Spectroscopic approaches to elucidating novel iron-sulfur chemistry in the "radical-Sam" protein superfamily

Radical SAM enzymes involved in the biosynthesis of purine-based natural products

The radical S-adenosyl-l-methionine (SAM) superfamily is a widely distributed group of iron-sulfur containing proteins that exploit the reactivity of the high energy intermediate, 5'-deoxyadenosyl radical, which is produced by the reductive cleavage of SAM, to carry-out complex radical-mediated transformations. The reactions catalyzed by radical SAM enzymes range from simple group migrations to complex reactions in protein and RNA modification. This review will highlight three radical SAM enzymes that catalyze reactions involving modified guanosines in the biosynthesis pathways of the hypermodified tRNA base wybutosine; secondary metabolites of 7-deazapurine structure, including the hypermodified tRNA base queuosine; and the redox cofactor F(420). This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.

Iron-sulfur cluster engineering provides insight into the evolution of substrate specificity among sulfonucleotide reductases

Assimilatory sulfate reduction supplies prototrophic organisms with reduced sulfur that is required for the biosynthesis of all sulfur-containing metabolites, including cysteine and methionine. The reduction of sulfate requires its activation via an ATP-dependent activation to form adenosine-5'-phosphosulfate (APS). Depending on the species, APS can be reduced directly to sulfite by APS reductase (APR) or undergo a second phosphorylation to yield 3'-phosphoadenosine-5'-phosphosulfate (PAPS), the substrate for PAPS reductase (PAPR). These essential enzymes have no human homologue, rendering them attractive targets for the development of novel antibacterial drugs. APR and PAPR share sequence and structure homology as well as a common catalytic mechanism, but the enzymes are distinguished by two features, namely, the amino acid sequence of the phosphate-binding loop (P-loop) and an iron-sulfur cofactor in APRs. On the basis of the crystal structures of APR and PAPR, two P-loop residues are proposed to determine substrate specificity; however, this hypothesis has not been tested. In contrast to this prevailing view, we report here that the P-loop motif has a modest effect on substrate discrimination. Instead, by means of metalloprotein engineering, spectroscopic, and kinetic analyses, we demonstrate that the iron-sulfur cluster cofactor enhances APS reduction by nearly 1000-fold, thereby playing a pivotal role in substrate specificity and catalysis. These findings offer new insights into the evolution of this enzyme family and extend the known functions of protein-bound iron-sulfur clusters.

S K-edge XAS and DFT calculations on SAM dependent pyruvate formate-lyase activating enzyme: nature of interaction between the Fe4S4 cluster and SAM and its role in reactivity

S K-edge X-ray absorption spectroscopy on the resting oxidized and the S-adenosyl-l-methionine (SAM) bound forms of pyruvate formate-lyase activating enzyme are reported. The data show an increase in pre-edge intensity, which is due to additional contributions from sulfide and thiolate of the Fe(4)S(4) cluster into the C-S σ* orbital. This experimentally demonstrates that there is a backbonding interaction between the Fe(4)S(4) cluster and C-S σ* orbitals of SAM in this inner sphere complex. DFT calculations that reproduce the data indicate that this backbonding is enhanced in the reduced form and that this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to the SAM, which otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier. This may provide a mechanism for generation of the 5'-deoxyadenosyl radical upon substrate binding.

Complex biotransformations catalyzed by radical S-adenosylmethionine enzymes

The radical S-adenosylmethionine (AdoMet) superfamily currently comprises thousands of proteins that participate in numerous biochemical processes across all kingdoms of life. These proteins share a common mechanism to generate a powerful 5'-deoxyadenosyl radical, which initiates a highly diverse array of biotransformations. Recent studies are beginning to reveal the role of radical AdoMet proteins in the catalysis of highly complex and chemically unusual transformations, e.g. the ThiC-catalyzed complex rearrangement reaction. The unique features and intriguing chemistries of these proteins thus demonstrate the remarkable versatility and sophistication of radical enzymology.

