Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution

Abstract

High-potential iron-sulfur protein (HiPIP) is a soluble electron carrier protein of photosynthetic bacteria with an Fe4S4 cluster. Although structural changes accompanying the electron transfer are important for understanding of the functional mechanism, the changes have not been clarified in sufficient detail. We previously reported the high-resolution crystal structures of HiPIP from a thermophilic purple bacterium Thermochromatium tepidum in the reduced state. In order to perform a detailed comparison between the structures in different redox states, the oxidized structure should also be revealed at high resolution. Therefore, in the present study we performed a crystallographic analysis of oxidized HiPIP and a structural comparison with the reduced form at a high resolution of 0.8 Å. The comparison highlighted small but significant contraction in the iron-sulfur cluster. The changes in Fe-S bond lengths were similar to that predicted by theoretical calculation, although some discrepancies were also found. Almost distances between the sulfur atoms of the iron-sulfur cluster and the protein environment are elongated upon the oxidation. Positional changes of hydrogen atoms in the protein environment, such as on the amide-hydrogen of Cys75 in the proximity of the iron-sulfur cluster, were also observed in the accurate analyses. None of the water molecules exhibited significant changes in position or anisotropy of atomic displacement parameter between the two states, while the orientations of some water molecules were different.

Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis

“…In the oxidized state, the distances between the sulfur atoms and hydrogen bond donors are slightly longer. This elongation indicates that all sulfur atoms undergo a change in electronic state caused by oxidation and follows the same trend as in our previous study of the x-ray structures at 0.8-Å resolution ( 32 ). In the redox protein, the hydrogen atoms that are coordinated to sulfur atoms play a major role in redox potential ( 26 , 41 , 42 ).…”

“…In HiPIP, subcluster 1 is largely responsible for electron storage (28). We have previously reported the x-ray crystal structures of reduced (~0.48-Å resolution) and oxidized (~0.80-Å resolution) HiPIP from a thermophilic purple bacterium, Thermochromatium tepidum (28)(29)(30)(31)(32)(33). The ultrahigh-resolution x-ray structure at 0.48-Å resolution in the reduced state revealed large distortions of the peptide bonds around the iron-sulfur cluster (28).…”

Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase

“…This effect can either arise if the cofactors in the NADH bound enzyme move or if they show a different scattering behaviour due to charge. High-resolution crystallographic characterisation of the high-potential iron-sulfur protein in different redox states, indicate a small (up to 0.03 Å) contraction of the oxidised [4Fe-4S] cluster 42 with regard to the reduced cluster. These movements are too small to be visualised in our 3D reconstructions and would also not explain the observed densities around molybdenum, phosphates or FMN.…”

The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins

“…Another crystallographic study demonstrated that a high-potential iron-sulfur protein (HiPIP) undergoes only minor structural changes upon toggling the redox state of the [4Fe4S] cluster between 2+ and 3+. 51 Therefore, we assumed the coordinates of the atoms in the EndoIII protein structure are the same for both the [4Fe4S] 3+ and [4Fe4S] 2+ cases. The binding energy resulting from electrostatic interactions between the positively charged [4Fe4S] cluster and the negatively-charged phosphate groups on the DNA backbone are calculated to be ca.…”