Database of ligand-induced domain movements in enzymes

The domain movements in the non-redundant database of protein domain movements are those found by applying the DynDom program to pairs of crystallographic structures contained in Protein Data Bank files. For each pair of structures cross-checking ligands in their Protein Data Bank files with the KEGG-LIGAND database and using methods that search for ligands that contact the enzyme in one conformation but not the other, the non-redundant database of protein domain movements was refined down to a set of 203 enzymes where a domain movement is apparently triggered by the binding of a functional ligand. For these cases, ligand binding information, including hydrogen bonds and salt-bridges between the ligand and specific residues on the enzyme is presented in the context of dynamical information such as the regions that form the dynamic domains, the hinge bending residues, and the hinge axes.The presentation at a single website of data on interactions between a ligand and specific residues on the enzyme alongside data on the movement that these interactions induce, should lead to new insights into the mechanisms of these enzymes in particular, and help in trying to understand the general process of ligand-induced domain closure in enzymes. The website can be found at: http://www.cmp.uea.ac.uk/dyndom/enzymeList.do webciteEnzymes are flexible molecules that change conformation upon ligand binding [1,2]. However, there is considerable variation in extent of that conformational change. A database study has shown that movements in enzymes upon substrate binding are generally small [3]. However, another recent study has shown that the extent of movement may depend on the actual reaction mechanism [4]. It is the obvious complexity and variability of conformational change that enzymes exhibit upon ligand binding that makes their study so difficult. In order to help overcome this, we report here on a database specifically devoted to enzymes with a domain movement upon ligand bindi