Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

BACKGROUND: For many metalloproteins, sequence motifs characteristic of metal-binding sites have not been found or are so short that they would not be expected to be metal-specific. Striking examples of such metalloproteins are those containing Mg(2+), one of the most versatile metal cofactors in cellular biochemistry. Even when Mg(2+)-proteins share insufficient sequence homology to identify Mg(2+)-specific sequence motifs, they may still share similarity in the Mg(2+)-binding site structure. However, no structural motifs characteristic of Mg(2+)-binding sites have been reported. Thus, our aims are (i) to develop a general method for discovering structural patterns/motifs characteristic of ligand-binding sites, given the 3D protein structures, and (ii) to apply it to Mg(2+)-proteins sharing <30% sequence identity. Our motif discovery method employs structural alphabet encoding to convert 3D structures to the corresponding 1D structural letter sequences, where the Mg(2+)-structural motifs are identified as recurring structural patterns. RESULTS: The structural alphabet-based motif discovery method has revealed the structural preference of Mg(2+)-binding sites for certain local/secondary structures: compared to all residues in the Mg(2+)-proteins, both first and second-shell Mg(2+)-ligands prefer loops to helices. Even when the Mg(2+)-proteins share no significant sequence homology, some of them share a similar Mg(2+)-binding site structure: 4 Mg(2+)-structural motifs, comprising 21% of the binding sites, were found. In particular, one of the Mg(2+)-structural motifs found maps to a specific functional group, namely, hydrolases. Furthermore, 2 of the motifs were not found in non metalloproteins or in Ca(2+)-binding proteins. The structural motifs discovered thus capture some essential biochemical and/or evolutionary properties, and hence may be useful for discovering proteins where Mg(2+ )plays an important biological role. CONCLUSION: The structural motif discovery method presented herein is general and can be applied to any set of proteins with known 3D structures. This new method is timely considering the increasing number of structures for proteins with unknown function that are being solved from structural genomics incentives. For such proteins, which share no significant sequence homology to proteins of known function, the presence of a structural motif that maps to a specific protein function in the structure would suggest likely active/binding sites and a particular biological function.