Additional file 2.
Evolutionary conservation and structure of the Link domain. (A) Alignment of Link 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. Residues in close contact with the rNTP or nascent transcripts are indicated by boxes and arrows. (B) Arrangement of the Link 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 Link domain in light purple, 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.
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Weinzierl BMC Biology 2010 8:134 doi:10.1186/1741-7007-8-134