position OB. (C) For comparison, from a similar structural alignment the known binding orientations for glycerol (from PDB: 3A2W (ApTrx, chains A and C with the glycerol molecules depicted in pink and green, respectively) are compared to the same binding of H2O2 (PDB: 3A2V). Note that for ApTrx chain A, the glycerol terminal oxygen aligns with position OA, while the glycerol molecule from ApTrx chain C has oxygen atoms aligning with positions OA and OB as was previously reported  All structural alignments derived from the alignment of the following conserved residues PxxxxTxxCP, as was done previously .
Qiu et al. BMC Structural Biology 2012 12:2 doi:10.1186/1472-6807-12-2