The manganese(IV)/iron(III) cofactor of Chlamydia trachomatis ribonucleotide reductase: structure, assembly, radical initiation, and evolution

Accessing a synthetic FeIIIMnIV core to model biological heterobimetallic active sites

Metalloproteins with dinuclear cores are known to bind and activate dioxygen, with a subclass of these proteins having active sites containing FeMn cofactors and activities ranging from long-range proton-coupled electron transfer (PCET) to post-translational peptide modification. While mechanistic studies propose that these metallocofactors access FeIIIMnIV intermediates, there is a dearth of related synthetic analogs. Herein, the first well-characterized synthetic FeIII-(μ-O)-MnIV complex is reported; this complex shows similar spectroscopic features as the catalytically competent FeIIIMnIV intermediate X found in Class Ic ribonucleotide reductase and demonstrates PCET function towards phenolic substrates. This complex is prepared from the oxidation of the isolable FeIII-(μ-O)-MnIII species, whose stepwise assembly is facilitated by a tripodal ligand containing phosphinic amido groups. Structural and spectroscopic studies found proton movement involving the FeIIIMnIII core, whereby the initial bridging hydroxido ligand is converted to an oxido ligand with concomitant protonation of one phosphinic amido group. This series of FeMn complexes allowed us to address factors that may dictate the preference of an active site for a heterobimetallic cofactor over one that is homobimetallic: comparisons of the redox properties of our FeMn complexes with those of the di-Fe analogs suggested that the relative thermodynamic ease of accessing an FeIIIMnIV core can play an important role in determining the metal ion composition when the key catalytic steps do not require an overly potent oxidant. Moreover, these complexes allowed us to demonstrate the effect of the hyperfine interaction from non-Fe nuclei on 57Fe Mössbauer spectra which is relevant to MnFe intermediates in proteins.

Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis

Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of para-aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen Chlamydia trachomatis. The pathway used by Chlamydiae for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from l-tyrosine. As a member of the emerging superfamily of heme oxygenase-like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O₂ activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the "substrate" Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in C. trachomatis, which will inform the design of novel therapeutics.

Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade

Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.

Billions of years ago, the Earth’s atmosphere had very little oxygen. It was only after some bacteria and early plants evolved to harness energy from sunlight that oxygen began to fill the Earth’s environment. Oxygen is highly reactive and can interfere with enzymes and other molecules that are essential to life. Organisms living at this point in history therefore had to adapt to survive in this new oxygen-rich world.

An ancient family of enzymes known as ribonucleotide reductases are used by all free-living organisms and many viruses to repair and replicate their DNA. Because of their essential role in managing DNA, these enzymes have been around on Earth for billions of years. Understanding how they evolved could therefore shed light on how nature adapted to increasing oxygen levels and other environmental changes at the molecular level.

One approach to study how proteins evolved is to use computational analysis to construct a phylogenetic tree. This reveals how existing members of a family are related to one another based on the chain of molecules (known as amino acids) that make up each protein. Despite having similar structures and all having the same function, ribonucleotide reductases have remarkably diverse sequences of amino acids. This makes it computationally very demanding to build a phylogenetic tree.

To overcome this, Burnim, Spence, Xu et al. created a phylogenetic tree using structural information from a part of the enzyme that is relatively similar in many modern-day ribonucleotide reductases. The final result took seven continuous months on a supercomputer to generate, and includes over 6,000 members of the enzyme family.

The phylogenetic tree revealed a new distinct group of ribonucleotide reductases that may explain how one adaptation to increasing levels of oxygen emerged in some family members, while another adaptation emerged in others. The approach used in this work also opens up a new way to study how other highly diverse enzymes and other protein families evolved, potentially revealing new insights about our planet’s past.

Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins

Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A Mn^III(μ-O)(μ-OH)Fe^III species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the Mn^III(μ-O)(μ-OH)Fe^III state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded Mn^III(μ-OH)Fe^III species. This final intermediate precedes formation of the Mn^III/Fe^III resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.

Mechanism of DOPA radical generation and transfer in metal-free class Ie ribonucleotide reductase based on density functional theory

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The mechanism of DOPA radical generation, transfer and regeneration is revealed.

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The superoxide O₂^•− should be protonated to HO₂^• prior to oxidizing Tyr126 to DOPA radical.

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The protonation of Asp88 is the prerequisite for the DOPA radical generation and radical transfer.

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Lys213 is a key residue for the transfer of the DOPA radical.

Quantum mechanical/molecular mechanical (QM/MM) calculations were carried out to investigate the mechanisms of the generation, transfer, and regeneration of the DOPA radical for metal-free class Ie ribonucleotide reductase. The crystal structure of MfR2 (Nature, 2018, 563, 416–420) was adopted for the calculations. The QM/MM calculations have revealed several key points that are vital for understanding the mechanisms. The superoxide O₂^•− provided by the flavoprotein NrdI cannot directly oxidize the residue Tyr126 to the DOPA radical. It should be protonated to HO₂^•. The calculation results suggest that the covalent modification of Tyr126 and the DOPA radical generation can be carried out with no involvement of metal cofactors. This addresses the concerns of the articles (Nature, 2018, 563, 416–420; PNAS, 2018, 115, 10022–10027). Another concern from the articles is that how the DOPA radical is transferred from the radical trap. The DFT calculations have demonstrated that Lys213 is a key residue for the radical transfer from the DOPA radical. The ε-amino group of Lys213 is used not only as a bridge for the electron transfer but also as a proton donor. It can provide a proton to DOPA126 via a water molecule, and thus the radical transfer from DOPA126 to Trp52 is facilitated. It has also been revealed that the protonation of Asp88 is the prerequisite for the DOPA radical generation and the radical transfer in class Ie. Once the radical is quenched, it can be regenerated via the oxidations by superoxide O₂^•− and hydroperoxyl radical HO₂^•.

Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation

Bimetallic active sites in enzymes catalyze small-molecule conversions that are among the top 10 challenges in chemistry. As different metal cofactors are typically incorporated in varying protein scaffolds, it is demanding to disentangle the individual contributions of the metal and the protein matrix to the activity. Here, we compared the structure, properties, and hydrogen peroxide reactivity of four homobimetallic cofactors (Mn(II)₂, Fe(II)₂, Co(II)₂, Ni(II)₂) that were reconstituted into a four-helix bundle protein. Reconstituted proteins were studied in solution and in crystals. All metals bind with high affinity and yield similar cofactor structures. Cofactor variants react with H₂O₂ but differ in their turnover rates, accumulated oxidation states, and trapped peroxide-bound intermediates. Varying the metal composition thus creates opportunities to tune the reactivity of the bimetallic cofactor and to study and functionalize reactive species.

Spontaneous Formation of an Fe/Mn Diamond Core: Models for the Fe/Mn Sites in Class 1c Ribonucleotide Reductases

A handful of oxygen-activating enzymes has recently been found to contain Fe/Mn active sites, like Class 1c ribonucleotide reductases and R2-like ligand-binding oxidase, which are closely related to their better characterized diiron cousins. These enzymes are proposed to form high-valent intermediates with Fe-O-Mn cores. Herein, we report the first examples of synthetic Fe/Mn complexes that mimic doubly bridged intermediates proposed for enzymatic oxygen activation. Fe K-edge extended X-ray absorption fine structure (EXAFS) analysis has been used to characterize the structures of each of these compounds. Linear compounds accurately model the Fe···Mn distances found in Fe/Mn proteins in their resting states, and doubly bridged diamond core compounds accurately model the distances found in high-valent biological intermediates. Unlike their diiron analogues, the paramagnetic nature of Fe/Mn compounds can be analyzed by EPR, revealing S = 1/2 signals that reflect antiferromagnetic coupling between the high-spin Fe(III) and Mn(III) units of heterobimetallic centers. These compounds undergo electron transfer with various ferrocenes, linear compounds being capable of oxidizing diacetyl ferrocene, a weak reductant, and diamond core compounds being capable of oxidizing acetyl ferrocene. Diamond core compounds can also perform HAT reactions from substrates with X-H bonds with bond dissociation free energies (BDFEs) up to 75 kcal/mol and are capable of oxidizing TEMPO-H at rates of 0.32-0.37 M^-1 s^-1, which are comparable to those reported for some mononuclear Fe^III-OH and Mn^III-OH compounds. However, such reactivity is not observed for the corresponding diiron compounds, a difference that Nature may have taken advantage of in evolving enzymes with heterobimetallic active sites.

Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets

Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.

Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein

Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater Mn^II affinity than Fe^II affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.

Fate of oxygen species from O2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry

Oxygen (O₂) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O₂ cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only ⁵⁷Fe(II) or Mn(II) plus ⁵⁷Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including ^16/18O and H/D exchange. ⁵⁷Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H₂O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH^-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas ¹⁸O from ¹⁸O₂ cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O₂ reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O₂ cleavage route in an enzyme.

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.

O–H and (CO)N–H bond weakening by coordination to Fe(ii)

Coordination of hydroxyl/amide groups to Fe(ii) diminishes BDFEs of O–H and (CO)N–H bonds down to 76.0 and 80.5 kcal mol⁻¹ respectively.

Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor

A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O₂^-) for activation, but it does not require the O₂^--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O₂^- to the Mn₂^II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.

Involvement of high-valent manganese-oxo intermediates in oxidation reactions: realisation in nature, nano and molecular systems

Manganese plays multiple role in many biological redox reactions in which it exists in different oxidation states from Mn(II) to Mn(IV). Among them the high-valent manganese-oxo intermediate plays important role in the activity of certain enzymes and lessons from the natural system provide inspiration for new developments of artificial systems for a sustainable energy supply and various organic conversions. This review describes recent advances and key lessons learned from the nature on high-valent Mn-oxo intermediates. Also we focus on the elemental science developed from the natural system, how the novel strategies are realised in nano particles and molecular sites at heterogeneous and homogeneous reaction conditions respectively. Finally, perspectives on the utilisation of the high-valent manganese-oxo species towards other organic reactions are proposed.

Oxoiron(IV) complexes as synthons for the assembly of heterobimetallic centers such as the Fe/Mn active site of Class Ic ribonucleotide reductases

Nonheme oxoiron(IV) complexes can serve as synthons for generating heterobimetallic oxo-bridged dimetal complexes by reaction with divalent metal complexes. The formation of Fe^III-O-Cr^III and Fe^III-O-Mn^III complexes is described herein. The latter complexes may serve as models for the Fe^III-X-Mn^III active sites of an emerging class of Fe/Mn enzymes represented by the Class 1c ribonucleotide reductase from Chlamydia trachomatis and the R2-like ligand-binding oxidase (R2lox) found in Mycobacterium tuberculosis. These synthetic complexes have been characterized by UV-Vis, resonance Raman, and X-ray absorption spectroscopy, as well as electrospray mass spectrometry. The Fe^III-O-Cr^III complexes exhibit a three-band UV-Vis pattern that differs from the simpler features associated with Fe^III-O-Fe^III complexes. The positions of these features are modulated by the nature of the supporting polydentate ligand on the iron center, and their bands intensify dramatically in two examples upon the binding of an axial cyanate or thiocyanate ligand trans to the oxo bridge. In contrast, the Fe^III-O-Mn^III complexes resemble Fe^III-O-Fe^III complexes more closely. Resonance Raman characterization of the Fe^III-O-M^III complexes reveals an ¹⁸O-sensitive vibration in the range of 760-890 cm^-1. This feature has been assigned to the asymmetric Fe^III-O-M^III stretching mode and correlates reasonably with the Fe-O bond distance determined by EXAFS analysis. The likely binding of an acetate as a bridging ligand to the Fe^III-O-Mn^III complex 12 lays the foundation for further efforts to model the heterobimetallic active sites of Fe/Mn enzymes.

Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog

Bifidobacteria comprises an important group/order of bacteria whose members have widespread usage in the food and health industry due to their health-promoting activity in the human gastrointestinal tract. However, little is known about the underlying molecular properties that are responsible for the probiotic effects of these bacteria. The enzyme ribonucleotide reductase (RNR) plays a key role in all organisms by reducing nucleoside di- or tri- phosphates into corresponding deoxyribose derivatives required for DNA synthesis, and RNR homologs belonging to classes I and III are present in either most or all Bifidobacteriales. Comparative analyses of these RNR homologs have identified several novel sequence features in the forms of conserved signature indels (CSIs) that are exclusively found in bifidobacterial RNRs. Specifically, in the large subunit of the aerobic class Ib RNR, three CSIs have been identified that are uniquely found in the Bifidobacteriales homologs. Similarly, the large subunit of the anaerobic class III RNR contains five CSIs that are also distinctive characteristics of bifidobacteria. Phylogenetic analyses indicate that these CSIs were introduced in a common ancestor of the Bifidobacteriales and retained by all descendants, likely due to their conferring advantageous functional roles. The identified CSIs in the bifidobacterial RNR homologs provide useful tools for further exploration of the novel functional aspects of these important enzymes that are exclusive to these bacteria. We also report here the results of homology modeling studies, which indicate that most of the bifidobacteria-specific CSIs are located within the surface loops of the RNRs, and of these, a large 43 amino acid insert in the class III RNR homolog forms an extension of the allosteric regulatory site known to be essential for protein function. Preliminary docking studies suggest that this large CSI may be playing a role in enhancing the stability of the RNR dimer complex. The possible significances of the identified CSIs, as well as the distribution of RNR homologs in the Bifidobacteriales, are discussed.

Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis

High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).

Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations

Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O₂) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O₂ reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal-ligand bond lengths, metal-metal distances, metal oxidation states, spin configurations, valence-level degeneracy, molecular orbital composition, nuclear quadrupole splitting energies, and vibrational normal modes for both cofactors. A protonation state with an axial water (H₂O) ligand at Mn or Fe in binding site 1 and a metal-bridging hydroxo group (μOH) in a hydrogen-bonded network is assigned. Our comprehensive picture of the molecular, electronic, and dynamic properties of the cofactors highlights reorientation of the unique axis along the Mn-OH₂ bond for the Mn1(III) Jahn-Teller ion but along the Fe-μOH bond for the octahedral Fe1(III). This likely corresponds to a more positive redox potential of the Mn(III)Fe(III) cofactor and higher proton affinity of its μOH group. Refined model structures for the Mn(III)Fe(III) and Fe(III)Fe(III) cofactors are presented. Implications of our findings for the site-specific metalation of R2lox and performance of the O₂ reduction and cross-link formation reactions are discussed.

Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis

Ribonucleotide reductases (RNRs) catalyze conversion of ribonucleotides to deoxyribonucleotides in all organisms via a free-radical mechanism that is essentially conserved. In class I RNRs, the reaction is initiated and terminated by radical translocation (RT) between the α and β subunits. In the class Ic RNR from Chlamydia trachomatis (Ct RNR), the initiating event converts the active S = 1 Mn(IV)/Fe(III) cofactor to the S = 1/2 Mn(III)/Fe(III) "RT-product" form in the β subunit and generates a cysteinyl radical in the α active site. The radical can be trapped via the well-described decomposition reaction of the mechanism-based inactivator, 2'-azido-2'-deoxyuridine-5'-diphosphate, resulting in the generation of a long-lived, nitrogen-centered radical (N(•)) in α. In this work, we have determined the distance between the Mn(III)/Fe(III) cofactor in β and N(•) in α to be 43 ± 1 Å by using double electron-electron resonance experiments. This study provides the first structural data on the Ct RNR holoenzyme complex and the first direct experimental measurement of the inter-subunit RT distance in any class I RNR.

Electronic structural flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins

The electronic structure of the Mn/Fe cofactor identified in a new class of oxidases (R2lox) described by Andersson and Högbom [Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5633] is reported. The R2lox protein is homologous to the small subunit of class Ic ribonucleotide reductase (R2c) but has a completely different in vivo function. Using multifrequency EPR and related pulse techniques, it is shown that the cofactor of R2lox represents an antiferromagnetically coupled Mn(III)/Fe(III) dimer linked by a μ-hydroxo/bis-μ-carboxylato bridging network. The Mn(III) ion is coordinated by a single water ligand. The R2lox cofactor is photoactive, converting into a second form (R2loxPhoto) upon visible illumination at cryogenic temperatures (77 K) that completely decays upon warming. This second, unstable form of the cofactor more closely resembles the Mn(III)/Fe(III) cofactor seen in R2c. It is shown that the two forms of the R2lox cofactor differ primarily in terms of the local site geometry and electronic state of the Mn(III) ion, as best evidenced by a reorientation of its unique (55)Mn hyperfine axis. Analysis of the metal hyperfine tensors in combination with density functional theory (DFT) calculations suggests that this change is triggered by deprotonation of the μ-hydroxo bridge. These results have important consequences for the mixed-metal R2c cofactor and the divergent chemistry R2lox and R2c perform.

Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins

The ferritin superfamily contains several protein groups that share a common fold and metal coordinating ligands. The different groups utilize different dinuclear cofactors to perform a diverse set of reactions. Several groups use an oxygen-activating di-iron cluster, while others use di-manganese or heterodinuclear Mn/Fe cofactors. Given the similar primary ligand preferences of Mn and Fe as well as the similarities between the binding sites, the basis for metal specificity in these systems remains enigmatic. Recent data for the heterodinuclear cluster show that the protein scaffold per se is capable of discriminating between Mn and Fe and can assemble the Mn/Fe center in the absence of any potential assembly machineries or metal chaperones. Here we review the current understanding of the assembly of the heterodinuclear cofactor in the two different protein groups in which it has been identified, ribonucleotide reductase R2c proteins and R2-like ligand-binding oxidases. Interestingly, although the two groups form the same metal cluster they appear to employ partly different mechanisms to assemble it. In addition, it seems that both the thermodynamics of metal binding and the kinetics of oxygen activation play a role in achieving metal specificity.