Probing the reaction mechanism of spore photoproduct lyase (SPL) via diastereoselectively labeled dinucleotide SP TpT substrates

5-Thyminyl-5,6-dihydrothymine (commonly called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is generated in the bacterial sporulation phase and repaired by a radical SAM enzyme, spore photoproduct lyase (SPL), at the early germination phase. SPL utilizes a special [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) to generate a reactive 5'-dA radical. The 5'-dA radical is proposed to abstract one of the two H-atoms at the C6 carbon of SP to initiate the repair process. Via organic synthesis and DNA photochemistry, we selectively labeled the 6-H(proS) or 6-H(proR) position with a deuterium in a dinucleotide SP TpT substrate. Monitoring the deuterium migration in enzyme catalysis (employing Bacillus subtilis SPL) revealed that it is the 6-H(proR) atom of SP that is abstracted by the 5'-dA radical. Surprisingly, the abstracted deuterium was not returned to the resulting TpT after enzymatic catalysis; an H-atom from the aqueous buffer was incorporated into TpT instead. This result questions the currently hypothesized SPL mechanism which excludes the involvement of protein residue(s) in SPL reaction, suggesting that some protein residue(s), which is capable of exchanging a proton with the aqueous buffer, is involved in the enzyme catalysis. Moreover, evidence has been obtained for a possible SAM regeneration after each catalytic cycle; however, such a regeneration process is more complex than currently thought, with one or even more protein residues involved as well. These observations have enabled us to propose a modified reaction mechanism for this intriguing DNA repair enzyme.

Characterization of NocL involved in thiopeptide nocathiacin I biosynthesis: a [4Fe-4S] cluster and the catalysis of a radical S-adenosylmethionine enzyme

The radical S-adenosylmethionine (AdoMet) enzyme superfamily is remarkable at catalyzing chemically diverse and complex reactions. We have previously shown that NosL, which is involved in forming the indole side ring of the thiopeptide nosiheptide, is a radical AdoMet enzyme that processes L-Trp to afford 3-methyl-2-indolic acid (MIA) via an unusual fragmentation-recombination mechanism. We now report the expansion of the MIA synthase family by characterization of NocL, which is involved in nocathiacin I biosynthesis. EPR and UV-visible absorbance spectroscopic analyses demonstrated the interaction between L-Trp and the [4Fe-4S] cluster of NocL, leading to the assumption of nonspecific interaction of [4Fe-4S] cluster with other nucleophiles via the unique Fe site. This notion is supported by the finding of the heterogeneity in the [4Fe-4S] cluster of NocL in the absence of AdoMet, which was revealed by the EPR study at very low temperature. Furthermore, a free radical was observed by EPR during the catalysis, which is in good agreement with the hypothesis of a glycyl radical intermediate. Combined with the mutational analysis, these studies provide new insights into the function of the [4Fe-4S] cluster of radical AdoMet enzymes as well as the mechanism of the radical-mediated complex carbon chain rearrangement catalyzed by MIA synthase.

The single-domain globin of Vitreoscilla: augmentation of aerobic metabolism for biotechnological applications

