Title: Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB
The radicalS-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon–carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys–Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys–Trp radical (Lys–Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys–Trp• intermediate by the redox-tuned [4Fe-4S]2+AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon–carbon bond-forming reactions.
Grell, Tsehai A. J.; Bell, Benjamin N.; Nguyen, Chi; Dowling, Daniel P.; Bruender, Nathan A.; Bandarian, Vahe; Drennan, Catherine L.(
, Protein Science)
Abstract
7‐Carboxy‐7‐deazaguanine synthase, QueE, catalyzes the radical mediated ring contraction of 6‐carboxy‐5,6,7,8‐tetrahydropterin, forming the characteristic pyrrolopyrimidine core of all 7‐deazaguanine natural products. QueE is a member of theS‐adenosyl‐L‐methionine (AdoMet) radical enzyme superfamily, which harnesses the reactivity of radical intermediates to perform challenging chemical reactions. Members of the AdoMet radical enzyme superfamily utilize a canonical binding motif, a CX3CXϕC motif, to bind a [4Fe‐4S] cluster, and a partial (β/α)6TIM barrel fold for the arrangement of AdoMet and substrates for catalysis. Although variations to both the cluster‐binding motif and the core fold have been observed, visualization of drastic variations in the structure of QueE fromBurkholderia multivoranscalled into question whether a re‐haul of the defining characteristics of this superfamily was in order. Surprisingly, the structure of QueE fromBacillus subtilisrevealed an architecture more reminiscent of the classical AdoMet radical enzyme. With these two QueE structures revealing varying degrees of alterations to the classical AdoMet fold, a new question arises: what is the purpose of these alterations? Here, we present the structure of a third QueE enzyme fromEscherichia coli,which establishes the middle range of the spectrum of variation observed in these homologs. With these three homologs, we compare and contrast the structural architecture and make hypotheses about the role of these structural variations in binding and recognizing the biological reductant, flavodoxin.
Broader impact statement: We know more about how enzymes are tailored for catalytic activity than about how enzymes are tailored to react with a physiological reductant. Here, we consider structural differences between three 7‐carboxy‐7‐deazaguanine synthases and how these differences may be related to the interaction between these enzymes and their biological reductant, flavodoxin.
Biomass is abundant, inexpensive and renewable, therefore, it is highly expected to play a significant role in our future energy and chemical landscapes. The US DOE has identified furanic compounds (furfural and 5-(hydroxymethyl)furfural (HMF)) as the top platform building-block chemicals that can be readily derived from biomass sources [1]. Electrocatalytic conversion of these furanic compounds is an emerging route for the sustainable production of valuable chemicals [2, 3].
In my presentation, I will first present our recent mechanistic study of electrocatlytic hydrogenation (ECH) of furfural through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies [4]. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions of each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. Understanding the underlying mechanisms enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important bio-based polymer precursors and fuels
We further studied the mechanisms on the Pb electrode, based on the potential regulated ECH and ER products. Isotopic incorporation studies and electrokinetics have confirmed ECH process to alcohol and alkyl product followed different pathways: alcohol was generated from Langmuir Hinshelwood step through surface-bound furfural and hydrogen, which is sensitive to surface structures. In contrast, alkyl product was formed through an Eley–Rideal step via surface-bound furfural and the inner-sphere protons. By modifying the electrode/electrolyte interface, we have elucidated H2O and H3O+ matters in forming alcohol and alkyl products, respectively. Dynamic oscillation studies and electron paramagnetic resonance (EPR) finally confirmed that the alcohol and dimer products shared the same intermediate. The dimer was formed through the intermediate desorption from the surface to form radicals and the self-coupling of two radicals at the bulk electrolyte.
Next, I will present electrocatalytic conversion of HMF to two biobased monomers in an H-type electrochemical cell [5]. HMF reduction (hydrogenation) to 2,5-bis(hydroxymethyl)furan (BHMF) was achieved under mild electrolyte conditions and ambient temperature using a Ag/C cathode. Meanwhile, HMF oxidation to 2,5-furandicarboxylic acid (FDCA) with ~100% efficiency was facilitated under the same conditions by a homogeneous nitroxyl radical redox mediator. We recently developed a three-electrode flow cell with an oxide-derived Ag (OD-Ag) cathode and catbon felt anode for paring elecatalytic oxidation and reduction of HMF [6]. The flow cell has a remarkably low cell voltage: from ~7.5 V to ~2.0 V by transferring the electrolysis from the H-type cell to the flow cell. This represents a more than fourfold increase in the energy efficiency at the 10 mA operation. A combined faradaic efficiency of 163% was obtained to BHMF and FDCA. Alternatively, the anodic hydrogen oxidation reaction on platinum further reduced the cell voltage to only ~0.85 V at 10 mA operation. These paired processes have shown potential for integrating renewable electricity and carbon for distributed chemical manufacturing in the future.
