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, and (17) O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged Fe(II) -Fe(III) diiron 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 Fe(II) -Fe(II) YtfE toward nitric oxide demonstrates that the prerequisite for N2 O 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 N2 O 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 N2 O transformation under low NO flux, which precedes nitrosative stress.

Structure, function and evolution of the hemerythrin‐like domain superfamily

“…These conserved positions, which represent a variation from the H‐HxxxE duplicate, contribute to the 5H/1E/1D ligation to iron (Table ) in hemerythrin from Themiste dyscritum, myohemerythrin fro m Themiste hennahi , bacteriohemerythrin from M. capsulatus , and the hemerythrin‐like domain of DcrH from D. vulgaris . These hemerythrin homologs are all involved in O 2 transport and storage through their ability to bind O 2 reversibly, and O 2 sensing in signal‐transduction proteins by autoxidation of the binuclear iron site upon O 2 binding . Sequences with an H‐HxxxE‐HxxxH‐HxxxxD motif are highly conserved as shown by the low number of divergent projections in the cluster map, which may indicate a recent divergence of this group (Fig.…”

“…Nitric oxide and reactive nitrogen species are deleterious products of denitrification and host immune system responses, particularly damaging to iron‐sulfur clusters and to DNA . The hemerythrin‐like domain of YtfE has been shown to catalyze the reduction of nitric oxide to nitrous oxide …”

“…However, the cation‐binding residues are not conserved in all solved hemerythrin structures (Table ). For instance, the catalytic site of hemerythrin in YtfE, a repair iron centers protein from Escherichia coli , has been shown to involve four instead of five histidine residues, and two carboxylate bridges from two glutamic residues instead of one glutamic and one aspartic acid residues. This arrangement results in a five‐coordinate/five‐coordinate binuclear Fe(II)‐binding site with nitric oxide‐reductase activity that is likely to be part of a defense mechanism against DNA damage associated with NO.…”

“…For instance, the catalytic site of hemerythrin in YtfE, a repair iron centers protein from Escherichia coli , has been shown to involve four instead of five histidine residues, and two carboxylate bridges from two glutamic residues instead of one glutamic and one aspartic acid residues. This arrangement results in a five‐coordinate/five‐coordinate binuclear Fe(II)‐binding site with nitric oxide‐reductase activity that is likely to be part of a defense mechanism against DNA damage associated with NO. A survey of the literature reveals that many other functionally characterized hemerythrin‐containing proteins have a cation‐binding motif that is different from the H‐HxxxE‐HxxxH‐HxxxxD motif of signal‐transduction and oxygen‐carrier hemerythrins.…”

EPR spectroscopy of complex biological iron–sulfur systems

“…Trace C is from similarly treated cells in which the gene yftE has been deleted. The protein YftE (recently proposed to be renamed as RIC for ‘repair of iron centers’ [45]) carries a dinuclear iron oxo cluster and has been implicated in repair of Fe–S clusters ([46] and refs quoted therein). The circa threefold higher amplitude of the [3Fe–4S] + signal in trace C versus B was interpreted as an indication that in the Δ yftE cells fumarase A was less well protected against oxidative damage by H 2 O 2 [44].…”