Figure 1.

RNase E of α-proteobacteria have a distinguishing S1 domain insert not found in RNase E of other bacterial classes. (A) Structure based sequence alignment of the E. coli and C. crescentus RNase E catalytic domains. The secondary structural elements of E. coli RNase E are shown on the lines above the sequence alignment using the PDB file 2BX2. The arrows indicate β-sheet, the coils indicate α-helices, TT indicates β turns and η indicates 3₁₀ helices. Red letters indicate homology and blue boxes show similarity. The red highlights indicate identity across the sequences. The green stars represent the antigenic peptide used in this study. Structural sub-domains of RNase E are coloured (RNase H: light blue; S1: purple; 5′ sensor: yellow; DNase I: dark grey; zinc link: red; small domain: dark blue). Alignments were prepared using CLUSTALW2 (http://www.ebi.ac.uk/Tools/clustalw2/index.html) and ESPript (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi). (B) E. coli RNase E NTD tetramer in complex with 13-mer RNA (pale orange). Structural sub-domains are highlighted for one protomer, coloured as in Figure 1A. The position of the S1 insert absent in E. coli RNase E catalytic domain is represented by the dashed loops.