Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO

Abstract

Molecular mechanisms underlying the repair of nitrosylated [Fe–S] clusters by the microbial protein YtfE remain poorly understood. The X-ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and17O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged FeII–FeIIIdiiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo-bridge. Structural analysis reveals that there are two solvent-accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced-form FeII–FeIIYtfE toward nitric oxide demonstrates that the prerequisite for N2O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO-trapping scavenger to promote the NO to N2O transformation under low NO flux, which precedes nitrosative stress.