Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase?
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combina...
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| Format: | Article |
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Frontiers Media S.A.
2018-10-01
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| Series: | Frontiers in Chemistry |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fchem.2018.00513/full |
| _version_ | 1818418394306707456 |
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| author | Amy Timmins Nicholas J. Fowler Jim Warwicker Grit D. Straganz Grit D. Straganz Sam P. de Visser |
| author_facet | Amy Timmins Nicholas J. Fowler Jim Warwicker Grit D. Straganz Grit D. Straganz Sam P. de Visser |
| author_sort | Amy Timmins |
| collection | DOAJ |
| description | In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases. |
| first_indexed | 2024-12-14T12:21:59Z |
| format | Article |
| id | doaj.art-245ce79ed0ad403a8140d726f00157ad |
| institution | Directory Open Access Journal |
| issn | 2296-2646 |
| language | English |
| last_indexed | 2024-12-14T12:21:59Z |
| publishDate | 2018-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Chemistry |
| spelling | doaj.art-245ce79ed0ad403a8140d726f00157ad2022-12-21T23:01:27ZengFrontiers Media S.A.Frontiers in Chemistry2296-26462018-10-01610.3389/fchem.2018.00513422704Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase?Amy Timmins0Nicholas J. Fowler1Jim Warwicker2Grit D. Straganz3Grit D. Straganz4Sam P. de Visser5The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United KingdomThe Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United KingdomThe Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United KingdomInstitute of Biochemistry, Graz University of Technology, Graz, AustriaInstitute of Molecular Biosciences, Graz University, Graz, AustriaThe Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United KingdomIn this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.https://www.frontiersin.org/article/10.3389/fchem.2018.00513/fullnonheme ironenzyme catalysisreaction mechanismQM/MMdensity functional theoryhalogenation |
| spellingShingle | Amy Timmins Nicholas J. Fowler Jim Warwicker Grit D. Straganz Grit D. Straganz Sam P. de Visser Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Frontiers in Chemistry nonheme iron enzyme catalysis reaction mechanism QM/MM density functional theory halogenation |
| title | Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? |
| title_full | Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? |
| title_fullStr | Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? |
| title_full_unstemmed | Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? |
| title_short | Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? |
| title_sort | does substrate positioning affect the selectivity and reactivity in the hectochlorin biosynthesis halogenase |
| topic | nonheme iron enzyme catalysis reaction mechanism QM/MM density functional theory halogenation |
| url | https://www.frontiersin.org/article/10.3389/fchem.2018.00513/full |
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