First Spectroscopic Characterization of FeII-Fur, the Physiological Active Form of the Fur Protein

Iron Insertion at the Assembly Site of the ISCU Scaffold Protein Is a Conserved Process Initiating Fe-S Cluster Biosynthesis

Iron-sulfur (Fe-S) clusters are prosthetic groups of proteins biosynthesized on scaffold proteins by highly conserved multi-protein machineries. Biosynthesis of Fe-S clusters into the ISCU scaffold protein is initiated by ferrous iron insertion, followed by sulfur acquisition, via a still elusive mechanism. Notably, whether iron initially binds to the ISCU cysteine-rich assembly site or to a cysteine-less auxiliary site via N/O ligands remains unclear. We show here by SEC, circular dichroism (CD), and Mössbauer spectroscopies that iron binds to the assembly site of the monomeric form of prokaryotic and eukaryotic ISCU proteins via either one or two cysteines, referred to the 1-Cys and 2-Cys forms, respectively. The latter predominated at pH 8.0 and correlated with the Fe-S cluster assembly activity, whereas the former increased at a more acidic pH, together with free iron, suggesting that it constitutes an intermediate of the iron insertion process. Iron not binding to the assembly site was non-specifically bound to the aggregated ISCU, ruling out the existence of a structurally defined auxiliary site in ISCU. Characterization of the 2-Cys form by site-directed mutagenesis, CD, NMR, X-ray absorption, Mössbauer, and electron paramagnetic resonance spectroscopies showed that the iron center is coordinated by four strictly conserved amino acids of the assembly site, Cys35, Asp37, Cys61, and His103, in a tetrahedral geometry. The sulfur receptor Cys104 was at a very close distance and apparently bound to the iron center when His103 was missing, which may enable iron-dependent sulfur acquisition. Altogether, these data provide the structural basis to elucidate the Fe-S cluster assembly process and establish that the initiation of Fe-S cluster biosynthesis by insertion of a ferrous iron in the assembly site of ISCU is a conserved mechanism.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Ferric uptake regulator (Fur) reversibly binds a [2Fe-2S] cluster to sense intracellular iron homeostasis in Escherichia coli

The ferric uptake regulator (Fur) is a global transcription factor that regulates intracellular iron homeostasis in bacteria. The current hypothesis states that when the intracellular "free" iron concentration is elevated, Fur binds ferrous iron, and the iron-bound Fur represses the genes encoding for iron uptake systems and stimulates the genes encoding for iron storage proteins. However, the "iron-bound" Fur has never been isolated from any bacteria. Here we report that the Escherichia coli Fur has a bright red color when expressed in E. coli mutant cells containing an elevated intracellular free iron content because of deletion of the iron-sulfur cluster assembly proteins IscA and SufA. The acid-labile iron and sulfide content analyses in conjunction with the EPR and Mössbauer spectroscopy measurements and the site-directed mutagenesis studies show that the red Fur protein binds a [2Fe-2S] cluster via conserved cysteine residues. The occupancy of the [2Fe-2S] cluster in Fur protein is ∼31% in the E. coli iscA/sufA mutant cells and is decreased to ∼4% in WT E. coli cells. Depletion of the intracellular free iron content using the membrane-permeable iron chelator 2,2´-dipyridyl effectively removes the [2Fe-2S] cluster from Fur in E. coli cells, suggesting that Fur senses the intracellular free iron content via reversible binding of a [2Fe-2S] cluster. The binding of the [2Fe-2S] cluster in Fur appears to be highly conserved, because the Fur homolog from Hemophilus influenzae expressed in E. coli cells also reversibly binds a [2Fe-2S] cluster to sense intracellular iron homeostasis.

Redox Sensing by Fe2+ in Bacterial Fur Family Metalloregulators

SIGNIFICANCE

Iron is required for growth and is often redox active under cytosolic conditions. As a result of its facile redox chemistry, iron homeostasis is intricately involved with oxidative stress. Bacterial adaptation to iron limitation and oxidative stress often involves ferric uptake regulator (Fur) proteins: a diverse set of divalent cation-dependent, DNA-binding proteins that vary widely in both metal selectivity and sensitivity to metal-catalyzed oxidation. Recent Advances: Bacteria contain two Fur family metalloregulators that use ferrous iron (Fe²⁺) as their cofactor, Fur and PerR. Fur functions to regulate iron homeostasis in response to changes in intracellular levels of Fe²⁺. PerR also binds Fe²⁺, which enables metal-catalyzed protein oxidation as a mechanism for sensing hydrogen peroxide (H₂O₂).