Extensive studies have revealed that large-scale, high-cell density bioreactor cultivations have significant impact on metabolic networks of oxygen-requiring production organisms. Oxygen transfer problems associated with fluid dynamics and inefficient mixing efficiencies result in oxygen gradients, which lead to reduced performance of the bioprocess, decreased product yields, and increased production costs. These problems can be partially alleviated by improving bioreactor configuration and setting, but significant improvements have been achieved by metabolic engineering methods, especially by heterologously expressing Vitreoscilla hemoglobin (VHb). Vast numbers of studies have been accumulating during the past 20 years showing the applicability of VHb to improve growth and product yields in a variety of industrially significant prokaryotic and eukaryotic hosts. The global view on the metabolism of globin-expressing Escherichia coli cells depicts increased energy generation, higher oxygen uptake rates, and a decrease in fermentative by-product excretion. Transcriptome and metabolic flux analysis clearly demonstrate the multidimensional influence of heterologous VHb on the expression of stationary phase-specific genes and on the regulation of cellular metabolic networks. The exact biochemical mechanisms by which VHb is able to improve the oxygen-limited growth remain poorly understood. The suggested mechanisms propose either the delivery of oxygen to the respiratory chain or the detoxification of reactive nitrogen species for the protection of cytochrome activity. The expression of VHb in E. coli bioreactor cultures is likely to assist bacterial growth through providing an increase in available intracellular oxygen, although to fully understand the exact role of VHb in vivo, further analysis will be required.

Mechanistic and functional versatility of radical SAM enzymes

Enzymes of the radical SAM (RS) superfamily catalyze a diverse assortment of reactions that proceed via intermediates containing unpaired electrons. The radical initiator is the common metabolite S-adenosyl-l-methionine (SAM), which is reductively cleaved to generate a 5′-deoxyadenosyl 5′-radical, a universal and obligate intermediate among enzymes within this class. A bioinformatics study that appeared in 2001 indicated that this superfamily contained over 600 members, many catalyzing reactions that were rich in novel chemical transformations. Since that seminal study, the RS superfamily has grown immensely, and new details about the scope of reactions and biochemical pathways in which its members participate have emerged. This review will highlight only a few of the most significant findings from the past 2-3 years, focusing primarily on: RS enzymes involved in complex metallocofactor maturation; characterized RS enzymes that lack the canonical CxxxCxxC motif; RS enzymes containing multiple iron-sulfur clusters; RS enzymes catalyzing reactions with compelling medical implications; and the energetics and mechanism of generating the 5′-deoxyadenosyl radical. A number of significant studies of RS enzymes will unfortunately be omitted, and it is hoped that the reader will access the relevant literature - particularly a number of superb review articles recently written on the subject - to acquire a deeper appreciation of this class of enzymes.

Pyruvate formate-lyase, evidence for an open conformation favored in the presence of its activating enzyme

Pyruvate formate-lyase-activating enzyme (PFL-AE) activates pyruvate formate-lyase (PFL) by generating a catalytically essential radical on Gly-734 of PFL. Crystal structures of unactivated PFL reveal that Gly-734 is buried 8 A from the surface of the protein in what we refer to here as the closed conformation of PFL. We provide here the first experimental evidence for an alternate open conformation of PFL in which: (i) the glycyl radical is significantly less stable; (ii) the activated enzyme exhibits lower catalytic activity; (iii) the glycyl radical undergoes less H/D exchange with solvent; and (iv) the T(m) of the protein is decreased. The evidence suggests that in the open conformation of PFL, the Gly-734 residue is located not in its buried position in the enzyme active site but rather in a more solvent-exposed location. Further, we find that the presence of the PFL-AE increases the proportion of PFL in the open conformation; this observation supports the idea that PFL-AE accesses Gly-734 for direct hydrogen atom abstraction by binding to the Gly-734 loop in the open conformation, thereby shifting the closed <--> open equilibrium of PFL to the right. Together, our results lead to a model in which PFL can exist in either a closed conformation, with Gly-734 buried in the active site of PFL and harboring a stable glycyl radical, or an open conformation, with Gly-734 more solvent-exposed and accessible to the PFL-AE active site. The equilibrium between these two conformations of PFL is modulated by the interaction with PFL-AE.

