Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

Abstract

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.

High Potency Zinc Modulation of Human P2X2 Receptors and Low Potency Zinc Modulation of Rat P2X2 Receptors Share a Common Molecular Mechanism

“…Of the highest likelihood candidates for binding zinc within the middle vestibule, mutation of Glu-326 and His-330 had only minor effects on zinc potency but the substantial effects of mutation of Glu-75 make it an appealing candidate for participation in zinc binding. If so, additional residues would be needed, and the most likely untested candidates are serines, which although extremely rare in nanomolar affinity structural zinc-binding sites (Ͻ0.1%) contribute to zinc binding in about 4% of the lower affinity catalytic zinc sites (23). Candidates are Ser-76, Ser-77, and Ser-106, all of which are close to Glu-75 in our homology model.…”

The Physiological, Biochemical, and Molecular Roles of Zinc Transporters in Zinc Homeostasis and Metabolism

“…The "zinc finger" motif was first found in the transcription factor TFIIIA of Xenopus (284). Zinc fingers are now grouped into more than 20 classes of structurally distinct modules and are known to be a functional motif that interacts with a variety of proteins, lipids, and nucleic acids (6,26,119,222,227) (TABLE 1), clearly indicating the importance of zinc in cellular biochemistry. In catalytic functions, zinc can activate substrates in enzymes by stabilizing negative charges, because of its strong Lewis acid property (264).…”

Structure and mechanism of Zn2+-transporting P-type ATPases

“…However, the Lys693 side-chain would be an unexpected ligand for Zn 2+ (Refs 16,17) and indeed Zn 2+ -binding is unaffected by the Lys693Ala mutation (Fig. 2b), suggesting that binding is rather established by the two cysteine thiolates and two oxygen ligands, possibly from Asp714 in a bidentate fashion; a recurrent coordination motif of Zn 2+ -binding sites 16,17 . Congruent with this role, the relative activity of the Asp714Glu mutant decreases with the increasing ionic radii and coordination distances of Zn 2+ , Cd 2+ and Pb 2+ (Fig.…”