CRITICAL ISSUES

To effectively regulate iron homeostasis, Fur has an Fe²⁺ affinity tuned to monitor the labile iron pool of the cell and may be under selective pressure to minimize iron oxidation, which would otherwise lead to an inappropriate increase in iron uptake under oxidative stress conditions. Conversely, Fe²⁺ is bound more tightly to PerR but exhibits high H₂O₂ reactivity, which enables a rapid induction of peroxide stress genes.

FUTURE DIRECTIONS

The features that determine the disparate reactivity of these proteins with oxidants are still poorly understood. A controlled, comparative analysis of the affinities of Fur/PerR proteins for their metal cofactors and their rate of reactivity with H₂O₂, combined with structure/function analyses, will be needed to define the molecular mechanisms that have facilitated this divergence of function between these two paralogous regulators.

Iron Binding Site in a Global Regulator in Bacteria - Ferric Uptake Regulator (Fur) Protein: Structure, Mössbauer Properties, and Functional Implication

Fur protein plays key roles in regulating numerous genes in bacteria and is essential for intracellular iron concentration regulation. However, atomic level pictures of the iron binding site and its functional mechanism remain to be established. Here we present results of the first quantum chemical investigation of various first- and second-shell models and experimental Mössbauer data of E. Coli Fur, including 1) the first robust evidence that site 2 is the Fe binding site with a 3His/2Glu ligand set, being the first case in non-heme proteins, with computed Mössbauer data in excellent accord with experiment; 2) the first discovery of a conservative hydrogen bonding interaction in the iron binding site based on X-ray and homology structures; 3) the first atomic level hypothesis of active site reorganization upon iron concentration increase, triggering the conformational change needed for its function. These results shall facilitate structural and functional studies of Fur family proteins.

Non-heme iron sensors of reactive oxygen and nitrogen species

SIGNIFICANCE

In bacteria, transcriptional responses to reactive oxygen and nitrogen species (ROS and RNS, respectively) are typically coordinated by regulatory proteins that employ metal centers or reactive thiols to detect the presence of those species. This review is focused on the structure, function and mechanism of three regulatory proteins (Fur, PerR, and NorR) that contain non-heme iron and regulate the transcription of target genes in response to ROS and/or RNS. The targets for regulation include genes encoding detoxification activities, and genes encoding proteins involved in the repair of the damage caused by ROS and RNS.

RECENT ADVANCES

Three-dimensional structures of several Fur proteins and of PerR are revealing important details of the metal binding sites of these proteins, showing a surprising degree of structural diversity in the Fur family.

CRITICAL ISSUES

Discussion of the interaction of Fur with ROS and RNS will illustrate the difficulty that sometimes exists in distinguishing between true physiological responses and adventitious reactions of a regulatory protein with a reactive ligand.

FUTURE DIRECTIONS

Consideration of these three sensor proteins illuminates some of the key questions that remain unanswered, for example, the nature of the biochemical determinants that dictate the sensitivity and specificity of the interaction of the sensor proteins with their cognate signals.

Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding

In Bacillus subtilis, the transcription factor PerR is an iron dependant sensor of H(2)O(2). The sensing mechanism relies on a selective metal catalysed oxidation of two histidine residues of the regulatory site. Here we present the first crystal structure of the active PerR protein in complex with a Mn(2+) ion. In addition, X-ray absorption spectroscopy experiments were performed to characterize the corresponding iron form of the protein. Both studies reveal a penta-coordinate arrangement of the regulatory site that involves three histidines and two aspartates. One of the histidine ligand belongs to the N-terminal domain. Binding of this residue to the regulatory metal allows the protein to adopt a caliper-like conformation suited to DNA binding. Since this histidine is conserved in all PerR and a vast majority of Fur proteins, it is likely that the allosteric switch induced by the regulatory metal is general for this family of metalloregulators.

