Characterization of Radical SAM Adenosylhopane Synthase,HpnH, which Catalyzes the 5′‐Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C35 Bacteriohopanepolyols

Adenosylhopane is a crucial intermediate in the biosynthesis of bacteriohopanepolyols, which are widespread prokaryotic membrane lipids. Herein, it is demonstrated that reconstituted HpnH, a putative radical S‐adenosyl‐l ‐methionine (SAM) enzyme, commonly encoded in the hopanoid biosynthetic gene cluster, converts diploptene into adenosylhopane in the presence of SAM, flavodoxin, flavodoxin reductase, and NADPH. NMR spectra of the enzymatic reaction product were identical to those of synthetic (22R)‐adenosylhopane, indicating that HpnH catalyzes stereoselective C?C formation between C29 of diploptene and C5′ of 5′‐deoxyadenosine. Further, the HpnH reaction in D₂O‐containing buffer revealed that a D atom was incorporated at the C22 position of adenosylhopane. Based on these results, we propose a radical addition reaction mechanism catalyzed by HpnH for the formation of the C₃₅ bacteriohopane skeleton.     

Characterization of Radical SAM Adenosylhopane Synthase,HpnH, which Catalyzes the 5′-Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C35 Bacteriohopanepolyols

Adenosylhopane is a crucial intermediate in the biosynthesis of bacteriohopanepolyols, which are widespread prokaryotic membrane lipids. Herein, it is demonstrated that reconstituted HpnH, a putative radical S-adenosyl-l -methionine (SAM) enzyme, commonly encoded in the hopanoid biosynthetic gene cluster, converts diploptene into adenosylhopane in the presence of SAM, flavodoxin, flavodoxin reductase, and NADPH. NMR spectra of the enzymatic reaction product were identical to those of synthetic (22R)-adenosylhopane, indicating that HpnH catalyzes stereoselective C−C formation between C29 of diploptene and C5′ of 5′-deoxyadenosine. Further, the HpnH reaction in D₂O-containing buffer revealed that a D atom was incorporated at the C22 position of adenosylhopane. Based on these results, we propose a radical addition reaction mechanism catalyzed by HpnH for the formation of the C₃₅ bacteriohopane skeleton.     

Sulfonium‐Based Homolytic Substitution Observed for the Radical SAM Enzyme HemN

Sulfur‐based homolytic substitution (S_H reaction) plays an important role in synthetic chemistry, yet whether such a reaction could occur on the positively charged sulfonium compounds remains unknown. In the study of the anaerobic coproporphyrinogen III oxidase HemN, a radical S‐adenosyl‐l ‐methionine (SAM) enzyme involved in heme biosynthesis, we observed the production of di‐(5′‐deoxyadenosyl)methylsulfonium, which supports a deoxyadenosyl (dAdo) radical‐mediated S_H reaction on the sulfonium center of SAM. The sulfonium‐based S_H reactions were then investigated in detail by density functional theory calculations and model reactions, which showed that this type of reactions is thermodynamically favorable and kinetically competent. These findings represent the first report of sulfonium‐based S_H reactions, which could be useful in synthetic chemistry. Our study also demonstrates the remarkable catalytic promiscuity of the radical SAM superfamily enzymes.     

The Catalytic Mechanism of the Class C Radical S‐Adenosylmethionine Methyltransferase NosN

S ‐Adenosylmethionine (SAM) is one of the most common co‐substrates in enzyme‐catalyzed methylation reactions. Most SAM‐dependent reactions proceed through an S_N2 mechanism, whereas a subset of them involves radical intermediates for methylating non‐nucleophilic substrates. Herein, we report the characterization and mechanistic investigation of NosN, a class C radical SAM methyltransferase involved in the biosynthesis of the thiopeptide antibiotic nosiheptide. We show that, in contrast to all known SAM‐dependent methyltransferases, NosN does not produce S ‐adenosylhomocysteine (SAH) as a co‐product. Instead, NosN converts SAM into 5′‐methylthioadenosine as a direct methyl donor, employing a radical‐based mechanism for methylation and releasing 5′‐thioadenosine as a co‐product. A series of biochemical and computational studies allowed us to propose a comprehensive mechanism for NosN catalysis, which represents a new paradigm for enzyme‐catalyzed methylation reactions.     

Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN

HemN is a radical S‐adenosyl‐l ‐methionine (SAM) enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, an intermediate in heme biosynthesis. HemN binds two SAM molecules in the active site, but how these two SAMs are utilized for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III remains largely elusive. Provided here is evidence showing that in HemN catalysis a SAM serves as a hydrogen relay which mediates a radical‐based hydrogen transfer from the propionate to the 5′‐deoxyadenosyl (dAdo) radical generated from another SAM in the active site. Also observed was an unexpected shunt product resulting from trapping of the SAM‐based methylene radical by the vinyl moiety of the mono‐decarboxylated intermediate, harderoporphyrinogen. These results suggest a major revision of the HemN mechanism and reveal a new paradigm of the radical‐mediated hydrogen transfer in radical SAM enzymology.     

Hydrogen Transfer in SAM‐Mediated Enzymatic Radical Reactions

S‐Adenosylmethionine (SAM) plays an essential role in a variety of enzyme‐mediated radical reactions. One‐electron reduction of SAM is currently believed to generate the C5′‐desoxyadenosyl radical, which subsequently abstracts a hydrogen atom from the actual substrate in a catalytic or a non‐catalytic fashion. Using a combination of theoretical and experimental bond dissociation energy (BDE) data, the energetics of these radical processes have now been quantified. SAM‐derived radicals are found to react with their respective substrates in an exothermic fashion in enzymes using SAM in a stoichiometric (non‐catalytic) way. In contrast, the catalytic use of SAM appears to be linked to a sequence of moderately endothermic and exothermic reaction steps. The use of SAM in spore photoproduct lyase (SPL) appears to fit neither of these general categories and appears to constitute the first example of a SAM‐initiated radical reaction propagated independently of the cofactor.     

Biochemical Characterization of an Arginine 2,3‐Aminomutase with Dual Substrate Specificity

The radical S‐adenosylmethionine (SAM) aminomutases represent an important pathway for the biosynthesis of β‐amino acids. In this study, we report biochemical characterization of BlsG involved in blasticidin S biosynthesis as a radical SAM arginine 2,3‐aminomutase. We showed that BlsG acts on both L‐arginine and L‐lysine with comparable catalytic efficiencies. Similar dual substrate specificity was also observed for the lysine 2,3‐aminomutase from Escherichia coli (LAM_EC). The catalytic efficiency of LAM_EC is similar to that of BlsG, but is significantly lower than that of the enzyme from Clostridium subterminale (LAM_CS), which acts only on L‐lysine rather than on L‐arginine. Moreover, we showed that enzymes can be grouped into two major phylogenetic clades, each corresponding to a certain C3 stereochemistry of the β‐amino acid product. Our study expands the radical SAM aminomutase members and provides insights into enzyme evolution, supporting a trade‐off between substrate promiscuity and catalytic efficiency.     

Substrate‐Tuned Catalysis of the Radical S‐Adenosyl‐L‐Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis

NosL is a radical S‐adenosyl‐L ‐methionine (SAM) enzyme that converts L ‐Trp to 3‐methyl‐2‐indolic acid, a key intermediate in the biosynthesis of a thiopeptide antibiotic nosiheptide. In this work we investigated NosL catalysis by using a series of Trp analogues as the molecular probes. Using a benzofuran substrate 2‐amino‐3‐(benzofuran‐3‐yl)propanoic acid (ABPA), we clearly demonstrated that the 5′‐deoxyadenosyl (dAdo) radical‐mediated hydrogen abstraction in NosL catalysis is not from the indole nitrogen but likely from the amino group of L ‐Trp. Unexpectedly, the major product of ABPA is a decarboxylated compound, indicating that NosL was transformed to a novel decarboxylase by an unnatural substrate. Furthermore, we showed that, for the first time to our knowledge, the dAdo radical‐mediated hydrogen abstraction can occur from an alcohol hydroxy group. Our study demonstrates the intriguing promiscuity of NosL catalysis and highlights the potential of engineering radical SAM enzymes for novel activities.     