A consensus mechanism for Radical SAM-dependent dehydrogenation? BtrN contains two [4Fe-4S] clusters

BtrN catalyzes the two-electron oxidation of the C3 secondary alcohol of 2-deoxy-scyllo-inosamine to the corresponding ketone and is a member of a subclass of radical S-adenosylmethionine (SAM) enzymes called radical SAM (RS) dehydrogenases. Like all RS enzymes, BtrN contains a [4Fe-4S] cluster that delivers an electron to SAM, inducing its cleavage to the common intermediate in RS reactions, the 5'-deoxyadenosyl 5'-radical. In this work, we show that BtrN contains an additional [4Fe-4S] cluster, thought to bind in contact with the substrate to facilitate loss of the second electron in the two-electron oxidation.

Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase

Spore photoproduct lyase (SP lyase), a member of the radical S-adenosylmethionine superfamily of enzymes, catalyzes the repair of 5-thyminyl-5,6-dihydrothymine [spore photoproduct (SP)], a type of UV-induced DNA damage unique to bacterial spores. The anaerobic purification and characterization of Clostridium acetobutylicum SP lyase heterologously expressed in Escherichia coli, and its catalytic activity in repairing stereochemically defined synthetic dinucleotide SPs was investigated. The purified enzyme contains between 2.3 and 3.1 iron atoms per protein. Electron paramagnetic resonance (EPR) spectroscopy reveals an isotropic signal centered at g = 1.99, characteristic of a [3Fe-4S](+) cluster accounting for 3-4% of the iron in the sample. Upon reduction, a nearly axial signal (g = 2.03, 1.93 and 1.92) characteristic of a [4Fe-4S](+) cluster is observed that accounts for 34-45% of total iron. Addition of S-adenosylmethionine to the reduced enzyme produces a rhombic signal (g = 2.02, 1.93, 1.82) unique to the S-adenosyl-L: -methionine complex while decreasing the overall EPR intensity. This reduced enzyme is shown to rapidly and completely repair the 5R diastereomer of a synthetic dinucleotide SP with a specific activity of 7.1 +/- 0.6 nmol min(-1) mg(-1), whereas no repair was observed for the 5S diastereomer.

The antiviral protein viperin is a radical SAM enzyme

Viperin, an interferon-inducible antiviral protein, is shown to bind an iron-sulfur cluster, based on iron analysis as well as UV-Vis and electron paramagnetic resonance spectroscopic data. The reduced protein contains a [4Fe-4S](1+) cluster whose g-values are altered upon addition of S-adenosylmethionine (SAM), consistent with SAM coordination to the cluster. Incubation of reduced viperin with SAM results in reductive cleavage of SAM to produce 5'-deoxyadenosine (5'-dAdo), a reaction characteristic of the radical SAM superfamily. The 5'-dAdo cleavage product was identified by a combination of HPLC and mass spectrometry analysis.

Pyrroloquinoline quinone biogenesis: demonstration that PqqE from Klebsiella pneumoniae is a radical S-adenosyl-L-methionine enzyme

Biogenesis of pyrroloquinoline quinone (PQQ) in Klebsiella pneumoniae requires the expression of six genes (pqqA-F). One of these genes (pqqE) encodes a 43 kDa protein (PqqE) that plays a role in the initial steps in PQQ formation [Veletrop, J. S., et al. (1995) J. Bacteriol. 177, 5088-5098]. PqqE contains two highly conserved cysteine motifs at the N- and C-termini, with the N-terminal motif comprised of a CX(3)CX(2)C consensus sequence that is unique to a family of proteins known as radical S-adenosyl-l-methionine (SAM) enzymes [Sofia, H. J., et al. (2001) Nucleic Acids Res. 29, 1097-1106]. PqqE from K. pneumoniae was cloned into Escherichia coli and expressed as the native protein and with an N-terminal His(6) tag. Anaerobic expression and purification of the His(6)-tagged PqqE results in an enzyme with a brownish-red hue indicative of Fe-S cluster formation. Spectroscopic and physical analyses indicate that PqqE contains a mixture of Fe-S clusters, with the predominant form of the enzyme containing two [4Fe-4S] clusters. PqqE isolated anaerobically yields an active enzyme capable of cleaving SAM to methionine and 5'-deoxyadenosine in an uncoupled reaction (k(obs) = 0.011 +/- 0.001 min(-1)). In this reaction, the 5'-deoxyadenosyl radical either abstracts a hydrogen atom from a solvent accessible position in the enzyme or obtains a proton and electron from buffer. The putative PQQ substrate PqqA has not yet been shown to be modified by PqqE, implying that PqqA must be modified before becoming the substrate for PqqE and/or that another protein in the biosynthetic pathway is critical for the initial steps in PQQ biogenesis.

Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily

RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of Asp88 of the small ribosomal protein S12 [Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831]. To date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modifications have been observed on tRNA. All members of the methylthiotransferase (MTTase) family, to which RimO belongs, have been shown to contain the canonical CxxxCxxC motif in their primary structures that is typical of the radical S-adenosylmethionine (SAM) family of proteins. MiaB, the only characterized MTTase, and the enzyme experimentally shown to be responsible for methylthiolation of N(6)-isopentenyladenosine of tRNA in E. coli and Thermotoga maritima, has been demonstrated to harbor two distinct [4Fe-4S] clusters. Herein, we report in vitro biochemical and spectroscopic characterization of RimO. We show by analytical and spectroscopic methods that RimO, overproduced in E. coli in the presence of iron-sulfur cluster biosynthesis proteins from Azotobacter vinelandii, contains one [4Fe-4S](2+) cluster. Reconstitution of this form of RimO (RimO(rcn)) with (57)Fe and sodium sulfide results in a protein that contains two [4Fe-4S](2+) clusters, similar to MiaB. We also show by mass spectrometry that RimO(rcn) catalyzes the attachment of a methylthio group to a peptide substrate analogue that mimics the loop structure bearing aspartyl 88 of the S12 ribosomal protein from E. coli. Kinetic analysis of this reaction shows that the activity of RimO(rcn) in the presence of the substrate analogue does not support a complete turnover. We discuss the possible requirement for an assembled ribosome for fully active RimO in vitro. Our findings are consistent with those of other enzymes that catalyze sulfur insertion, such as biotin synthase, lipoyl synthase, and MiaB.

The iron-sulfur cluster of pyruvate formate-lyase activating enzyme in whole cells: cluster interconversion and a valence-localized [4Fe-4S]2+ state

Pyruvate formate-lyase activating enzyme (PFL-AE) catalyzes the generation of a catalytically essential glycyl radical on pyruvate formate-lyase (PFL). Purified PFL-AE contains an oxygen-sensitive, labile [4Fe-4S] cluster that undergoes cluster interconversions in vitro, with only the [4Fe-4S](+) cluster state being catalytically active. Such cluster interconversions could play a role in regulating the activity of PFL-AE, and thus of PFL, in response to oxygen levels in vivo. Here we report a Mossbauer investigation on whole cells overexpressing PFL-AE following incubation under aerobic and/or anaerobic conditions and provide evidence that PFL-AE undergoes cluster interconversions in vivo. After 2 h aerobic induction of PFL-AE expression, approximately 44% of the total iron is present in [4Fe-4S](2+) clusters, 6% in [2Fe-2S](2+) clusters, and the remainder as noncluster Fe(III) (29%) and Fe(II) (21%) species. Subsequent anaerobic incubation of the culture results in approximately 75% of the total iron being present as [4Fe-4S](2+) clusters, with no detectable [2Fe-2S](2+). Ensuing aerobic incubation of the culture converts the iron species nearly back to the original composition (42% [4Fe-4S](2+), 10% [2Fe-2S](2+), 19% Fe(III), and 29% Fe(II)). The results provide evidence for changes in cluster composition of PFL-AE in response to the redox state of the cell. Furthermore, the Mossbauer spectra reveal that the [4Fe-4S](2+) cluster of PFL-AE in whole cells contains a valence-localized Fe(III)Fe(II) pair which has not been previously observed in the purified enzyme. Addition of certain small molecules containing adenosyl moieties, including 5'-deoxyadenosine, AMP, ADP, and methylthioadenosine, to purified PFL-AE reproduces the valence-localized state of the [4Fe-4S](2+) cluster. It is speculated that the [4Fe-4S](2+) cluster of PFL-AE in whole cells may be coordinated by a small molecule, probably AMP, and that such coordination may protect this labile cluster from oxidative damage.

Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins

Radical S-adenosine-L-methionine (SAM or AdoMet) proteins are involved in chemically difficult reactions including the synthesis of cofactors, the generation of protein radicals, and the maturation of complex organometallic catalytic sites. In the first and common step of the reaction, a conserved [Fe4S4] cluster donates an electron to perform the reductive cleavage of AdoMet into methionine and a reactive radical 5'-dA. species. The latter extracts a hydrogen atom from substrate eliciting one of the about 40 reactions so far characterized for this family of proteins. It has been suggested that the radical-generating mechanism differs depending on whether AdoMet is a cofactor or a substrate. It has also been speculated that electron transfer from the [Fe4S4] cluster to AdoMet is sulfur-based. Here we have used protein crystallography and theoretical calculations to show that regardless whether AdoMet serves as a cofactor or a substrate, the 5'-dA. generating mechanism should be common to the radical SAM proteins studied so far, and that electron transfer is mediated by a unique Fe from the conserved [Fe4S4] cluster. This unusual electron transfer is determined by the sulfonium ion in AdoMet.

Cleavage of [4Fe-4S]-type clusters: breaking the symmetry

The cleavage of [4Fe-4S]-type clusters is thought to be important in proteins such as Fe-S scaffold proteins and nitrogenase. However, most [4Fe-4S](2+) clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe(2.5+)-Fe(2.5+) pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe-4S] core into two [2Fe-2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe(3+)-Fe(2+) pairs. Cleavage first through the weak Fe(2+)-S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe(4)S(4)L(4)](2-) (L = SCH(3), Cl, H) and heteroligand [Fe(4)S(4)(SCH(3))(2)L(2)](2-) (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe-4S] cluster in their biological function might have spin-localized [4Fe-4S] clusters.

Subunit structure of benzylsuccinate synthase

Benzylsuccinate synthase is a member of the glycyl radical family of enzymes. It catalyzes the addition of toluene to fumarate to form benzylsuccinate as the first step in the anaerobic pathway of toluene fermentation. The enzyme comprises three subunits, alpha, beta, and gamma, that in Thauera aromatica strain T1 are encoded by the tutD, tutG, and tutF genes, respectively. The large alpha-subunit contains the essential glycine and cysteine residues that are conserved in all glycyl radical enzymes. However, the function of the small beta- and gamma-subunits has remained unclear. We have overexpressed all three subunits of benzylsuccinate synthase in Escherichia coli, both individually and in combination. Coexpression of the gamma-subunit (but not the beta-subunit) is essential for efficient expression of the alpha-subunit. The benzylsuccinate synthase complex lacking the glycyl radical could be purified as an alpha(2)beta(2)gamma(2) hexamer by nickel affinity chromatography through a "His(6)" affinity tag engineered onto the C-terminus of the alpha-subunit. Unexpectedly, BSS was found to contain two iron-sulfur clusters, one associated with the beta-subunit and the other with the gamma-subunit that appear to be necessary for the structural integrity of the complex. The spectroscopic properties of these clusters suggest that they are most likely [4Fe-4S] clusters. Removal of iron with chelating agents results in dissociation of the complex; similarly, a mutant gamma-subunit lacking the [4Fe-4S] cluster is unable to stabilize the alpha-subunit when the proteins are coexpressed.