A comparative analysis of perturbations caused by a gene knock-out, a dominant negative allele, and a set of peptide aptamers

The study of protein function mostly relies on perturbing regulatory networks by acting upon protein expression levels or using transdominant negative agents. Here we used the Escherichia coli global transcription regulator Fur (ferric uptake regulator) as a case study to compare the perturbations exerted by a gene knock-out, the expression of a dominant negative allele of a gene, and the expression of peptide aptamers that bind a gene product. These three perturbations caused phenotypes that differed quantitatively and qualitatively from one another. The Fur peptide aptamers inhibited the activity of their target to various extents and reduced the virulence of a pathogenic E. coli strain in Drosophila. A genome-wide transcriptome analysis revealed that the "penetrance" of a peptide aptamer was comparable to that of a dominant negative allele but lower than the penetrance of the gene knock-out. Our work shows that comparative analysis of phenotypic and transcriptome responses to different types of perturbation can help decipher complex regulatory networks that control various biological processes.

Reversible Redox- and Zinc-Dependent Dimerization of theEscherichia coliFur Protein

Fur is a bacterial regulator using iron as a cofactor to bind to specific DNA sequences. This protein exists in solution as several oligomeric states, of which the dimer is generally assumed to be the biologically relevant one. We describe the equilibria that exist between dimeric Escherichia coli Fur and higher oligomers. The dissociation constant for the dimer-tetramer equilibrium is estimated to be in the millimolar range. Oligomerization is enhanced at low ionic strength and pH. The as-isolated monomeric form of Fur is not in equilibrium with the dimer and contains two disulfide bridges (C92-C95 and C132-C137). Binding of the monomer to DNA is metal-dependent and sequence specific with an apparent affinity 5.5 times lower than that of the dimer. Size exclusion chromatography, EDC cross-linking, and CD spectroscopy show that reconstitution of the dimer from the monomer requires reduction of the disulfide bridges and coordination of Zn2+. Reduction of the disulfide bridges or Zn2+ alone does not promote dimerization. EDC and DMA cross-links reveal that the N-terminal NH2 group of one subunit is in an ionic interaction with acidic residues of the C-terminal tail and close to Lys76 and Lys97 of the other. Furthermore, the yields of cross-link drastically decrease upon binding of metal in the activation site, suggesting that the N-terminus is involved in the conformational change. Conversely, oxidizing reagents, H2O2 or diamide, disrupt the dimeric structure leading to monomer formation. These results establish that coordination of the zinc ion and the redox state of the cysteines are essential for holding E. coli Fur in a dimeric state.

Iron(II) triggered conformational changes in Escherichia coli fur upon DNA binding: a study using molecular modeling

In order to identify the Fur dimerization domain, a three-dimensional structure of the ferric uptake regulation protein from Escherichia coli (Fur EC) was determined using homology modeling and energy minimization. The Fur monomer consists of turn- helix -turn motif on the N-terminal domain, followed by another helix-turn-helix-turn motif, and two beta-strands separated by a turn which forms the wing. The C-terminal domain, separated by a long coil from the N-terminal, and consisting of two anti parallel beta strands, and a turn-helix-turn-helix-turn motif. Residues in central domain were found to aid the dimer formation, residues 45-70 as evident in the calculated distances; this region is rich in hydrophobic residues. Most interactions occur between residues Val55, Leu53, Gln52, Glu49 and Tyr56 with closest contacts occurring at residues 49-56. These residues are part of an alpha-helix (alpha(4)) near the N-terminal. Upon raising the Fe(2+) concentration the binding of Fur dimer to DNA was enhanced, this was evident when, the Fur EC dimer was docked onto DNA "iron box" (it was found to bind the AT-rich region) and upon addition of Fe(2+) the helices near the N-terminal bound to the major groove of the DNA. Addition of high Fe(2+) concentration triggered further conformational changes in the Fur dimer as was measured by distances between the two subunits, Fe(2+) mediated the Fur binding to DNA by attaching itself to the DNA. At the same time DNA changed conformation as was evident in the distortion in the backbone and the shrinking of major groove distance from 11.4 to 9.3A. Two major Fe(2+) sites were observed on the C-terminal domain: site 1, the traditional Zn site, the cavity contains the residues Cys92, Cys95, Asp137, Asp141, Arg139, Glu 140, His 145 and His 143 at distances range from 1.3 to 2.2A. Site 2 enclave consists of His71, Ile50, Asn72, Gly97, Asp105 and Ala109 at very close proximity to Fe(2+). The closest contacts between Fur dimer and DNA at the AT-rich region were at residues Ala11, Gly12, Leu13, Pro18 and Arg19 mostly hydrophobic residues near the N-terminal domain. Close contacts repeated at His87, His88 and Arg112, and a third region near the C-terminal at Asn137, Arg 139, Glu140, Asn141, His143, Asn141 and His145. Fur dimer has three major contact regions with DNA, the first on the N-terminal domain, a second smaller region at His87, His88 and Arg112 mediated by Fe(2+) ions, and a third region on the C-terminal domain consisting mainly of hydrophobic contacts and mediated by Fe(2+) ions at high concentration.