Mechanistic Insights into the Radical S‐adenosyl‐l‐methionine Enzyme NosL From a Substrate Analogue and the Shunt Products

The radical S‐adenosyl‐l ‐methionine (SAM) enzyme NosL catalyzes the transformation of l ‐tryptophan into 3‐methyl‐2‐indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2‐methyl‐3‐(indol‐3‐yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D₂O and H₂O unambiguously indicated that the 5′‐deoxyadenosyl (dAdo)‐radical‐mediated hydrogen abstraction is from the amino group of l ‐tryptophan and not a protein residue. Surprisingly, the dAdo‐radical‐mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β‐unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes.     

Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM

The radical S‐adenosylmethionine (SAM) superfamily enzymes cleave SAM reductively to generate a highly reactive 5′‐deoxyadenosyl (dAdo) radical, which initiates remarkably diverse reactions. Unlike most radical SAM enzymes, the class C radical SAM methyltransferase NosN binds two SAMs in the active site, using one SAM to produce a dAdo radical and the second as a methyl donor. Here, we report a mechanistic investigation of NosN in which an allyl analogue of SAM (allyl‐SAM) was used. We show that NosN cleaves allyl‐SAM efficiently and the resulting dAdo radical can be captured by the olefin moieties of allyl‐SAM or 5′‐allylthioadenosine (ATA), the latter being a derivative of allyl‐SAM. Remarkably, we found that NosN produced two distinct sets of products in the presence and absence of the methyl acceptor substrate, thus suggesting substrate‐triggered production of ATA from allyl‐SAM. We also show that NosN produces S‐adenosylhomocysteine from 5′‐thioadenosine and homoserine lactone. These results support the idea that 5′‐methylthioadenosine is the direct methyl donor in NosN reactions, and demonstrate great potential to modulate radical SAM enzymes for novel catalytic activities.     

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues

Radical S‐adenosyl‐l ‐methionine (SAM) enzymes utilize a [4Fe‐4S] cluster to bind SAM and reductively cleave its carbon–sulfur bond to produce a highly reactive 5′‐deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical‐based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical‐based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside‐containing compounds by using radical SAM‐dependent reactions.     

Sulfonium-Based Homolytic Substitution Observed for the Radical SAM Enzyme HemN

Sulfur-based homolytic substitution (S_H reaction) plays an important role in synthetic chemistry, yet whether such a reaction could occur on the positively charged sulfonium compounds remains unknown. In the study of the anaerobic coproporphyrinogen III oxidase HemN, a radical S-adenosyl-l -methionine (SAM) enzyme involved in heme biosynthesis, we observed the production of di-(5′-deoxyadenosyl)methylsulfonium, which supports a deoxyadenosyl (dAdo) radical-mediated S_H reaction on the sulfonium center of SAM. The sulfonium-based S_H reactions were then investigated in detail by density functional theory calculations and model reactions, which showed that this type of reactions is thermodynamically favorable and kinetically competent. These findings represent the first report of sulfonium-based S_H reactions, which could be useful in synthetic chemistry. Our study also demonstrates the remarkable catalytic promiscuity of the radical SAM superfamily enzymes.     

DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations

Radical S‐adenosyl‐L‐methionine (SAM) enzymes have emerged as one of the last superfamilies of enzymes discovered to date. Arguably, it is the most versatile group of enzymes involved in at least 85 biochemical transformations. One of the founding members of this enzyme superfamily is the spore photoproduct (SP) lyase, a DNA repair enzyme catalyzing the direct reversal repair of a unique DNA lesion, the so‐called spore photoproduct, back into two thymidine residues. Discovered more than 20 years ago in the bacterium Bacillus subtilis, SP lyase has been shown to be widespread in the endospore‐forming Firmicutes from the Bacilli and Clostridia classes and to use radical‐based chemistry to perform C‐C bond breakage, a chemically challenging reaction. This review describes how the work on SP lyase has illuminated a unique strategy for DNA repair and provided major advances in our understanding of the emerging radical SAM superfamily of enzymes, from a biochemical and structural perspective.     

