A 2.8 Å Fe-Fe separation in the Fe2(III/IV) intermediate, X, from Escherichia coli ribonucleotide reductase

• Published in: Journal of the American Chemical Society Vol. 135; no. 45; pp. 16758 - 16761
• Main Authors: Dassama, Laura M K, Silakov, Alexey, Krest, Courtney M, Calixto, Julio C, Krebs, Carsten, Bollinger, Jr, J Martin, Green, Michael T
• Format: Journal Article
• Language: English
• Published: United States 13.11.2013
• Subjects: Crystallography, X-Ray; Escherichia coli - chemistry; Escherichia coli - enzymology; Iron - chemistry; Iron - metabolism; Models, Molecular; Oxidation-Reduction; Ribonucleotide Reductases - chemistry; Ribonucleotide Reductases - metabolism; Spectroscopy, Mossbauer; Tyrosine - analogs & derivatives; Tyrosine - metabolism
• ISSN: 1520-5126
• DOI: 10.1021/ja407438p

A class Ia ribonucleotide reductase (RNR) employs a μ-oxo-Fe2(III/III)/tyrosyl radical cofactor in its β subunit to oxidize a cysteine residue ~35 Å away in its α subunit; the resultant cysteine radical initiates substrate reduction. During self-assembly of the Escherichia coli RNR-β cofactor, reaction of the protein's Fe2(II/II) complex with O2 results in accumulation of an Fe2(III/IV) cluster, termed X, which oxidizes the adjacent tyrosine (Y122) to the radical (Y122(•)) as the cluster is converted to the μ-oxo-Fe2(III/III) product. As the first high-valent non-heme-iron enzyme complex to be identified and the key activating intermediate of class Ia RNRs, X has been the focus of intensive efforts to determine its structure. Initial characterization by extended X-ray absorption fine structure (EXAFS) spectroscopy yielded a Fe-Fe separation (d(Fe-Fe)) of 2.5 Å, which was interpreted to imply the presence of three single-atom bridges (O(2-), HO(-), and/or μ-1,1-carboxylates). This short distance has been irreconcilable with computational and synthetic models, which all have d(Fe-Fe) ≥ 2.7 Å. To resolve this conundrum, we revisited the EXAFS characterization of X. Assuming that samples containing increased concentrations of the intermediate would yield EXAFS data of improved quality, we applied our recently developed method of generating O2 in situ from chlorite using the enzyme chlorite dismutase to prepare X at ~2.0 mM, more than 2.5 times the concentration realized in the previous EXAFS study. The measured d(Fe-Fe) = 2.78 Å is fully consistent with computational models containing a (μ-oxo)2-Fe2(III/IV) core. Correction of the d(Fe-Fe) brings the experimental data and computational models into full conformity and informs analysis of the mechanism by which X generates Y122(•).