Structural Changes of Escherichia coli Ferric Uptake Regulator during Metal-dependent Dimerization and Activation Explored by NMR and X-ray Crystallography

Ferric uptake regulator (Fur) is a global bacterial regulator that uses iron as a cofactor to bind to specific DNA sequences. Escherichia coli Fur is usually isolated as a homodimer with two metal sites per subunit. Metal binding to the iron site induces protein activation; however the exact role of the structural zinc site is still unknown. Structural studies of three different forms of the Escherichia coli Fur protein (nonactivated dimer, monomer, and truncated Fur-(1-82)) were performed. Dimerization of the oxidized monomer was followed by NMR in the presence of a reductant (dithiothreitol) and Zn(II). Reduction of the disulfide bridges causes only local structure variations, whereas zinc addition to reduced Fur induces protein dimerization. This demonstrates for the first time the essential role of zinc in the stabilization of the quaternary structure. The secondary structures of the mono- and dimeric forms are almost conserved in the N-terminal DNA-binding domain, except for the first helix, which is not present in the nonactivated dimer. In contrast, the C-terminal dimerization domain is well structured in the dimer but appears flexible in the monomer. This is also confirmed by heteronuclear Overhauser effect data. The crystal structure at 1.8A resolution of a truncated protein (Fur-(1-82)) is described and found to be identical to the N-terminal domain in the monomeric and in the metal-activated state. Altogether, these data allow us to propose an activation mechanism for E. coli Fur involving the folding/unfolding of the N-terminal helix.

Spectroscopic description of the two nitrosyl-iron complexes responsible for fur inhibition by nitric oxide

Ferric uptake regulation protein (Fur) is a global regulator, ubiquitous in Gram negative bacteria, that acts as a transcriptional repressor when it binds ferrous ion. Fur is involved in responses to several types of stress related to iron metabolism, such as stress induced by nitric oxide (NO) generated by macrophages against bacterial invasion. NO was recently shown to react with Fe(2+) ions in FeFur (iron substituted Fur protein) leading to an Fur bound iron-nitrosyl complex, unable to bind DNA, and characterized by a g = 2.03 EPR signal, associated with an S = (1)/(2) ground state. This electronic configuration could arise from either a mononitrosyl-iron [Fe(NO)](7) or a dinitrosyl-iron [Fe(NO)(2)](9) complex. The use of several spectroscopic tools such as EPR, ENDOR, FTIR, Mössbauer, and UV-visible spectroscopies as well as mass spectrometry analysis was necessary to characterize the iron-nitrosyl species in Fur. Furthermore, changes of C132 and C137 into glycines by site directed mutagenesis reveal that neither of the two cysteines is required for the formation of the g = 2.03 signal. Altogether, we found that two species are responsible for Fur inhibition in NO stress conditions: the major species, S(1/2), is an [Fe(NO)(2)](9) (S = (1)/(2)) complex without bound thiolate and the minor species is probably a diamagnetic [Fe(NO)(2)](8) (S = 0) complex. This is the first characterization of these physiologically relevant species potentially linking iron metabolism and the response to NO toxicity in bacteria.