Ribonucleotide reductase metallocofactor: assembly, maintenance and inhibition

Ribonucleotide reductase (RNR) supplies cellular deoxyribonucleotide triphosphates (dNTP) pools by converting ribonucleotides to the corresponding deoxy forms using radical-based chemistry. Eukaryotic RNR comprises α and β subunits: α contains the catalytic and allosteric sites; β houses a diferric-tyrosyl radical cofactor (Fe^III₂-Y•) that is required to initiates nucleotide reduction in α. Cells have evolved multi-layered mechanisms to regulate RNR level and activity in order to maintain the adequate sizes and ratios of their dNTP pools to ensure high-fidelity DNA replication and repair. The central role of RNR in nucleotide metabolism also makes it a proven target of chemotherapeutics. In this review, we discuss recent progress in understanding the function and regulation of eukaryotic RNRs, with a focus on studies revealing the cellular machineries involved in RNR metallocofactor biosynthesis and its implication in RNR-targeting therapeutics.

The role of water-based hydrogen atom wires in long-range electron-transfer reactions in aqueous media for the FeII-FeIII self-exchange and related systems

Extended reach: A calculated mechanism for long-range proton-coupled electron transfer (PCET, see picture) through an array of structured water molecules between Fe(III)-Fe(III) complexes accounts for the reaction enthalpy and kinetic isotope effect previously measured for this reaction. This mechanism may be general and occur for other hydroxo-metal complexes.

Experimental and computational X-ray emission spectroscopy as a direct probe of protonation states in oxo-bridged Mn(IV) dimers relevant to redox-active metalloproteins

The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-μ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kβ emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kβ(2,5) peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kβ" peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated μ-oxo bridges dominate this spectral region. The energies of the Kβ" features differ by ~3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (μ-O)(μ-OH2) motif can be distinguished from a symmetric (μ-OH)2 one. The results reported here highlight the sensitivity of Kβ valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.

Geometric and electronic structure of the Mn(IV)Fe(III) cofactor in class Ic ribonucleotide reductase: correlation to the class Ia binuclear non-heme iron enzyme

The class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (Ct) utilizes a Mn/Fe heterobinuclear cofactor, rather than the Fe/Fe cofactor found in the β (R2) subunit of the class Ia enzymes, to react with O2. This reaction produces a stable Mn(IV)Fe(III) cofactor that initiates a radical, which transfers to the adjacent α (R1) subunit and reacts with the substrate. We have studied the Mn(IV)Fe(III) cofactor using nuclear resonance vibrational spectroscopy (NRVS) and absorption (Abs)/circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD spectroscopies to obtain detailed insight into its geometric/electronic structure and to correlate structure with reactivity; NRVS focuses on the Fe(III), whereas MCD reflects the spin-allowed transitions mostly on the Mn(IV). We have evaluated 18 systematically varied structures. Comparison of the simulated NRVS spectra to the experimental data shows that the cofactor has one carboxylate bridge, with Mn(IV) at the site proximal to Phe127. Abs/CD/MCD/VTVH MCD data exhibit 12 transitions that are assigned as d-d and oxo and OH(-) to metal charge-transfer (CT) transitions. Assignments are based on MCD/Abs intensity ratios, transition energies, polarizations, and derivative-shaped pseudo-A term CT transitions. Correlating these results with TD-DFT calculations defines the Mn(IV)Fe(III) cofactor as having a μ-oxo, μ-hydroxo core and a terminal hydroxo ligand on the Mn(IV). From DFT calculations, the Mn(IV) at site 1 is necessary to tune the redox potential to a value similar to that of the tyrosine radical in class Ia RNR, and the OH(-) terminal ligand on this Mn(IV) provides a high proton affinity that could gate radical translocation to the α (R1) subunit.

L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

Synthesis of open-shell, bimetallic Mn/Fe trinuclear clusters

Concomitant deprotonation and metalation of hexadentate ligand platform (tbs)LH6 ((tbs)LH6 = 1,3,5-C6H9(NHC6H4-o-NHSiMe2(t)Bu)3) with divalent transition metal starting materials Fe2(Mes)4 (Mes = mesityl) or Mn3(Mes)6 in the presence of tetrahydrofuran (THF) resulted in isolation of homotrinuclear complexes ((tbs)L)Fe3(THF) and ((tbs)L)Mn3(THF), respectively. In the absence of coordinating solvent (THF), the deprotonation and metalation exclusively afforded dinuclear complexes of the type ((tbs)LH2)M2 (M = Fe or Mn). The resulting dinuclear species were utilized as synthons to prepare bimetallic trinuclear clusters. Treatment of ((tbs)LH2)Fe2 complex with divalent Mn source (Mn2(N(SiMe3)2)4) afforded the bimetallic complex ((tbs)L)Fe2Mn(THF), which established the ability of hexamine ligand (tbs)LH6 to support mixed metal clusters. The substitutional homogeneity of ((tbs)L)Fe2Mn(THF) was determined by (1)H NMR, (57)Fe Mössbauer, and X-ray fluorescence. Anomalous scattering measurements were critical for the unambiguous assignment of the trinuclear core composition. Heating a solution of ((tbs)LH2)Mn2 with a stoichiometric amount of Fe2(Mes)4 (0.5 mol equiv) affords a mixture of both ((tbs)L)Mn2Fe(THF) and ((tbs)L)Fe2Mn(THF) as a result of the thermodynamic preference for heavier metal substitution within the hexa-anilido ligand framework. These results demonstrate for the first time the assembly of mixed metal cluster synthesis in an unbiased ligand platform.

