Journal:JBIC:11

A Cryo-Crystallographic Time Course for Peroxide Reduction by Rubrerythrin from Pyrococcus furiosus

Bret Dillard, Jonathan Demick, Michael Adams and William Lanzilotta^[1]

Molecular Tour

Oxidative damage is a major problem for all organisms and not surprisingly a number of protection systems exist in cells across all kingdoms of life. For organisms that respire using anaerobic processes oxidative damage can be an even more pressing problem as these cells may be destroyed by the simple presence of molecular oxygen. It is not that surprising that strict anaerobes have developed a system for the rapid reduction and removal of molecular oxygen in two steps. The first involves reduction of oxygen to peroxide followed by peroxide reduction to water. The terminal enzyme in this systems, rubrerythrin, has been well characterized in a number of bacteria that live at ambient temperatures. In this work, we report the first time course that monitors peroxide reduction by a rubrerythrin isolated from an organism that lives at an optimal temperature of one-hundred degrees centigrade. The slow turnover of the enzyme at room temperature has allowed us to trap intermediates and track the atomic details of this important enzyme reaction.

Rubrerythrin peroxide binding site containing two iron atoms is formed by 2 adjacent monomers A (colored darkmagenta) and B (colored magenta). Rubrerythrin in the reduced, resting (all-ferrous) state has two water molecules near the diiron center (3pwf). Rubrerythrin in the fully oxidized all-ferric state (3mps), after 20 s exposure to peroxide, has μ-oxo bridge. Monomers of oxidized rubrerythrin A (colored skyblue) and B (colored cyan). This exposure causes significant conformational changes of residues within the peroxide binding site. Movement of E114 upon oxidation of the all-ferrous diiron center to the fully oxidized all-ferric state results in a significant distortion of an alpha-helix. The movement of backbone carbon atoms is over 1.7 A in some cases. 10-s exposure of rubrerythrin crystals to peroxide reveals small srtuctural changes (3pza). 15-s explosure also reveals small srtuctural changes (3qvd). Both these exposures identified previously unobserved intermediates in the reaction cycle.

Reaction scheme for rubrerythrins.

PDB reference: Peroxide Bound Oxidized Rubrerythrin from Pyrococcus furiosus, 3mps; High resolution structure of the fully reduced form of rubrerythrin from P. furiosus, 3pwf; Fully Reduced (All-ferrous) Pyrococcus rubrerythrin after a 10 second exposure to peroxide, 3pza; Exposure of rubrerythrin from Pyrococcus furiosus to peroxide, fifteen second time point, 3qvd.