Activation of zinc uptake regulator by zinc binding to three regulatory sites

• Published in: Nucleic acids research 2024-05, Vol.52 (8), p.4185-4197
• Main Authors: Choi, Yunchan, Koh, Junseock, Cha, Sun-Shin, Roe, Jung-Hye
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Gene Expression Regulation, Bacterial; Gene regulation, Chromatin and Epigenetics; Histidine - chemistry; Histidine - metabolism; Protein Binding; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism; Streptomyces coelicolor - genetics; Streptomyces coelicolor - metabolism; Zinc - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkae079

Zur is a Fur-family metalloregulator that is widely used to control zinc homeostasis in bacteria. In Streptomyces coelicolor, Zur (ScZur) acts as both a repressor for zinc uptake (znuA) gene and an activator for zinc exporter (zitB) gene. Previous structural studies revealed three zinc ions specifically bound per ScZur monomer; a structural one to allow dimeric architecture and two regulatory ones for DNA-binding activity. In this study, we present evidence that Zur contains a fourth specific zinc-binding site with a key histidine residue (H36), widely conserved among actinobacteria, for regulatory function. Biochemical, genetic, and calorimetric data revealed that H36 is critical for hexameric binding of Zur to the zitB zurbox and further binding to its upstream region required for full activation. A comprehensive thermodynamic model demonstrated that the DNA-binding affinity of Zur to both znuA and zitB zurboxes is remarkably enhanced upon saturation of all three regulatory zinc sites. The model also predicts that the strong coupling between zinc binding and DNA binding equilibria of Zur drives a biphasic activation of the zitB gene in response to a wide concentration change of zinc. Similar mechanisms may be pertinent to other metalloproteins, expanding their response spectrum through binding multiple regulatory metals.