Understanding Zinc’s Functional Role in Metalloproteins via Categorization of Zinc Coordination

Metal binding proteins or metalloproteins chelate a metal ion cofactor such as iron, zinc, or copper and play key roles in human cellular metabolism and signaling. In particular, upwards of 10% of human proteins are predicted to bind zinc. These various proteins use zinc in a variety of structural, catalytic, and signal transduction functions. Zinc also appears in all six classes of enzymes. Despite the importance of zinc binding proteins, the functional role of zinc in many of these proteins is still unknown. Clues as to the functional use of zinc in zinc binding proteins can be obtained through analysis of the worldwide Protein Data Bank (PDB) and other databases. The PDB is a rapidly growing database of 3-D structures of various biomacromolecules, with the vast majority being proteins. We have identified and analyzed 5965 proteins bound to zinc in the PDB. Our analysis classified the coordination geometry of each zinc site as either tetrahedral, trigonal bipyramidal, or octahedral. This analysis also classified sites based on the number of residues that contribute ligands to the site, by the specific residue combination that ligates the zinc, and their involvement in zinc clusters. The Enzyme Commission (EC) numbers, which describe the enzymatic activity of the protein or chain, are then obtained for each zinc site. By analyzing the prevalence of each EC number in each category, we observed the propensities of certain categories to exhibit specific types of enzymatic activity or the lack of enzymatic activity