Figure 3.

Alignment of nitrile hydratase (NHase) with nitrile hydratase leader peptide (NHLP) sequences. (A) Fourteen members of the NHase alpha subunit protein family (TIGR01323), identified by locus tags, are shown aligned to the leader sequences of 28 members of the NHLP family (TIGR03793). Along the top of the figure is a colour-coded region depicting the anticipated secondary structure for that region (red, alpha-helix; blue, loop; green, beta-sheet). Relative to NHase, the NHLP sequences exhibit a 63-residue deletion that carries the residues required for iron/cobalt ligation, the CxxCSC motif. Without the ability to bind the required catalytic metal, the truncation seen in NHLP is presumed to abolish NHase activity. Shown in the truncated region is the canonical metal coordination architecture, with two of the three Cys thiol ligands being oxidized to sulphenic and sulphinic acids. Also shown is the putative leader sequence cleavage site for NHLP, which is not conserved with full-length NHase. (B) Crystal structure of the NHase from Bacillus smithii, the most closely related NHase to the NHLP family with a known structure [38]. The N- and C-termini have been labelled, the metal centre is shown as a cyan sphere and the beta subunit has been omitted for clarity. The colour coding is by secondary structure as in panel A with the addition of the N- and C-terminal extensions (grey) that are not included in the alignment. The final residue of the NHase alignment, Arg, is shown in blue stick format. (C) Same as in panel B, but with the insertion-deletion region omitted in NHLP's shown in wheat. This figure was generated using a previously described, web-based program [36] and PyMOL.

Haft et al. BMC Biology 2010 8:70   doi:10.1186/1741-7007-8-70
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