Structural basis for assembly of the Mn(IV)/Fe(III) cofactor in the class Ic ribonucleotide reductase from Chlamydia trachomatis

The class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (Ct) employs a Mn(IV)/Fe(III) cofactor in each monomer of its β2 subunit to initiate nucleotide reduction. The cofactor forms by reaction of Mn(II)/Fe(II)-β2 with O2. Previously, in vitro cofactor assembly from apo β2 and divalent metal ions produced a mixture of two forms, with Mn at site 1 (Mn(IV)/Fe(III)) or site 2 (Fe(III)/Mn(IV)), of which the more active Mn(IV)/Fe(III) product predominates. Here we have addressed the basis for metal site selectivity by determining X-ray crystal structures of apo, Mn(II), and Mn(II)/Fe(II) complexes of Ct β2. A structure obtained anaerobically with equimolar Mn(II), Fe(II), and apoprotein reveals exclusive incorporation of Mn(II) at site 1 and Fe(II) at site 2, in contrast to the more modest site selectivity achieved previously. Site specificity is controlled thermodynamically by the apoprotein structure, as only minor adjustments of ligands occur upon metal binding. Additional structures imply that, by itself, Mn(II) binds in either site. Together, the structures are consistent with a model for in vitro cofactor assembly in which Fe(II) specificity for site 2 drives assembly of the appropriately configured heterobimetallic center, provided that Fe(II) is substoichiometric. This model suggests that use of a Mn(IV)/Fe(III) cofactor in vivo could be an adaptation to Fe(II) limitation. A 1.8 Å resolution model of the Mn(II)/Fe(II)-β2 complex reveals additional structural determinants for activation of the cofactor, including a proposed site for side-on (η(2)) addition of O2 to Fe(II) and a short (3.2 Å) Mn(II)-Fe(II) interionic distance, promoting formation of the Mn(IV)/Fe(IV) activation intermediate.

Hydrogen-bonding effects on the reactivity of [X-Fe(III)-O-Fe(IV)═O] (X = OH, F) complexes toward C-H bond cleavage

Complexes 1-OH and 1-F are related complexes that share similar [X-Fe(III)-O-Fe(IV)═O](3+) core structures with a total spin S of ½, which arises from antiferromagnetic coupling of an S = 5/2 Fe(III)-X site and an S = 2 Fe(IV)═O site. EXAFS analysis shows that 1-F has a nearly linear Fe(III)-O-Fe(IV) core compared to that of 1-OH, which has an Fe-O-Fe angle of ~130° due to the presence of a hydrogen bond between the hydroxo and oxo groups. Both complexes are at least 1000-fold more reactive at C-H bond cleavage than 2, a related complex with a [OH-Fe(IV)-O-Fe(IV)═O](4+) core having individual S = 1 Fe(IV) units. Interestingly, 1-F is 10-fold more reactive than 1-OH. This raises an interesting question about what gives rise to the reactivity difference. DFT calculations comparing 1-OH and 1-F strongly suggest that the H-bond in 1-OH does not significantly change the electrophilicity of the reactive Fe(IV)═O unit and that the lower reactivity of 1-OH arises from the additional activation barrier required to break its H-bond in the course of H-atom transfer by the oxoiron(IV) moiety.

Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase

Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.

Novel Approaches for the Accumulation of Oxygenated Intermediates to Multi-Millimolar Concentrations

Metalloenzymes that utilize molecular oxygen as a co-substrate catalyze a wide variety of chemically difficult oxidation reactions. Significant insight into the reaction mechanisms of these enzymes can be obtained by the application of a combination of rapid kinetic and spectroscopic methods to the direct structural characterization of intermediate states. A key limitation of this approach is the low aqueous solubility (< 2 mM) of the co-substrate, O2, which undergoes further dilution (typically by one-third or one-half) upon initiation of reactions by rapid-mixing. This situation imposes a practical upper limit on [O2] (and therefore on the concentration of reactive intermediate(s) that can be rapidly accumulated) of ∼1-1.3 mM in such experiments as they are routinely carried out. However, many spectroscopic methods benefit from or require significantly greater concentrations of the species to be studied. To overcome this problem, we have recently developed two new approaches for the preparation of samples of oxygenated intermediates: (1) direct oxygenation of reduced metalloenzymes using gaseous O2 and (2) the in situ generation of O2 from chlorite catalyzed by the enzyme chlorite dismutase (Cld). Whereas the former method is applicable only to intermediates with half lives of several minutes, owing to the sluggishness of transport of O2 across the gas-liquid interface, the latter approach has been successfully applied to trap several intermediates at high concentration and purity by the freeze-quench method. The in situ approach permits generation of a pulse of at least 5 mM O2 within ∼ 1 ms and accumulation of O2 to effective concentrations of up to ∼ 11 mM (i.e. ∼ 10-fold greater than by the conventional approach). The use of these new techniques for studies of oxygenases and oxidases is discussed.

Radical-translocation intermediates and hurdling of pathway defects in "super-oxidized" (Mn(IV)/Fe(IV)) Chlamydia trachomatis ribonucleotide reductase

A class I ribonucleotide reductase (RNR) uses either a tyrosyl radical (Y(•)) or a Mn(IV)/Fe(III) cluster in its β subunit to oxidize a cysteine residue ∼35 Å away in its α subunit, generating a thiyl radical that abstracts hydrogen (H(•)) from the substrate. With either oxidant, the inter-subunit "hole-transfer" or "radical-translocation" (RT) process is thought to occur by a "hopping" mechanism involving multiple tyrosyl (and perhaps one tryptophanyl) radical intermediates along a specific pathway. The hopping intermediates have never been directly detected in a Mn/Fe-dependent (class Ic) RNR nor in any wild-type (wt) RNR. The Mn(IV)/Fe(III) cofactor of Chlamydia trachomatis RNR assembles via a Mn(IV)/Fe(IV) intermediate. Here we show that this cofactor-assembly intermediate can propagate a hole into the RT pathway when α is present, accumulating radicals with EPR spectra characteristic of Y(•)'s. The dependence of Y(•) accumulation on the presence of substrate suggests that RT within this "super-oxidized" enzyme form is gated by the protein, and the failure of a β variant having the subunit-interfacial pathway Y substituted by phenylalanine to support radical accumulation implies that the Y(•)(s) in the wt enzyme reside(s) within the RT pathway. Remarkably, two variant β proteins having pathway substitutions rendering them inactive in their Mn(IV)/Fe(III) states can generate the pathway Y(•)'s in their Mn(IV)/Fe(IV) states and also effect nucleotide reduction. Thus, the use of the more oxidized cofactor permits the accumulation of hopping intermediates and the "hurdling" of engineered defects in the RT pathway.

Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study

How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.

Aqueous speciation and electrochemical properties of a water-soluble manganese phthalocyanine complex

The speciation behavior of a water-soluble manganese(III) tetrasulfonated phthalocyanine complex was investigated with UV-visible and electron paramagnetic resonance (EPR) spectroscopies, as well as cyclic voltammetry. Parallel-mode EPR (in dimethylformamide : pyridine solvent mix) reveals a six-line hyperfine signal, centered at a g-value of 8.8, for the manganese(III) monomer, characteristic of the d(4)S = 2 system. The color of an aqueous solution containing the complex is dependent upon the pH of the solution; the phthalocyanine complex can exist as a water-bound monomer, a hydroxide-bound monomer, or an oxo-bridged dimer. Addition of coordinating bases such as borate or pyridine changes the speciation behavior by coordinating the manganese center. From the UV-visible spectra, complete speciation diagrams are plotted by global analysis of the pH-dependent UV-visible spectra, and a complete set of pK(a) values is obtained by fitting the data to a standard pK(a) model. Electrochemical studies reveal a pH-independent quasi-reversible oxidation event for the monomeric species, which likely involves oxidation of the organic ligand to the radical cation species. Adsorption of the phthalocyanine complex on the carbon working electrode was sometimes observed. The pK(a) values and electrochemistry data are discussed in the context of the development of mononuclear water-oxidation catalysts.

Role of arginine 293 and glutamine 288 in communication between catalytic and allosteric sites in yeast ribonucleotide reductase

Ribonucleotide reductases (RRs) catalyze the rate-limiting step of de novo deoxynucleotide (dNTP) synthesis. Eukaryotic RRs consist of two proteins, RR1 (α) that contains the catalytic site and RR2 (β) that houses a diferric-tyrosyl radical essential for ribonucleoside diphosphate reduction. Biochemical analysis has been combined with isothermal titration calorimetry (ITC), X-ray crystallography and yeast genetics to elucidate the roles of two loop 2 mutations R293A and Q288A in Saccharomyces cerevisiae RR1 (ScRR1). These mutations, R293A and Q288A, cause lethality and severe S phase defects, respectively, in cells that use ScRR1 as the sole source of RR1 activity. Compared to the wild-type enzyme activity, R293A and Q288A mutants show 4% and 15%, respectively, for ADP reduction, whereas they are 20% and 23%, respectively, for CDP reduction. ITC data showed that R293A ScRR1 is unable to bind ADP and binds CDP with 2-fold lower affinity compared to wild-type ScRR1. With the Q288A ScRR1 mutant, there is a 6-fold loss of affinity for ADP binding and a 2-fold loss of affinity for CDP compared to the wild type. X-ray structures of R293A ScRR1 complexed with dGTP and AMPPNP-CDP [AMPPNP, adenosine 5-(β,γ-imido)triphosphate tetralithium salt] reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type. Our in vivo functional analyses demonstrated that R293A cannot support mitotic growth, whereas Q288A can, albeit with a severe S phase defect. Taken together, our structure, activity, ITC and in vivo data reveal that the arginine 293 and glutamine 288 residues of ScRR1 are crucial in facilitating ADP and CDP substrate selection.

O(2)-evolving chlorite dismutase as a tool for studying O(2)-utilizing enzymes

The direct interrogation of fleeting intermediates by rapid-mixing kinetic methods has significantly advanced our understanding of enzymes that utilize dioxygen. The gas's modest aqueous solubility (<2 mM at 1 atm) presents a technical challenge to this approach, because it limits the rate of formation and extent of accumulation of intermediates. This challenge can be overcome by use of the heme enzyme chlorite dismutase (Cld) for the rapid, in situ generation of O(2) at concentrations far exceeding 2 mM. This method was used to define the O(2) concentration dependence of the reaction of the class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis, in which the enzyme's Mn(IV)/Fe(III) cofactor forms from a Mn(II)/Fe(II) complex and O(2) via a Mn(IV)/Fe(IV) intermediate, at effective O(2) concentrations as high as ~10 mM. With a more soluble receptor, myoglobin, an O(2) adduct accumulated to a concentration of >6 mM in <15 ms. Finally, the C-H-bond-cleaving Fe(IV)-oxo complex, J, in taurine:α-ketoglutarate dioxygenase and superoxo-Fe(2)(III/III) complex, G, in myo-inositol oxygenase, and the tyrosyl-radical-generating Fe(2)(III/IV) intermediate, X, in Escherichia coli RNR, were all accumulated to yields more than twice those previously attained. This means of in situ O(2) evolution permits a >5 mM "pulse" of O(2) to be generated in <1 ms at the easily accessible Cld concentration of 50 μM. It should therefore significantly extend the range of kinetic and spectroscopic experiments that can routinely be undertaken in the study of these enzymes and could also facilitate resolution of mechanistic pathways in cases of either sluggish or thermodynamically unfavorable O(2) addition steps.

