Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes

In order to search for a common structural motif in the phosphate-binding s ites of protein-mononucleotide complexes, we investigated the structural va riety of phosphate-binding schemes by an all-against-all comparison of 491 binding sites found in the Protein Data Bank. We found four frequently occu rring structural moths composed of protein atoms interacting with phosphate groups, each of which appears in different protein superfamilies with diff erent folds. The most frequently occurring motif, which we call the structu ral P-loop, is shared by 13 superfamilies and is characterized by a four-re sidue fragment, GXXX, interacting with a phosphate group through the backbo ne atoms. Various sequence moths, including Walker's A moth or the P-loop, turn out to be a structural P-loop found in a few specific superfamilies, T he other three motifs are found in pairs of superfamilies: protein kinase a nd glutathione synthetase ATPase domain like, actin-like ATPase domain and nucleotidyltransferase, and FMN-linked oxidoreductase and PRTase.