Iron–Sulfur Cluster Repair ProteinYtfE

Abstract

YtfE, a repair of iron centers protein, plays roles in the response of the bacteria to oxidative and nitrosative stress. The 2.10 Å resolution crystal structure of the isolated Escherichia coli YtfE reveals two‐domain architecture with the L‐shape of a C‐terminal nonheme iron‐containing hemerythrin‐like (Hr‐like) domain linked to an N‐terminal ScdA_N domain via a highly flexible pentapeptide loop. The geometry of the diiron core of YtfE is symmetrical with two five‐coordinate irons. Each iron has a bridging oxygen atom, two bridging carboxylates derived from Glu33/Glu208, and two histidines; His84/His204 are bound to Fe(II) and His129/His160 are bound to Fe(III). Structural analysis of YtfE reveals that the diiron core is connected to the solvent regions by two roughly orthogonal tunnels. Both tunnels have small radii, ranging from 1.2 to 2.4 Å, indicating that the possible substrates (or products) for YtfE are small molecules or ions. The long hydrophobic tunnel can facilitate electron transfer to active site, and the hydrophilic tunnel gated by a negatively glutamate triad may trap proton entry or center iron ion to exit. The mixed‐valence Fe(II)–Fe(III) core of the isolated YtfE bridged by μ‐oxo was characterized by UV–vis, electron paramagnetic resonance (EPR)/electron spin echo envelope modulation (ESEEM) experiments, magnetic circular dichroism (MCD), Mössbauer spectroscopy, resonance Raman, and extended X‐ray absorption fine structure (EXAFS) spectroscopy. In spite of the isolated YtfE exhibiting the Fe(II)–Fe(III) state, the whole‐cell EPR spectrum shows that the YtfE protein exists in the reduced Fe(II)–Fe(II) state under normal cellular conditions. With regard to the repair function, YtfE may act as a ferrous‐ion donor, interacting with IscS or SufS to reassemble the Fe–S cluster of iron–sulfur proteins damaged by oxidative or nitrosative stress. Also, the Fe(II)–Fe(II) core of YtfE serves as an NO‐trapping scavenger to convert NO to N 2 O under the participation of electrons and protons.

Bioinorganic Chemistry of the Natural [Fe(NO)2] Motif: Evolution of a Functional Model for NO-Related Biomedical Application and Revolutionary Development of a Translational Model

“…Moreover, subsequent two-electron reduction of the [{Fe­(NO) 7 -{Fe­(NO) 7 ] YtfE, instead of the [{Fe­(NO) 7 -Fe III ] state, leads to the formation of N 2 O along with the recovery of the [Fe II –Fe II ] state and lends support to the “super-reduced” pathway in NO reductase. This crystallographic and single-turnover reactivity study of YtfE toward NO-to-N 2 O conversion discloses the cooperative effect of the carboxylate-bridged diiron center for the buildup of the proposed “super-reduced” [{Fe­(NO) 8 -{Fe­(NO) 8 ] intermediate to promote NO-to-N 2 O conversion. , …”

“…Regarding the proposed formation of [Fe III -{Fe­(NO) 2 } 9 ] and [Fe III Fe III (hyponitrite)] intermediates, in addition to the proposed intermediates diferrous dinitrosyl [{Fe­(NO)} 7 ] 2 and the super-reduced [{Fe­(NO)} 8 ] 2 species, during the catalytic reaction, NO reduction reactivity was attempted in the synthetic and biomimetic study of {Fe­(NO) 2 } 9 and {Fe­(NO) 2 } 10 DNICs. − The strong antiferromagnetic coupling between the high-spin Fe center and NO ligands forcing parallel spins in the NO ligands within the [Fe­(NO) 2 ] core, however, excluded its reactivity toward N–N bond formation and hyponitrite formation to afford N 2 O . Despite the absence of NO-to-N 2 O reactivity in the [Fe­(NO) 2 ] motif, the research experiences and spectroscopic tools developed during the bioinorganic journey in DNICs inspires our endeavor to seek and unveil control of NO reduction through collaboration on the reactivity and crystallographic investigation of YtfE protein belonging to the RIC family. , …”

“…Crystallographic study of YtfE in a 2.10-Å resolution reveals that the cofactor-free N-terminal ScdA_N domain and the C-terminal nonheme diiron hemerythrin-like (Hr-l) domain are linked through a highly flexible pentapeptide in an L shape. , Four α-helices in a tight and globular bundle are assembled by the N-terminal 61 amino acids in the ScdA_N domain, whereas a nonheme diiron center embedded in the four-helix-bundle Hr-l domain is anchored near the ScdA_N domain. Regarding the proposed function of YtfE to donate Fe for the assembly of [Fe-S] clusters and to achieve NO-to-N 2 O conversion as a NO-trapping scavenger, one hydrophobic channel and one hydrophilic channel with 1.2–2.4-Å-wide radii are discovered in YtfE for connection between the diiron core and the solvent bulk and for the trafficking of small molecules (i.e., NO, N 2 O, H 2 O, H + , and Fe 2+ ).…”

Nitrosylation of the Diiron Core Mediated by the N Domain of YtfE

“…The Escherichia coli YtfE protein is involved in the repair of damaged iron–sulfur clusters. , Expression of the YtfE protein is highly induced during anaerobic growth under conditions of nitrosative stress . A recent crystal structure of YtfE (Figure A) revealed its two-domain architecture featured by an N-terminal ScdA_N domain (NTD) linked to a C-terminal nonheme diiron-containing hemerythrin-like domain (CTD) via a highly flexible pentapeptide loop (residues 61–65; see also Figure S1).…”

“…The resulting coordination geometry is a distorted octahedron with vacancies on each iron in positions trans to the bridging oxygen. YtfE acts as a nitric oxide (NO) reductase that catalyzes the reduction of NO to nitrous oxide (N 2 O) at the diiron core in the CTD, protecting [Fe–S] clusters from nitrosylation under conditions of low NO flux . Having no characterized function, the NTD is annotated as a “domain of unknown function” (DUF542).…”