coli together with protein-protein docking experiments using the docking algorithm BiGGER. The studies showed that the conserved residues are not evenly distributed but clustered around the proposed nickel binding residues Glu16 and His93 (HybD – E. coli)  and around the conserved “”HOXBOX”" region for all three cases. In HupW and HybD conserved surface areas could also be found
along alpha helix 1, beta sheet 2 and alpha helix 4 [16, 17] (Figure 7a-b). Figure 7 HybD (1CFZ.pdb) from E. coli PI3K inhibitor and the 3D-structure model of HoxW from Nostoc PCC 7120. Illustration showing the crystallised structure of HybD (1CFZ.pdb) from E. coli (top) and the 3D structure model of HoxW from Nostoc PCC 7120 (bottom). A. Ribbon diagram of HybD (E.coli) and HoxW (Nostoc PCC 7120). Colour guide; green: amino acids believed to be involved in binding to the nickel in the active site of the large subunit, orange: the differently conserved residues i.e. the “”HOXBOX”"
in HybD (DGG) and HoxW (HQL). Abbreviations; H: α-helix, S: βEpigenetics inhibitor -sheet. B. The position of conserved amino acid residues on the surface of a representative of hydrogenase specific proteases from group 1 (HybD-1CFZ.pdb) and 3d (HoxW-3D model). Colour guide; red: residues conserved AMN-107 supplier among all (100%) of the strains within a group, blue: residues found to be conserved or similar among 80% of the strains in each group. C. Protein-protein docking result of hydrogenase specific proteases to the large subunit of the [NiFe]-hydrogenase. HybC (large subunit) and HybD (protease) from E. coli. HoxH (large subunit) and HoxW (protease) from Nostoc PCC 7120. Colour guide;
orange: conserved residues, i.e. the “”HOXBOX”" region, blue: 4-Aminobutyrate aminotransferase identical and similar residues shared by 80% of the strains in group 1 and group 3d respectively. Light blue arrow indicates direction as seen in (B). Three of the structures (HybC, HoxH and HoxW) were modelled by using the online program SWISS-MODEL. D. Space filling structure of HybC (E. coli). Colour guide; green: active site with the four cysteins involved in the binding of nickel and iron, red: the C-terminal histidine (His552), orange: region on the large subunit which might be in contact with the HOXBOX. Protein docking experiments resulted in 11 hits for HybC-HybD (E. coli), 84 hits for HybB-HynC (Desulfovibrio vulgaris str. Miyazaki F) and 28 hits for HoxH-HoxW (Nostoc PCC 7120). The best hit for HybD in E. coli and HoxW in Nostoc PCC 7120 can be seen in Figure 7c, a target-probe complex whereby the HOXBOX of the protease is in a less favourable position for C-terminal cleavage. This means that the HOXBOX is either facing away from the C-terminal or that other residues are blocking making it difficult for physical contact to occur without major conformation changes.