The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR

Abstract

NikR is a nickel-responsive metalloregulator protein that controls the level of Ni²⁺ ions in living cells. Previous studies have shown that NikR can bind a series of first-row transition metal ions but binds to DNA with high affinity only as a Ni²⁺ complex. To understand this metal selectivity, S K-edge X-ray absorption spectroscopy of NikR bound to different metal ions was used to evaluate the different electronic structures. The experimental results are coupled with density functional theory calculations on relevant models. This study shows that both the Z_eff of the metal ion and the donor nature of the ligands determine the electronic structure of the metal site. This impacts the geometric structure of the metal site and thus the conformation of the protein. This contribution of electronic structure to geometric structure can be extended to other metal selective metalloregulators.

Figure 1.

Expansion of the NikR-DNA binding region based on PDB code 2HZV. The DNA, two α3 helices, and one Ni site with 4 ligands from 2 different subunits are shown. Another Ni site is faded in the back.

Figure 2,

S K-edge XAS of the metal varied NikR proteins, with the pre-edge region enlarged in insert.

Figure 3.

LUMO of the low-spin Ni-NikR active site, mainly showing the d_x²-_y² σ* interaction with the ligands.