Additional file 1.
Evolutionary conservation and structure of the β-D II domain. (A) Alignment of β-D II domain sequences from bacteria (E. coli K12, T. thermophilus) and eukaryotes (S. cerevisiae and H. sapiens) against the archaeon M. jannaschii. Residues identical to the archaeal sequence are shown in red. The numbers flanking the sequences represent the location of the sequences within the open reading frame of the complete subunit. One of the residues in close contact with the nascent transcripts is boxed and identified with an arrow. (B) Arrangement of the β-D II domain relative to the RNAP active site. Most structures are shown in space-filling mode to emphasize spatial connections. The Bridge Helix is shown in green (with the BH-HN region (corresponding to mjA' M808-E812) highlighted in yellow), the β-D II domain in turquoise, the template DNA is pale blue, the RNA is red, the NTP in the insertion site shown as a pink stick model and catalytic metal ions as magenta spheres. The rNTP binding pocket is indicated with a white-dashed oval. (C) Close-up view of the β-D II domain. Note the extensive contacts between the β-D II domain with the rNTP and the i-1 position of the nascent transcript. Two potential β-D II/Bridge Helix contacts are mediated via residues orthologous to mjA' R811 and L814. ((PDB #2E2H); visualized with PyMOL).
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Weinzierl BMC Biology 2010 8:134 doi:10.1186/1741-7007-8-134