Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization
(A) Cartoon representation of the ϕDI Dut dimer with protomers coloured in pink and orange, respectively (left). The secondary structural elements are numbered and labeled in order from the N to C terminus (the ‘ indicates elements from the second protomer). A molecule of dUPNPP (sticks coloured by atom type) and two Mg ions (green spheres) occupies the active center of each protomer. In an orthogonal view (right) the conserved and variable (motif VI) regions of the dimeric Duts from S. aureus phages are colored in pink and yellow tones, respectively. The structural elements exploited to dimerize (helices α2 and α6, and the latch) are highlighted in dark tones. Notice that the nucleotide binding sites and the motifs VI map in opposite faces of the dimer. (B) Sequence of the ϕDI Dut, with residues that interact with the substrate highlighted with red stars and residues that interact across the dimer interface in blue text. The Ala residue mutated in the ϕDIA73L is indicated in red. The locations of the five conserved motifs in the dimeric Duts are indicated. Structural elements are shown above the sequence coloured as (A) right panel. (C) Detailed view of the ϕDI Dut active center. The substrate dUPNPP is represented in stick with carbon atoms in cyan. The residues interacting with the nucleotide are shown in stick representation, with carbon atoms coloured according to the protomer to which they correspond and are labeled with a similar color text with the exception of A73 that is highlighted with red text. Nitrogen, oxygen, phosphorus atoms are coloured in dark blue, red and orange, respectively. The Mg ions are represented as green spheres.