Iron Binding Site in a Global Regulator in Bacteria–Ferric Uptake Regulator (Fur) Protein: Structure, Mössbauer Properties, and Functional Implication

Abstract

Fur protein plays key roles in regulating numerous genes in bacteria and is essential for intracellular iron concentration regulation. However, atomic level pictures of the iron binding site and its functional mechanism remain to be established. Here we present results of the first quantum chemical investigation of various first- and second-shell models and experimental Mössbauer data of E. Coli Fur, including 1) the first robust evidence that site 2 is the Fe binding site with a 3His/2Glu ligand set, being the first case in non-heme proteins, with computed Mössbauer data in excellent accord with experiment; 2) the first discovery of a conservative hydrogen bonding interaction in the iron binding site based on X-ray and homology structures; 3) the first atomic level hypothesis of active site reorganization upon iron concentration increase, triggering the conformational change needed for its function. These results shall facilitate structural and functional studies of Fur family proteins.

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

“…Moreover, all of the residues involved in metal ion binding are conserved across Fur proteins from different species. In agreement with the previously reported Mössbauer data of E. coli Fur, site 1 is the Fe 2+ -binding site with a 3His/2Glu ligand set 36 . Another study 13 indicated that E. coli Fur has a similar affinity for Mn 2+ and Fe 2+ .…”

Single Glutamate to Aspartate Mutation Makes Ferric Uptake Regulator (Fur) as Sensitive to H2O2 as Peroxide Resistance Regulator (PerR)

“…The only reported structures have a Zn 2+ ion in place of the regulatory metal9–12 and with its d 10 electronic structure Zn 2+ is insensitive to ligand field and thus cannot reveal subtle changes in the coordination sphere of the regulatory metal. To understand this structural change at the molecular level we used a combination of Mössbauer spectroscopy and density functional theory (DFT) calculations, which have recently been used in concert to derive spectroscopically validated structural properties 13–16. To get insights into the coordination changes brought about by the Asp/Glu substitutions, we decided to study PerR and Fur variants possessing the three carboxylate combinations Asp/Asp, Asp/Glu, and Glu/Glu in the 85 and 104 positions (with Bs PerR numbering).…”

Silica-Induced Protein (Sip) in Thermophilic Bacterium Thermus thermophilus Responds to Low Iron Availability

“…HpFur, for example, has three metal-binding sites, referred to as S1, S2, and S3 (38). Nearly all of the residues involved in metal binding are conserved in the Fur-like proteins of Thermus (39,40).…”