Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis

Abstract

Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

“… 32 , 33 The thiolates of the cysteine pair are orientated toward this channel and the di-iron site and are prone to oxidation, resulting in a disulfide bond. 26 , 32 A second channel, predominantly hydrophilic in nature, connects the di-iron center to the surrounding solvent. 26 , 32 …”

“… 26 , 32 A second channel, predominantly hydrophilic in nature, connects the di-iron center to the surrounding solvent. 26 , 32 …”

Repair of Iron Center Proteins—A Different Class of Hemerythrin-like Proteins

“…The currently available X-ray structures of RICs are of that the wild type and mutated E. coli YtfE (PDB 7BHA, 5FNN, 5FNP, 5FNY) [31,40]. All structures could only be obtained when harboring the double mutation C30AC31 for reasons that remain unclear.…”

“…The YtfE crystal structure contains two molecules in the asymmetric unit and all molecules show the two domains A and B, which correspond to the ScdA N-terminal domain and the hemerythrin-like domain, respectively. Different YtfE crystal structures were observed to fit in distinct space groups (P2 1 , I4 1 , and P2 1 2 1 2), indicating high variability in their inter-domain flexibility [31,40]. Domain A has a globular shape, is composed of 4 α-helices, and contains the conserved motif DfCCgG in the loop between helices 2 and 3.…”

“…E. coli YtfE (PDB 7BHA, 5FNN, 5FNP, 5FNY) [31,40]. All structures could only be obtain when harboring the double mutation C30AC31 for reasons that remain unclear.…”