Anaerobic functionalization of unactivated C-H bonds

The functionalization of alkanes was once thought to lie strictly within the domain of enzymes that activate dioxygen in order to generate an oxidant with suitable potency to cleave inert C-H bonds. The emergence of the radical SAM superfamily of enzymes-those which use S-adenosyl-l-methionine as a precursor to a 5'-deoxyadenosyl 5'-radical-has kindled a renaissance in the study of radical-dependent enzymatic reactions, and is ushering in a wealth of new and intriguing chemistry that remains to be elucidated. This review will focus on a special subclass of radical SAM enzymes that functionalize inert C-H bonds, highlighting the functional groups and the chemistry that leads to their insertion. Within this class are first, enzymes that catalyze sulfur insertion, the prototype of which is biotin synthase; second, enzymes that catalyze P-methylation or C-methylation, such as P-methylase or Fom3; third, enzymes that catalyze oxygen insertion, such as the anaerobic magnesium protoporphyrin-IX oxidative cyclase (BchE); and fourth, enzymes that functionalize n-hexane or other alkanes as the first step in the metabolism of these inert compounds by certain bacteria. In addition to surveying reactions that have been studied at various levels of detail, this review will speculate on the mechanisms of other types of reactions that this chemistry lends itself to.

Control of radical chemistry in the AdoMet radical enzymes

The radical AdoMet superfamily comprises a diverse set of >2800 enzymes that utilize iron-sulfur clusters and S-adenosylmethionine (SAM or AdoMet) to initiate a diverse set of radical-mediated reactions. The intricate control these enzymes exercise over the radical transformations they catalyze is an amazing feat of elegance and sophistication in biochemistry. This review focuses on the accumulating evidence for how these enzymes control this remarkable chemistry, including controlling the reactivity between the iron-sulfur cluster and AdoMet, and controlling the subsequent radical transformations.

Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme

Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.

Iron–sulfur proteins as initiators of radical chemistry

Iron-sulfur proteins are very versatile biological entities for which many new functions are continuously being unravelled. This review focus on their role in the initiation of radical chemistry, with special emphasis on radical-SAM enzymes, since several members of the family catalyse key steps in the biosynthetic pathways of cofactors such as biotin, lipoate, thiamine, heme and the molybdenum cofactor. It will also include other examples to show the chemical logic which is emerging from the presently available data on this family of enzymes. The common step in all the (quite different) reactions described here is the monoelectronic reductive cleavage of SAM by a reduced [4Fe-4S](1+) cluster, producing methionine and a highly oxidising deoxyadenosyl radical, which can initiate chemically difficult reactions. This set of enzymes, which represent a means to perform oxidation under reductive conditions, are often present in anaerobic organisms. Some other, non-SAM-dependent, radical reactions obeying the same chemical logic are also covered.

Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms

The photobiological production of H2 gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H(2) production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O2 sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications.

Maturation of hydrogenases

Enzymes possessing the capacity to oxidize molecular hydrogen have developed convergently three class of enzymes leading to: [FeFe]-, [NiFe]-, and [FeS]-cluster-free hydrogenases. They differ in the composition and the structure of the active site metal centre and the sequence of the constituent structural polypeptides but they show one unifying feature, namely the existence of CN and/or CO ligands at the active site Fe. Recent developments in the analysis of the maturation of [FeFe]- and [NiFe]- hydrogenases have revealed a remarkably complex pattern of mostly novel biochemical reactions. Maturation of [FeFe]-hydrogenases requires a minimum of three auxiliary proteins, two of which belong to the class of Radical-SAM enzymes and other to the family of GTPases. They are sufficient to generate active enzyme when their genes are co-expressed with the structural genes in a heterologous host, otherwise deficient in [FeFe]-hydrogenase expression. Maturation of the large subunit of [NiFe]-hydrogenases depends on the activity of at least seven core proteins that catalyse the synthesis of the CN ligand, have a function in the coordination of the active site iron, the insertion of nickel and the proteolytic maturation of the large subunit. Whereas this core maturation machinery is sufficient to generate active hydrogenase in the cytoplasm, like that of hydrogenase 3 from Escherichia coli, additional proteins are involved in the export of the ready-assembled heterodimeric enzyme to the periplasm via the twin-arginine translocation system in the case of membrane-bound hydrogenases. A series of other gene products with intriguing putative functions indicate that the minimal pathway established for E. coli [NiFe]-hydrogenase maturation may possess even higher complexity in other organisms.

