Figure 1. Overview of the hbp regulatory system and tertiary structure modeling of the HbpR A-domain using a previously established XylR model as template.

(A) Organization of the hbp genes and the location of the HbpR binding sites (UAS, upstream activating sequences) in front of the P_C and P_D promoters. HbpR domains are depicted to scale according to the predictions by Jaspers et al [7]. (B) to (E) Fitting used swiss-model and was performed on XylR A-domain PDB coordinates as calculated by Devos et al [22]. (B) Ribbon model of HbpR A-domain residues 11–209, with predicted coils, alpha-helices and beta-sheets indicated. (C) Superposition of the predicted HbpR and XylR A-domains in the same configuration as A. (D) Tertiary structure model of HbpR A-domain with calculated molecular surface at 1.4Å and 40% transparency, in order to see the helical, coil and sheets. Model turned into a position which enables visualization of the proposed tunnel entry (b). C-terminal end of coil ending the A-domain indicated with an arrow at (a). Pinkish region in the centre of the A-domain illustrates a predicted cavity within the A-domain. (E), as C but now for the XylR A-domain, with exception of the ten most C-terminal residues, which otherwise are predicted to occlude the tunnel.