OhrR: Difference between revisions

The Consurf Server was used to predict which regions of OhrR ''Xc'' are most  high conserved. Briefly, this freely-available tool performed a multiple sequence alignment of the input sequence and based on this alignment assigned residues a conservation score of 1 to 10. The structure of reduced OhrR (colored based on the output of this server) is available to the left with residues colored similar to output script files from ConSurf. Red spheres indicates the most highly conserved residues (10). Bright pink spheres indicate highly conserved residues (9). Light pink spheres indicate residues that are highly conserved but are more likely to substitution than those colored in bright pink.

The most conserved region of OhrR ''Xc'' is the helix-turn-helix region. This is not surprising in that this is a transcription factor and if it is unable to bind DNA, then this function has been severely inhibited. What  was surprising, however, is that the reactive cysteine (C22) of the protein and the residues it interacted with (C127) were not highly conserved. The conservation score for C22 was 7 (out of 9) and the C127 was 2 out of 9. Such a low rating for 1 of the 2 available cysteines in the entire protein suggests that disulfide bond formation may not be a conserved mechanism in the homologues included in this query. The regions of the protein that are in contact in the dimer are also conserved, with conservation scores most often between 6 and 7 (out of 10). This is logical in that this interaction interface must be conserved to allow these regions of the protein to facilitate dimerization. The least conserved portions of the protein are those that do not interact with either the DNA opposite unit of the dimer. This is logical in that these regions do not need to conserve a very strict chemistry of geometry in order to serve as a “linker” between the two DNA binding and interaction domain of a individual chain.