Binuclear manganese compounds of potential biological significance. Part 2. Mechanistic study of hydrogen peroxide disproportionation by dimanganese complexes: the two oxygen atoms of the peroxide end up in a dioxo intermediate

The dimanganese(II,II) complexes 1a [Mn(2)(L)(OAc)(2)(CH(3)OH)](ClO(4)) and 1b [Mn(2)(L)(OBz)(2)(H(2)O)](ClO(4)), where HL is the unsymmetrical phenol ligand 2-(bis-(2-pyridylmethyl)aminomethyl)-6-((2-pyridylmethyl)(benzyl)aminomethyl)-4-methylphenol, react with hydrogen peroxide in acetonitrile solution. The disproportionation reaction was monitored by electrospray ionization mass spectrometry (ESI-MS) and EPR and UV-visible spectroscopies. Extensive EPR studies have shown that a species (2) exhibiting a 16-line spectrum at g approximately 2 persists during catalysis. ESI-MS experiments conducted similarly during catalysis associate 2a with a peak at 729 (791 for 2b) corresponding to the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) ([Mn(III)Mn(IV)(L)(O)(2)(OBz)](+) for 2b). At the end of the reaction, it is partly replaced by a species (3) possessing a broad unfeatured signal at g approximately 2. ESI-MS associates 3a with a peak at 713 (775 for 3b) corresponding to the formula [Mn(II)Mn(III)(L)(O)(OAc)](+) ([Mn(II)Mn(III)(L)(O)(OBz)](+) for 3b). In the presence of H(2)(18)O, these two peaks move to 733 and to 715 indicating the presence of two and one oxo ligands, respectively. When H(2)(18)O(2) is used, 2a and 3a are labeled showing that the oxo ligands come from H(2)O(2). Interestingly, when an equimolar mixture of H(2)O(2) and H(2)(18)O(2) is used, only unlabeled and doubly labeled 2a/b are formed, showing that its two oxo ligands come from the same H(2)O(2) molecule. All these experiments lead to attribute the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) to 2a and to 3a the formula [Mn(II)Mn(III)(L)(O)(OAc)](+). Freeze-quench/EPR experiments revealed that 2a appears at 500 ms and that another species with a 6-line spectrum is formed transiently at ca. 100 ms. 2a was prepared by reaction of 1a with tert-butyl hydroperoxide as shown by EPR and UV-visible spectroscopies and ESI-MS experiments. Its structure was studied by X-ray absorption experiments which revealed the presence of two or three O atoms at 1.87 A and three or two N/O atoms at 2.14 A. In addition one N atom was found at a longer distance (2.3 A) and one Mn at 2.63 A. 2a can be one-electron oxidized at E(1/2) = 0.91 V(NHE) (DeltaE(1/2) = 0.08 V) leading to its Mn(IV)Mn(IV) analogue. The formation of 2a from 1a was monitored by UV-visible and X-ray absorption spectroscopies. Both concur to show that an intermediate Mn(II)Mn(III) species, resembling 4a [Mn(2)(L)(OAc)(2)(H(2)O)](ClO(4))(2), the one-electron-oxidized form of 1a, is formed initially and transforms into 2a. The structures of the active intermediates 2 and 3 are discussed in light of their spectroscopic properties, and potential mechanisms are considered and discussed in the context of the biological reaction.

Characterization of chromodulin by X-ray absorption and electron paramagnetic resonance spectroscopies and magnetic susceptibility measurements

The biologically active form of the essential trace element chromium is believed to be the oligopeptide chromodulin. Chromodulin binds four chromic ions before binding at or near the active site of activating insulin receptor and subsequently potentiating the tyrosine kinase activity of the receptor. Charge balance arguments and preliminary spectroscopic studies suggested that the chromic centers might be part of a multinuclear assembly. Using a combination of X-ray absorption and electron paramagnetic resonance spectroscopies and variable-temperature magnetic susceptibility measurements, we found that holochromodulin is shown to possess an antiferromagnetically coupled trinuclear assembly which probably weakly interacts with a fourth chromium center. The chromium centers possess octahedron coordination comprised of oxygen-based ligation, presumably derived primarily from oligopeptide-supplied carboxylate groups. X-ray absorption data cannot be reproduced with the presence of sulfur atom(s), indicating that the cysteine thiolate group does not coordinate to the chromium centers. Thus, chromodulin possesses a unique type of multinuclear assembly, distinct from those known in other bioinorganic systems.