C3′‐Deoxygenation of Paromamine Catalyzed by a Radical S‐Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3

C3′‐deoxygenation of aminoglycosides results in their decreased susceptibility to phosphorylation thereby increasing their efficacy as antibiotics. However, the biosynthetic mechanism of C3′‐deoxygenation is unknown. To address this issue, aprD4 and aprD3 genes from the apramycin gene cluster in Streptomyces tenebrarius were expressed in E. coli and the resulting gene products were characterized in vitro. AprD4 is shown to be a radical S‐adenosylmethionine (SAM) enzyme, catalyzing homolysis of SAM to 5′‐deoxyadenosine (5′‐dAdo) in the presence of paromamine. [4′‐²H]‐Paromamine was prepared and used to show that its C4′‐H is transferred to 5′‐dAdo by AprD4, during which the substrate is dehydrated to a product consistent with 4′‐oxolividamine. In contrast, paromamine is reduced to a deoxy product when incubated with AprD4/AprD3/NADPH. These results show that AprD4 is the first radical SAM diol‐dehydratase and, along with AprD3, is responsible for 3′‐deoxygenation in aminoglycoside biosynthesis.     

Thuricin Z: A Narrow‐Spectrum Sactibiotic that Targets the Cell Membrane

Sactionine‐containing antibiotics (sactibiotics) are a growing class of peptide antibiotics belonging to the ribosomally synthesized and post‐translationally modified peptide (RiPP) superfamily. We report the characterization of thuricin Z, a novel sactibiotic from Bacillus thuringiensis. Unusually, the biosynthesis of thuricin Z involves two radical S‐adenosylmethionine (SAM) enzymes, ThzC and ThzD. Although ThzC and ThzD are highly divergent from each other, these two enzymes produced the same sactionine ring in the precursor peptide ThzA in vitro. Thuricin Z exhibits narrow‐spectrum antibacterial activity against Bacillus cereus. A series of analyses, including confocal laser scanning microscopy, ultrathin‐sectioning transmission electron microscopy, scanning electron microscopy, and large‐unilamellar‐vesicle‐based fluorescence analysis, suggested that thuricin Z binds to the bacterial cell membrane and leads to membrane permeabilization.     

Quantum chemistry studies of adenosine 2503 methylation by S‐adenosylmethionine‐dependent enzymes

Ribosome methylation is important for life processes and is mainly catalyzed by radical S‐Adenosylmethionine (SAM) enzymes. Two SAM molecules serve as the cofactor by providing the 5 ′‐deoxyadenosyl radical for substrate activation and the methyl. Recently, Booker and coworkers (Science 2011, 332, 604) proposed an alternative mechanism for a pair of radical SAM enzymes, RlmN and Cfr, which respectively methylate the C2 and C8 of adenosine 2503. Their deuterium labeling experiments reveal that methyl group does not transfer directly from SAM to adenosine, instead it passes to Cys³⁵⁵ first, then onto adenosine. In this article, this new reaction mechanism is studied using density functional theory with B3LYP hybrid functional. The reaction system is simulated using small model compounds in the gas phase, and the protein environment is approximated using polarizable continuum model. The structures of the transition states and the intermediates are identified, and their free energies are calculated. The activation barriers indicate that the proposed reaction mechanism is plausible. The formation of a disulfide bond is found to be the rate‐limiting step. © 2012 Wiley Periodicals, Inc.     

Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin

BtrN encoded in the butirosin biosynthetic gene cluster possesses a CXXXCXXC motif conserved within the radical S-adenosyl methionine (SAM) superfamily. Its gene disruption in the butirosin producer Bacillus circulans caused the interruption of the biosynthetic pathway between 2-deoxy-scyllo-inosamine (DOIA) and 2-deoxystreptamine (DOS). Further, in vitro assay of the overexpressed enzyme revealed that BtrN catalyzed the oxidation of DOIA under the strictly anaerobic conditions along with consumption of an equimolar amount of SAM to produce 5'-deoxyadenosine, methionine, and 3-amino-2,3-dideoxy-scyllo-inosose (amino-DOI). Kinetic analysis showed substrate inhibition by DOIA but not by SAM, which suggests that the reaction is the Ordered Bi Ter mechanism and that SAM is the first substrate and DOIA is the second. The BtrN reaction with [3-2H]DOIA generated nonlabeled, monodeuterated and dideuterated 5'-deoxyadenosines, while no deuterium was incorporated by incubation of nonlabeled DOIA in the deuterium oxide buffer. These results indicated that the hydrogen atom at C-3 of DOIA was directly transferred to 5'-deoxyadenosine to give the radical intermediate of DOIA. Generation of nonlabeled and dideuterated 5'-deoxyadenosines proved the reversibility of the hydrogen abstraction step. The present study suggests that BtrN is an unusual radical SAM dehydrogenase catalyzing the oxidation of the hydroxyl group by a radical mechanism. This is the first report of the mechanistic study on the oxidation of a hydroxyl group by a radical SAM enzyme.     

A Water‐Bridged H‐Bonding Network Contributes to the Catalysis of the SAM‐Dependent C‐Methyltransferase HcgC

[Fe]‐hydrogenase hosts an iron‐guanylylpyridinol (FeGP) cofactor. The FeGP cofactor contains a pyridinol ring substituted with GMP, two methyl groups, and an acylmethyl group. HcgC, an enzyme involved in FeGP biosynthesis, catalyzes methyl transfer from S ‐adenosylmethionine (SAM) to C3 of 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol ( 2 ). We report on the ternary structure of HcgC/S ‐adenosylhomocysteine (SAH, the demethylated product of SAM) and 2 at 1.7 Å resolution. The proximity of C3 of substrate 2 and the S atom of SAH indicates a catalytically productive geometry. The hydroxy and carboxy groups of substrate 2 are hydrogen‐bonded with I115 and T179, as well as through a series of water molecules linked with polar and a few protonatable groups. These interactions stabilize the deprotonated state of the hydroxy groups and a keto form of substrate 2 , through which the nucleophilicity of C3 is increased by resonance effects. Complemented by mutational analysis, a structure‐based catalytic mechanism was proposed.     

Enzymatic Cascade Reactions in Biosynthesis

Enzyme‐mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron‐based enzymes use O₂ to generate high valent iron‐oxo species to homolyze unactivated C?H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S‐adenosylmethionine (SAM) to generate the 5′‐deoxyadenosyl radical as a powerful oxidant to initiate C?H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as “thwarted oxygenases”.     

Mechanistic Studies of the Radical S‐Adenosylmethionine Enzyme DesII with TDP‐D‐Fucose

DesII is a radical S‐adenosylmethionine (SAM) enzyme that catalyzes the C4‐deamination of TDP‐4‐amino‐4,6‐dideoxyglucose through a C3 radical intermediate. However, if the C4 amino group is replaced with a hydroxy group (to give TDP‐quinovose), the hydroxy group at C3 is oxidized to a ketone with no C4‐dehydration. It is hypothesized that hyperconjugation between the C4 C? N/O bond and the partially filled p orbital at C3 of the radical intermediate modulates the degree to which elimination competes with dehydrogenation. To investigate this hypothesis, the reaction of DesII with the C4‐epimer of TDP‐quinovose (TDP‐fucose) was examined. The reaction primarily results in the formation of TDP‐6‐deoxygulose and likely regeneration of TDP‐fucose. The remainder of the substrate radical partitions roughly equally between C3‐dehydrogenation and C4‐dehydration. Thus, changing the stereochemistry at C4 permits a more balanced competition between elimination and dehydrogenation.