Characterization of an Active Spore Photoproduct Lyase, a DNA Repair Enzyme in the Radical S-Adenosylmethionine Superfamily

The major photoproduct in UV-irradiated Bacillus spore DNA is a unique thymine dimer called spore photoproduct (SP, 5-thyminyl-5,6-dihydrothymine). The enzyme spore photoproduct lyase (SP lyase) has been found to catalyze the repair of SP dimers to thymine monomers in a reaction that requires S-adenosylmethionine. We present here the first detailed characterization of catalytically active SP lyase, which has been anaerobically purified from overexpressing Escherichia coli. Anaerobically purified SP lyase is monomeric and is red-brown in color. The purified enzyme contains approximately 3.1 iron and 3.0 acid-labile S(2-) per protein and has a UV-visible spectrum characteristic of iron-sulfur proteins (410 nm (11.9 mM(-1) cm(-1)) and 450 nm (10.5 mM(-1) cm(-1))). The X-band EPR spectrum of the purified enzyme shows a nearly isotropic signal (g = 2.02) characteristic of a [3Fe-4S]1+ cluster; reduction of SP lyase with dithionite results in the appearance of a new EPR signal (g = 2.03, 1.93, and 1.89) with temperature dependence and g values consistent with its assignment to a [4Fe-4S]1+ cluster. The reduced purified enzyme is active in SP repair, with a specific activity of 0.33 micromol/min/mg. Only a catalytic amount of S-adenosylmethionine is required for DNA repair, and no irreversible cleavage of S-adenosylmethionine into methionine and 5'-deoxyadenosine is observed during the reaction. Label transfer from [5'-3H]S-adenosylmethionine to repaired thymine is observed, providing evidence to support a mechanism in which a 5'-deoxyadenosyl radical intermediate directly abstracts a hydrogen from SP C-6 to generate a substrate radical, and subsequent to radical-mediated beta-scission, a product thymine radical abstracts a hydrogen from 5'-deoxyadenosine to regenerate the 5'-deoxyadenosyl radical. Together, our results support a mechanism in which S-adenosylmethionine acts as a catalytic cofactor, not a substrate, in the DNA repair reaction.

New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria

During the last decade, an increasing number of new enzymes containing glycyl radicals in their active sites have been identified and biochemically characterised. These include benzylsuccinate synthase (Bss), 4-hydroxyphenylacetate decarboxylase (Hpd) and the coenzyme B12-independent glycerol dehydratase (Gdh). These are involved in metabolic pathways as different as anaerobic toluene metabolism, fermentative production of p-cresol and glycerol fermentation. Some features of these newly discovered enzymes are described and compared with those of the previously known glycyl radical enzymes pyruvate formate-lyase (Pfl) and anaerobic ribonucleotide reductase (Nrd). Among the new enzymes, Bss and Hpd share the presence of small subunits, the function of which in the catalytic mechanisms is still enigmatic, and both enzymes contain metal centres in addition to the glycyl radical prosthetic group. The activating enzymes of the novel systems also deviate from the standard type, containing at least one additional Fe-S cluster. Finally, the available whole-genome sequences of an increasing number of strictly or facultative anaerobic bacteria revealed the presence of many more hitherto unknown glycyl radical enzyme (GRE) systems. Recent studies suggest that the particular types of these enzymes represent the ends of different evolutionary lines, which emerged early in evolution and diversified to yield remarkably versatile biocatalysts for chemical reactions that are otherwise difficult to perform in anoxic environments.