Evidence that the β subunit of Chlamydia trachomatis ribonucleotide reductase is active with the manganese ion of its manganese(IV)/iron(III) cofactor in site 1

The reaction of a class I ribonucleotide reductase (RNR) begins when a cofactor in the β subunit oxidizes a cysteine residue ~35 Å away in the α subunit, generating a thiyl radical. In the class Ic enzyme from Chlamydia trachomatis (Ct), the cysteine oxidant is the Mn(IV) ion of a Mn(IV)/Fe(III) cluster, which assembles in a reaction between O(2) and the Mn(II)/Fe(II) complex of β. The heterodinuclear nature of the cofactor raises the question of which site, 1 or 2, contains the Mn(IV) ion. Because site 1 is closer to the conserved location of the cysteine-oxidizing tyrosyl radical of class Ia and Ib RNRs, we suggested that the Mn(IV) ion most likely resides in this site (i.e., (1)Mn(IV)/(2)Fe(III)), but a subsequent computational study favored its occupation of site 2 ((1)Fe(III)/(2)Mn(IV)). In this work, we have sought to resolve the location of the Mn(IV) ion in Ct RNR-β by correlating X-ray crystallographic anomalous scattering intensities with catalytic activity for samples of the protein reconstituted in vitro by two different procedures. In samples containing primarily Mn(IV)/Fe(III) clusters, Mn preferentially occupies site 1, but some anomalous scattering from site 2 is observed, implying that both (1)Mn(II)/(2)Fe(II) and (1)Fe(II)/(2)Mn(II) complexes are competent to react with O(2) to produce the corresponding oxidized states. However, with diminished Mn(II) loading in the reconstitution, there is no evidence for Mn occupancy of site 2, and the greater activity of these "low-Mn" samples on a per-Mn basis implies that the (1)Mn(IV)/(2)Fe(III)-β is at least the more active of the two oxidized forms and may be the only active form.

High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases

Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(μO)(2)Fe(III)L(4) (metal-metal distance of ~2.75Å, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(μO)(μOH)Fe(III)L(4) (~2.90Å) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55Å) with a L(4)Fe(IV)(μO)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1Å) and Mn,Fe(III)Fe(II) species (~3.3-3.4Å) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(μO)(μOH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1.

Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo

Incorporation of metallocofactors essential for the activity of many enyzmes is a major mechanism of posttranslational modification. The cellular machinery required for these processes in the case of mono- and dinuclear nonheme iron and manganese cofactors has remained largely elusive. In addition, many metallocofactors can be converted to inactive forms, and pathways for their repair have recently come to light. The class I ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and require dinuclear metal clusters for activity: an Fe(III)Fe(III)-tyrosyl radical (Y•) cofactor (class Ia), a Mn(III)Mn(III)-Y• cofactor (class Ib), and a Mn(IV)Fe(III) cofactor (class Ic). The class Ia, Ib, and Ic RNRs are structurally homologous and contain almost identical metal coordination sites. Recent progress in our understanding of the mechanisms by which the cofactor of each of these RNRs is generated in vitro and in vivo and by which the damaged cofactors are repaired is providing insight into how nature prevents mismetallation and orchestrates active cluster formation in high yields.

Substrate-triggered activation of a synthetic [Fe2(μ-O)2] diamond core for C-H bond cleavage

An [Fe(IV)(2)(μ-O)(2)] diamond core structure has been postulated for intermediate Q of soluble methane monooxygenase (sMMO-Q), the oxidant responsible for cleaving the strong C-H bond of methane and its hydroxylation. By extension, analogous species may be involved in the mechanisms of related diiron hydroxylases and desaturases. Because of the paucity of well-defined synthetic examples, there are few, if any, mechanistic studies on the oxidation of hydrocarbon substrates by complexes with high-valent [Fe(2)(μ-O)(2)] cores. We report here that water or alcohol substrates can activate synthetic [Fe(III)Fe(IV)(μ-O)(2)] complexes supported by tetradentate tris(pyridyl-2-methyl)amine ligands (1 and 2) by several orders of magnitude for C-H bond oxidation. On the basis of detailed kinetic studies, it is postulated that the activation results from Lewis base attack on the [Fe(III)Fe(IV)(μ-O)(2)] core, resulting in the formation of a more reactive species with a [X-Fe(III)-O-Fe(IV)═O] ring-opened structure (1-X, 2-X, X = OH(-) or OR(-)). Treatment of 2 with methoxide at -80 °C forms the 2-methoxide adduct in high yield, which is characterized by an S = 1/2 EPR signal indicative of an antiferromagnetically coupled [S = 5/2 Fe(III)/S = 2 Fe(IV)] pair. Even at this low temperature, the complex undergoes facile intramolecular C-H bond cleavage to generate formaldehyde, showing that the terminal high-spin Fe(IV)═O unit is capable of oxidizing a C-H bond as strong as 96 kcal mol(-1). This intramolecular oxidation of the methoxide ligand can in fact be competitive with intermolecular oxidation of triphenylmethane, which has a much weaker C-H bond (D(C-H) 81 kcal mol(-1)). The activation of the [Fe(III)Fe(IV)(μ-O)(2)] core is dramatically illustrated by the oxidation of 9,10-dihydroanthracene by 2-methoxide, which has a second-order rate constant that is 3.6 × 10(7)-fold larger than that for the parent diamond core complex 2. These observations provide strong support for the DFT-based notion that an S = 2 Fe(IV)═O unit is much more reactive at H-atom abstraction than its S = 1 counterpart and suggest that core isomerization could be a viable strategy for the [Fe(IV)(2)(μ-O)(2)] diamond core of sMMO-Q to selectively attack the strong C-H bond of methane in the presence of weaker C-H bonds of amino acid residues that define the diiron active site pocket.

