Experimental Correlation of Substrate Position with Reaction Outcome in the Aliphatic Halogenase, SyrB2

Martinie, Ryan J.; Livada, Jovan; Chang, Wei‐chen; Green, Michael T.; Krebs, Carsten; Bollinger, J. Martin; Silakov, Alexey

doi:10.1021/jacs.5b03370

Cited by 100 publications

(225 citation statements)

References 54 publications

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“…[44,232] Recent experiments fit well into the overall picture. [233] At the same time, it seems that intrinsic properties of the metal complex may also play a role here, as it was found that the synthetic [Fe IV (O)(TPA)Cl] + complex has an appreciable preference toward rebound to the ligand in the cis position with respect to the amine nitrogen of TPA, as a result of the different bond strengths. [234] However, it is noteworthy that the rebound reactivity/selectivity of low-weight synthetic complexes can be considerably influenced by radical escape from the solvent cage and its reaction with other species in solution.…”

Section: Chemoselectivitymentioning

confidence: 87%

Mono- and binuclear non-heme iron chemistry from a theoretical perspective

et al. 2016

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In this minireview, we provide an account of the current state-of-the-art developments in the area of mono-and binuclear non-heme enzymes (NHFe and NHFe2) and the smaller NHFe(2) synthetic models, mostly from a theoretical and computational perspective. The sheer complexity, and at the same time the beauty, of the NHFe(2) world represent a challenge for both experimental as well as theoretical methods. We emphasize that the concerted progress on both theoretical and experimental side is a conditio sine qua non for future understanding, exploration and utilization of the NHFe(2) systems.After briefly discussing the current challenges and advances in the computational methodology, we review the recent spectroscopic and computational studies of NHFe(2) enzymatic and inorganic systems and highlight the correlations between various experimental data (spectroscopic, kinetic, thermodynamic, electrochemical) and computations. Throughout, we attempt to keep in mind the most fascinating and attractive phenomenon in the NHFe(2) chemistry which is the fact that despite the strong oxidative power of many reactive intermediates, the NHFe(2) enzymes perform catalysis with high selectivity. We conclude with our personal viewpoint and hope that further developments in quantum chemistry and especially in the field of multireference wave function methods are needed to have a solid theoretical basis for the NHFe(2) studies, mostly by providing benchmarking and calibration of the computationally efficient and easy-to-use DFT methods.

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Section: Chemoselectivitymentioning

confidence: 87%

Mono- and binuclear non-heme iron chemistry from a theoretical perspective

et al. 2016

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“…Some characterized examples include the nonheme dinuclear iron ribonucleotide reductase (RNR R2) (18,19) and mononuclear iron halogenase SyrB2 (20-22). The mechanisms for RNR and SyrB2 highlight the importance of quaternary structural elements, an extensive 35-Å proton-coupled electron transfer pathway in RNR (23), and extremely subtle (subangstrom) substrate positional tuning (SyrB2) (21,22), to enable efficient circumvention from the monooxygenation reaction coordinate.P450-I has also been linked to a number of important transformations in which an oxygen rebound step is not readily observed, including the desaturation of pharmaceuticals by liver P450s to afford hepatotoxic metabolites (24) and the C−C lyase activity of human P450 aromatase that is critical for estrogen biosynthesis (25), among others (26, 27). However, unambiguous determination of the oxidant responsible and operant mechanism for these aberrant P450 transformations has met significant challenges.…”

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confidence: 99%

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confidence: 99%

Catalytic strategy for carbon−carbon bond scission by the cytochrome P450 OleT

Grant

Mitchell

Makris

2016

Proc. Natl. Acad. Sci. U.S.A.

