Phosphorus Binding Sites in Proteins: Structural Preorganization and Coordination

Abstract

Phosphorus is a ubiquitous element of the cell, which is found throughout numerous key molecules related to cell structure, energy and information storage and transfer, and a diverse array of other cellular functions. In this work, we adopt an approach often used for characterizing metal binding and selectivity of metalloproteins in terms of interactions in a first shell (direct residue interactions with the metal) and a second shell (residue interactions with first shell residues) and use it to characterize binding of phosphorus compounds. Similar analyses of binding have previously been limited to individual structures that bind to phosphate groups; here, we investigate a total of 8307 structures obtained from the RCSB Protein Data Bank (PDB). An analysis of the binding site amino acid propensities reveals very characteristic first shell residue distributions, which are found to be influenced by the characteristics of the phosphorus compound and by the presence of cobound cations. The second shell, which supports the coordinating residues in the first shell, is found to consist mainly of protein backbone groups. Our results show how the second shell residue distribution is dictated mainly by the first shell of the binding site, especially by cobound cations and that the main function of the second shell is to stabilize the first shell residues.