Identification of the 7-hydroxymethyl chlorophyll a reductase of the chlorophyll cycle in Arabidopsis

The interconversion of chlorophyll a and chlorophyll b, referred to as the chlorophyll cycle, plays a crucial role in the processes of greening, acclimation to light intensity, and senescence. The chlorophyll cycle consists of three reactions: the conversions of chlorophyll a to chlorophyll b by chlorophyllide a oxygenase, chlorophyll b to 7-hydroxymethyl chlorophyll a by chlorophyll b reductase, and 7-hydroxymethyl chlorophyll a to chlorophyll a by 7-hydroxymethyl chlorophyll a reductase. We identified 7-hydroxymethyl chlorophyll a reductase, which is the last remaining unidentified enzyme of the chlorophyll cycle, from Arabidopsis thaliana by genetic and biochemical methods. Recombinant 7-hydroxymethyl chlorophyll a reductase converted 7-hydroxymethyl chlorophyll a to chlorophyll a using ferredoxin. Both sequence and biochemical analyses showed that 7-hydroxymethyl chlorophyll a reductase contains flavin adenine dinucleotide and an iron-sulfur center. In addition, a phylogenetic analysis elucidated the evolution of 7-hydroxymethyl chlorophyll a reductase from divinyl chlorophyllide vinyl reductase. A mutant lacking 7-hydroxymethyl chlorophyll a reductase was found to accumulate 7-hydroxymethyl chlorophyll a and pheophorbide a. Furthermore, this accumulation of pheophorbide a in the mutant was rescued by the inactivation of the chlorophyll b reductase gene. The downregulation of pheophorbide a oxygenase activity is discussed in relation to 7-hydroxymethyl chlorophyll a accumulation.

Conversion of fatty aldehydes to alka(e)nes and formate by a cyanobacterial aldehyde decarbonylase: cryptic redox by an unusual dimetal oxygenase

Cyanobacterial aldehyde decarbonylase (AD) catalyzes conversion of fatty aldehydes (R-CHO) to alka(e)nes (R-H) and formate. Curiously, although this reaction appears to be redox-neutral and formally hydrolytic, AD has a ferritin-like protein architecture and a carboxylate-bridged dimetal cofactor that are both structurally similar to those found in di-iron oxidases and oxygenases. In addition, the in vitro activity of the AD from Nostoc punctiforme (Np) was shown to require a reducing system similar to the systems employed by these O(2)-utilizing di-iron enzymes. Here, we resolve this conundrum by showing that aldehyde cleavage by the Np AD also requires dioxygen and results in incorporation of (18)O from (18)O(2) into the formate product. AD thus oxygenates, without oxidizing, its substrate. We posit that (i) O(2) adds to the reduced cofactor to generate a metal-bound peroxide nucleophile that attacks the substrate carbonyl and initiates a radical scission of the C1-C2 bond, and (ii) the reducing system delivers two electrons during aldehyde cleavage, ensuring a redox-neutral outcome, and two additional electrons to return an oxidized form of the cofactor back to the reduced, O(2)-reactive form.

Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like 'di-iron-carboxylate' proteins

Enzymes that activate dioxygen at carboxylate-bridged non-heme diiron clusters residing within ferritin-like, four-helix-bundle protein architectures have crucial roles in, among other processes, the global carbon cycle (e.g. soluble methane monooxygenase), fatty acid biosynthesis [plant fatty acyl-acyl carrier protein (ACP) desaturases], DNA biosynthesis [the R2 or β2 subunits of class Ia ribonucleotide reductases (RNRs)], and cellular iron trafficking (ferritins). Classic studies on class Ia RNRs showed long ago how this obligatorily oxidative di-iron/O2 chemistry can be used to activate an enzyme for even a reduction reaction, and more recent investigations of class Ib and Ic RNRs, coupled with earlier studies on dimanganese catalases, have shown that members of this protein family can also incorporate either one or two Mn ions and use them in place of iron for redox catalysis. These two strategies--oxidative activation for non-oxidative reactions and use of alternative metal ions--expand the catalytic repertoire of the family, probably to include activities that remain to be discovered. Indeed, a recent study has suggested that fatty aldehyde decarbonylases (ADs) from cyanobacteria, purported to catalyze a redox-neutral cleavage of a Cn aldehyde to the Cn-1 alkane (or alkene) and CO, also belong to this enzyme family and are most similar in structure to two other members with heterodinuclear (Mn-Fe) cofactors. Here, we first briefly review both the chemical principles underlying the O2-dependent oxidative chemistry of the 'classical' di-iron-carboxylate proteins and the two aforementioned strategies that have expanded their functional range, and then consider what metal ion(s) and what chemical mechanism(s) might be employed by the newly discovered cyanobacterial ADs.

Crystals in which some metal atoms are more equal than others: inequalities from crystal packing and their spectroscopic/magnetic consequences

Crystal structures of the heterometallic compounds CrCrFe(dpa)(4)Cl(2) (1), CrCrMn(dpa)(4)Cl(2) (2), and MoMoMn(dpa)(4)Cl(2) (3) (dpa = 2,2'-dipyridylamide) show disorder in the metal atom positions such that the linear M(A)[quadruple bond]M(A)···M(B) array for a given molecule in the crystal is oriented in one of two opposing directions. Despite the fact that the direct coordination sphere of the metals in the two crystallographically independent orientations is identical, subtle differences in some metal-ligand bond distances are observed in 1 and 3 due to differences in the orientation of a solvent molecule of crystallization. The Fe(II) and Mn(II) ions serve as sensitive local spectroscopic probes that have been interrogated by Mössbauer spectroscopy and high-field EPR spectroscopy, respectively. The subtle differences in the two independent Fe and Mn sites in 1 and 3 unexpectedly give rise to unusually large differences in the measured Fe quadrupole splitting (ΔE(Q)) in 1 and Mn zero-field splitting (D) in 3. Variable-temperature/single-crystal EPR spectroscopy has allowed us to determine that the temperature-dependent D tensors in 3 are oriented along the metal-metal axis and that they show significantly different dynamic behavior with temperature. The differences in ΔE(Q) and D are reproduced by density functional calculations on truncated models for 1 and 3 that lack the quadruply bonded M(A)[quadruple bond]M(A) groups, though the magnitude of the calculated effect is not as large as that observed experimentally. We suggest that the large observed differences in ΔE(Q) and D for the individual sites could be due to the influence of the strong diamagnetic anisotropy of the quadruply bonded M[quadruple bond]M unit.