Luo, Jian; Davenport, Michael T.; Ess, Daniel H.; Liu, T. Leo(
, Angewandte Chemie)
Abstract
Paired redox‐neutral electrolysis offers an attractive green platform for organic synthesis by avoiding sacrificial oxidants and reductants. Carboxylates are non‐toxic, stable, inexpensive, and widely available, making them ideal nucleophiles for C−C cross‐coupling reactions. Here, we report the electro/Ni dual‐catalyzed redox‐neutral decarboxylative C(sp3)−C(sp2) cross‐coupling reactions of pristine carboxylates with aryl bromides. At a cathode, a NiII(Ar)(Br) intermediate is formed through the activation of Ar−Br bond by a NiI‐bipyridine catalyst and subsequent reduction. At an anode, the carboxylates, including amino acid, benzyl carboxylic acid, and 2‐phenoxy propionic acid, undergo oxidative decarboxylation to form carbon‐based free radicals. The combination of NiII(Ar)(Br) intermediate and carbon radical results in the formation of C(sp3)−C(sp2) cross‐coupling products. The adaptation of this electrosynthesis method to flow synthesis and valuable molecule synthesis was demonstrated. The reaction mechanism was systematically studied through electrochemical voltammetry and density functional theory (DFT) computational studies. The relationships between the electrochemical properties of carboxylates and the reaction selectivity were revealed. The electro/Ni dual‐catalyzed cross‐coupling reactions described herein expand the chemical space of paired electrochemical C(sp3)−C(sp2) cross‐coupling and represent a promising method for the construction of the C(sp3)−C(sp2) bonds because of the ubiquitous carboxylate nucleophiles and the innate scalability and flexibility of electrochemical flow‐synthesis technology.
We report relatively persistent, open‐shell thiophene‐based double helices, radical cations 1•+‐TMS12and 2•+‐TMS8. Closed‐shell neutral double helices, 1‐TMS12and 2‐TMS8, have nearly identical first oxidation potentials,E+/0 ≈ +1.33 V, corresponding to reversible oxidation to their radical cations. The radical cations are generated, using tungsten hexachloride in dichloromethane (DCM) as an oxidant,E+/0 ≈ +1.56 V. EPR spectra consist of a relatively sharp singlet peak with an unusually lowg‐value of 2.001–2.002, thus suggesting exclusive delocalization of spin density over π‐conjugated system consisting of carbon atoms only. DFT computations confirm these findings, as only negligible fraction of spin density is found on sulfur and silicon atoms and the spin density is delocalized over a single tetrathiophene moiety. For radical cation, 1•+‐TMS12, energy level of the singly occupied molecular orbital (SOMO) lies below the four highest occupied molecular orbitals (HOMOs), thus indicating the SOMO–HOMO inversion (SHI) and therefore, violating the Aufbau principle. 1•+‐TMS12has a half‐life of the order of only 5 min at room temperature. EPR peak intensity of 2•+‐TMS8, which does not show SHI, is practically unchanged over at least 2 h.
Benner, Florian; Demir, Selvan(
, Chemical Science)
The discovery of singular organic radical ligands is a formidable challenge due to high reactivity arising from the unpaired electron. Matching radical ligands with metal ions to engender magnetic coupling is crucial for eliciting preeminent physical properties such as conductivity and magnetism that are crucial for future technologies. The metal-radical approach is especially important for the lanthanide ions exhibiting deeply buried 4f-orbitals. The radicals must possess a high spin density on the donor atoms to promote strong coupling. Combining diamagnetic 89 Y ( I = 1/2) with organic radicals allows for invaluable insight into the electronic structure and spin-density distribution. This approach is hitherto underutilized, possibly owing to the challenging synthesis and purification of such molecules. Herein, evidence of an unprecedented bisbenzimidazole radical anion (Bbim 3− ˙) along with its metalation in the form of an yttrium complex, [K(crypt-222)][(Cp* 2 Y) 2 (μ-Bbim˙)] is provided. Access of Bbim 3− ˙ was feasible through double-coordination to the Lewis acidic metal ion and subsequent one-electron reduction, which is remarkable as Bbim 2− was explicitly stated to be redox-inactive in closed-shell complexes. Two molecules containing Bbim 2− (1) and Bbim 3− ˙ (2), respectively, were thoroughly investigated by X-ray crystallography, NMR and UV/Vis spectroscopy. Electrochemical studies unfolded a quasi-reversible feature and emphasize the role of the metal centre for the Bbim redox-activity as neither the free ligand nor the Bbim 2− complex led to analogous CV results. Excitingly, a strong delocalization of the electron density through the Bbim 3− ˙ ligand was revealed via temperature-dependent EPR spectroscopy and confirmed through DFT calculations and magnetometry, rendering Bbim 3− ˙ an ideal candidate for single-molecule magnet design.
Balo, Aidin R., Caruso, Alessio, Tao, Lizhi, Tantillo, Dean J., Seyedsayamdost, Mohammad R., and Britt, R. David. Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proceedings of the National Academy of Sciences 118.21 Web. doi:10.1073/pnas.2101571118.
Balo, Aidin R., Caruso, Alessio, Tao, Lizhi, Tantillo, Dean J., Seyedsayamdost, Mohammad R., & Britt, R. David. Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proceedings of the National Academy of Sciences, 118 (21). https://doi.org/10.1073/pnas.2101571118
Balo, Aidin R., Caruso, Alessio, Tao, Lizhi, Tantillo, Dean J., Seyedsayamdost, Mohammad R., and Britt, R. David.
"Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB". Proceedings of the National Academy of Sciences 118 (21). Country unknown/Code not available: Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2101571118.https://par.nsf.gov/biblio/10228914.
@article{osti_10228914,
place = {Country unknown/Code not available},
title = {Trapping a cross-linked lysine–tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB},
url = {https://par.nsf.gov/biblio/10228914},
DOI = {10.1073/pnas.2101571118},
abstractNote = {The radicalS-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon–carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys–Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys–Trp radical (Lys–Trp•) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys–Trp• intermediate by the redox-tuned [4Fe-4S]2+AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon–carbon bond-forming reactions.},
journal = {Proceedings of the National Academy of Sciences},
volume = {118},
number = {21},
publisher = {Proceedings of the National Academy of Sciences},
author = {Balo, Aidin R. and Caruso, Alessio and Tao, Lizhi and Tantillo, Dean J. and Seyedsayamdost, Mohammad R. and Britt, R. David},
}
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