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Louka S, Barry SM, Heyes DJ, Mubarak MQE, Ali HS, Alkhalaf LM, Munro AW, Scrutton NS, Challis GL, de Visser SP. Catalytic Mechanism of Aromatic Nitration by Cytochrome P450 TxtE: Involvement of a Ferric-Peroxynitrite Intermediate. J Am Chem Soc 2020; 142:15764-15779. [PMID: 32811149 PMCID: PMC7586343 DOI: 10.1021/jacs.0c05070] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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The
cytochromes P450 are heme-dependent enzymes that catalyze many
vital reaction processes in the human body related to biodegradation
and biosynthesis. They typically act as mono-oxygenases; however,
the recently discovered P450 subfamily TxtE utilizes O2 and NO to nitrate aromatic substrates such as L-tryptophan.
A direct and selective aromatic nitration reaction may be useful in
biotechnology for the synthesis of drugs or small molecules. Details
of the catalytic mechanism are unknown, and it has been suggested
that the reaction should proceed through either an iron(III)-superoxo
or an iron(II)-nitrosyl intermediate. To resolve this controversy,
we used stopped-flow kinetics to provide evidence for a catalytic
cycle where dioxygen binds prior to NO to generate an active iron(III)-peroxynitrite
species that is able to nitrate l-Trp efficiently. We show
that the rate of binding of O2 is faster than that of NO
and also leads to l-Trp nitration, while little evidence
of product formation is observed from the iron(II)-nitrosyl complex.
To support the experimental studies, we performed density functional
theory studies on large active site cluster models. The studies suggest
a mechanism involving an iron(III)-peroxynitrite that splits homolytically
to form an iron(IV)-oxo heme (Compound II) and a free NO2 radical via a small free energy of activation. The latter activates
the substrate on the aromatic ring, while compound II picks up the ipso-hydrogen to form the product. The calculations give
small reaction barriers for most steps in the catalytic cycle and,
therefore, predict fast product formation from the iron(III)-peroxynitrite
complex. These findings provide the first detailed insight into the
mechanism of nitration by a member of the TxtE subfamily and highlight
how the enzyme facilitates this novel reaction chemistry.
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Affiliation(s)
- Savvas Louka
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Mancheste M13 9PL, United Kingdom
| | - Sarah M Barry
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Derren J Heyes
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - M Qadri E Mubarak
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Mancheste M13 9PL, United Kingdom
| | - Hafiz Saqib Ali
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew W Munro
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Nigel S Scrutton
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom.,Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia.,ARC Centre for Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC 3800, Australia
| | - Sam P de Visser
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Mancheste M13 9PL, United Kingdom
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Ugur I, Chandrasekhar P. Proton relay network in P450cam formed upon docking of putidaredoxin. Proteins 2019; 88:558-572. [PMID: 31597203 DOI: 10.1002/prot.25835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/13/2019] [Accepted: 09/28/2019] [Indexed: 11/08/2022]
Abstract
Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor-bound): (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)-docked-WT, FeOO state. (d) Pdx-docked WT, Cpd(0). (e) Pdx-docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH 2 O⋯D251 in WT; FeOO(H)⋯nH 2 O⋯D251 in T252A mutant; both occur with Pdx docking. (c) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H-bonding network, second protonation appears to be facilitated.
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Affiliation(s)
- Ilke Ugur
- Research Division, Ashwin-Ushas Corporation, Marlboro, New Jersey
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