Site-selective EXAFS in mixed-valence compounds using high-resolution fluorescence detection: a study of iron in Prussian Blue

A quantitative analysis is presented for the site-selective Fe K-edge absorption spectra of Prussian Blue: Fe(4)[Fe(CN)(6)](3) x xH(2)O (x = 14-16). The site-selective spectra were recorded using high-resolution fluorescence detection of the K beta emission from a polycrystalline sample. The K beta fluorescence lines arising from the high-spin and low-spin sites are shifted in energy. Since the emission features partially overlap, fluorescence-detected absorption spectra using different emission energies represent different linear combinations of the pure high-spin and low-spin EXAFS. A numerical method was used to extract the individual site EXAFS spectra from the experimental data. The analysis yields a range of solutions. A unique solution can be obtained if homovalent model compounds are used to simulate the K beta fluorescence emission from the two Fe sites in Prussian Blue. EXAFS analysis of the range of spectra obtained in the numerical method yields almost identical interatomic distances for the different spectra while the Debye-Waller factors vary considerably. The distances obtained in the EXAFS fit correspond to the crystallographic distances.

Characterization of the metal receptor sites in Escherichia coli Zur, an ultrasensitive zinc(II) metalloregulatory protein

The Escherichia coli Zur protein is a Fur homologue that regulates expression of Zn(II) uptake systems. The zinc-loaded form of Zur is proposed to bind DNA and repress transcription of the znuABC genes. Recent in vitro data indicate that the transcriptional activity of Zur is half-maximal when free Zn(II) concentrations are in the sub-femtomolar range, making it the most sensitive Zn(II) metalloregulatory protein reported to date. Previous results indicate that Zur binds at least one zinc; however, little else is known about Zn(II) binding. We have purified E. coli Zur to homogeneity and found that it has two Zn(II) binding sites per monomer with different coordination environments. Using Zn(II) binding assays, ICP-AES analysis, and Zn EXAFS analysis, we show that one zinc is tightly bound in an S(3)(N/O) coordination environment. Both Co(II) and Zn(II) were substituted into the second metal binding site and probed by EXAFS and UV-visible absorption spectroscopy. These studies indicate that Co(II) is bound in an S(N/O)(3) coordination environment with tetrahedral geometry. The Zn(II) EXAFS of Zn(2)Zur, which is consistent with the results for both sites, indicates an average coordination environment of S(2)(N/O)(2), presumably due to one S(N/O)(3) site and one S(3)(N/O) site. These studies reveal the coordination environments that confer such exceptional zinc sensitivity and may provide the foundation for understanding the molecular basis of metal ion selectivity. A comparison of the metal binding sites in Zur with its Fe(II)-sensing homologue Fur provides clues as to why these two proteins with similar structures respond to two very different metal ions.

Conformational changes of the ferric uptake regulation protein upon metal activation and DNA binding; first evidence of structural homologies with the diphtheria toxin repressor

Fur (ferric uptake regulation protein) is a bacterial global regulator that uses iron as a cofactor to bind to specific DNA sequences. It has been suggested that metal binding induces a conformational change in the protein, which is subsequently able to recognize DNA. This mechanism of activation has been investigated here using selective chemical modification monitored by mass spectrometry. The reactivity of each lysine residue of the Fur protein was studied, first in the apo form of the protein, then after metal activation and finally after DNA binding. Of particular interest is Lys76, which was shown to be highly protected from modification in the presence of target DNA. Hydrogen-deuterium exchange experiments were performed to map with higher resolution the conformational changes induced by metal binding. On the basis of these results, together with a secondary structure prediction, the presence in Fur of a non-classical helix-turn-helix motif is proposed. Experimental results show that activation upon metal binding induces conformational modification of this specific motif. The recognition helix, interacting directly with the major groove of the DNA, would include the domain [Y55-F61]. This helix would be followed by a small "wing" formed between two beta strands, containing Lys76, which might interact directly with DNA. These results suggest that Fur and DtxR (diphtheria toxin repressor), another bacterial repressor, share not only the function of being iron concentration regulators, and the structure of their DNA-binding domain.