102

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OleT is a cytochrome P450 that catalyzes the hydrogen peroxidedependent metabolism of C n chain-length fatty acids to synthesize C n-1 1-alkenes. The decarboxylation reaction provides a route for the production of drop-in hydrocarbon fuels from a renewable and abundant natural resource. This transformation is highly unusual for a P450, which typically uses an Fe 4+ −oxo intermediate known as compound I for the insertion of oxygen into organic substrates. OleT, previously shown to form compound I, catalyzes a different reaction. A large substrate kinetic isotope effect (≥8) for OleT compound I decay confirms that, like monooxygenation, alkene formation is initiated by substrate C−H bond abstraction. Rather than finalizing the reaction through rapid oxygen rebound, alkene synthesis proceeds through the formation of a reaction cycle intermediate with kinetics, optical properties, and reactivity indicative of an Fe 4+ −OH species, compound II. The direct observation of this intermediate, normally fleeting in hydroxylases, provides a rationale for the carbon−carbon scission reaction catalyzed by OleT.C ytochrome P450 (CYP) enzymes catalyze an extraordinary breadth of physiologically important oxidations for xenobiotic detoxification and specialized biosynthetic pathways (1, 2). The metabolic diversity of CYP enzymes originates from a sophisticated interplay of substrate molecular recognition with precise tuning of metal oxygen species formed at the enzyme active site. CYPs use a thiolate-ligated heme iron cofactor to activate molecular oxygen and produce short-lived ferric superoxo (3-5), ferric (hydro)peroxo (6-8), and ferryl (9, 10) intermediates. Coordinated efforts over several decades have resulted in isolation of each intermediate, including recent characterization of the principal oxidant thought to be responsible for the vast majority of P450 oxidations, the Fe 4+ −oxo pi−cation radical species commonly referred to as compound I (or P450-I) (10).The archetypal P450 hydroxylation involves C−H bond abstraction by P450-I and ensuing rapid oxygen insertion through a recombination process termed "oxygen rebound" (11, 12). The hydrogen abstraction/rebound mechanism describes the strategy used for most P450 transformations, and is thought to describe catalysis by numerous metal-dependent oxygenases and synthetic bio-inspired metal−oxo complexes (e.g., refs. 13-17). Despite the ubiquity of this mechanism, in some metalloenzymes, a metal−oxo species is formed that is not ultimately destined for incorporation into a substrate. Some characterized examples include the nonheme dinuclear iron ribonucleotide reductase (RNR R2) (18,19) and mononuclear iron halogenase SyrB2 (20-22). The mechanisms for RNR and SyrB2 highlight the importance of quaternary structural elements, an extensive 35-Å proton-coupled electron transfer pathway in RNR (23), and extremely subtle (subangstrom) substrate positional tuning (SyrB2) (21,22), to enable efficient circumvention from the monooxygenation reaction coordinate.P450-I has also been link...

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“…Transposon mutagenesis performed by Xu and Gross (1988) and Zhang and Gross (1995) has proven that a chromosomal region larger than 25 kb is involved in the biosynthesis of SRE. Within this region, four genes, namely, syrB, syrC, syrD and syrP have been sequenced and partially characterized (Martinie et al, 2015;Singh et al, 2007;Gross, 1991;Zhang and Gross, 1997;Quigley et al, 1993). SyrD has similar sequence to the ATP binding cassette transporter superfamily, thus, it is hypothesized that syrD product is involved in the transportation of SRE across the cytoplasmic membrane (Quigley et al, 1993).…”

Section: Discussionmentioning

confidence: 99%

Enhancing the production of syringomycin E in Pseudomonas syringae pv syringae by random mutagenesis and molecular characterization of the SyrB1 gene

Trieu¹,

Huyen²,

Tra³

et al. 2017

Afr. J. Biotechnol.

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Syringomycin E (SRE) is a phytotoxin produced by Pseudomonas syringae pv syringae with high potential as a safe and effective therapy for the control of human fungal infections and as a preservative for the food industry. In this study, 27 strains of P. syringae pv syringae were isolated from plums, potatoes, apricots and peaches, of which P. syringae pv syringae 120 (PS120) showed the highest SRE production levels. Furthermore, random mutagenesis induced by ultraviolet (UV) radiation resulted in the generation of a P. syringae pv syringae mutant that produced 30% more SRE than the parental strain PS120. To elucidate molecular mechanism underlying the higher SRE production ability of the mutant strain, syrB1 and syrB2 genes, which are known to be involved in SRE production, were cloned and sequenced. The nucleotide and amino acid sequences analysis showed that UV radiation induced numerous mutations at the AMP binding site on adenylation domain of syrB1, while no mutation was detected in syrB2 gene. Real-time polymerase chain reaction (PCR) results showed that expression of syrB1 gene in mutant strain was six-fold higher than that of PS120 strain. Taken together, these results suggest that the mutations at AMP binding site and overexpression of syrB1 were responsible for increased biosynthesis of SRE in P. syringae pv syringae.

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Experimental Correlation of Substrate Position with Reaction Outcome in the Aliphatic Halogenase, SyrB2

Cited by 100 publications

References 54 publications

Mono- and binuclear non-heme iron chemistry from a theoretical perspective

Mono- and binuclear non-heme iron chemistry from a theoretical perspective

Catalytic strategy for carbon−carbon bond scission by the cytochrome P450 OleT

Enhancing the production of syringomycin E in Pseudomonas syringae pv syringae by random mutagenesis and molecular characterization of the SyrB1 gene

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