Figure 3

Structure-based sequence alignment of the nuclease(-like) domains of RecB and RecC. Nuclease(-like) domain sequences of RecB (above, group 1) and RecC (below, group 2) were chosen from diverse representative species and extracted from complete alignments of COG database [31] entries for RecB or RecC. Purple indicates the E. coli sequences crystallized as the RecBCD complex (PDB code 1w36; [18]). Other sequences are labelled with Genbank numbers and sequence codes Bb, Borrelia burgdorferi; Cp, Chlamydophila pneumoniae; Mt, Mycobacterium tuberculosis; Xf, Xylella fastidiosa. Red colouring indicates conservation within each group while green is used for three important catalytic residues of RecB – H956, D1067 and D1080 [18]. Elements of regular secondary structure are shown above (RecB) and below (RecC) the alignment, where spirals represent α-helices and arrows β-strands. The three key regions (numbered 1–3) involved in adaptation of the RecC nuclease-like domain to its new function, as discussed in the text (see also Fig 2), are boxed and labelled. Purple underlining indicates zones that can be simultaneously structurally aligned (rms deviation of 2.19Å for 71 Cα atoms).