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Turlington ZR, Vaz Ferreira de Macedo S, Perry K, Belsky SL, Faust JA, Snider MJ, Hicks KA. Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights. Arch Biochem Biophys 2024; 752:109859. [PMID: 38104959 DOI: 10.1016/j.abb.2023.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
6-Hydroxynicotinic acid 3-monooxygenase (NicC) is a bacterial enzyme involved in the degradation of nicotinic acid. This enzyme is a Class A flavin-dependent monooxygenase that catalyzes a unique decarboxylative hydroxylation. The unliganded structure of this enzyme has previously been reported and studied using steady- and transient-state kinetics to support a comprehensive kinetic mechanism. Here we report the crystal structure of the H47Q NicC variant in both a ligand-bound (solved to 2.17 Å resolution) and unliganded (1.51 Å resolution) form. Interestingly, in the liganded form, H47Q NicC is bound to 2-mercaptopyridine (2-MP), a contaminant present in the commercial stock of 6-mercaptopyridine-3-carboxylic acid(6-MNA), a substrate analogue. 2-MP binds weakly to H47Q NicC and is not a substrate for the enzyme. Based on kinetic and thermodynamic characterization, we have fortuitously captured a catalytically inactive H47Q NicC•2-MP complex in our crystal structure. This complex reveals interesting mechanistic details about the reaction catalyzed by 6-hydroxynicotinic acid 3-monooxygenase.
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Affiliation(s)
- Zachary R Turlington
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States
| | | | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, United States
| | - Sam L Belsky
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Jennifer A Faust
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States.
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Phillips SK, Brancato SG, MacMillan SN, Snider MJ, Roering AJ, Hicks KA. Synthesis and crystallographic characterization of 6-hydroxy-1,2-dihydropyridin-2-one. Acta Crystallogr E Crystallogr Commun 2023; 79:1147-1150. [PMID: 38313119 PMCID: PMC10833402 DOI: 10.1107/s205698902300974x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/07/2023] [Indexed: 02/06/2024]
Abstract
The title compound, C5H5NO2, is a hy-droxy-lated pyridine ring that has been studied for its involvement in microbial degradation of nicotinic acid. Here we describe its synthesis as a formic acid salt, rather than the standard hydro-chloride salt that is commercially available, and its spectroscopic and crystallographic characterization.
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Affiliation(s)
- Sara K. Phillips
- Department of Chemistry, The State University of New York at Cortland, Cortland, New York 13045, USA
| | - Savannah G. Brancato
- Department of Chemistry, The State University of New York at Cortland, Cortland, New York 13045, USA
| | - Samantha N. MacMillan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Mark J. Snider
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, USA
| | - Andrew J. Roering
- Department of Chemistry, The State University of New York at Cortland, Cortland, New York 13045, USA
| | - Katherine A. Hicks
- Department of Chemistry, The State University of New York at Cortland, Cortland, New York 13045, USA
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Perkins SW, Hlaing MZ, Hicks KA, Rajakovich LJ, Snider MJ. Mechanism of the Multistep Catalytic Cycle of 6-Hydroxynicotinate 3-Monooxygenase Revealed by Global Kinetic Analysis. Biochemistry 2023; 62:1553-1567. [PMID: 37130364 DOI: 10.1021/acs.biochem.2c00514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The class A flavoenzyme 6-hydroxynicotinate 3-monooxygenase (NicC) catalyzes a rare decarboxylative hydroxylation reaction in the degradation of nicotinate by aerobic bacteria. While the structure and critical residues involved in catalysis have been reported, the mechanism of this multistep enzyme has yet to be determined. A kinetic understanding of the NicC mechanism would enable comparison to other phenolic hydroxylases and illuminate its bioengineering potential for remediation of N-heterocyclic aromatic compounds. Toward these goals, transient state kinetic analyses by stopped-flow spectrophotometry were utilized to follow rapid changes in flavoenzyme absorbance spectra during all three stages of NicC catalysis: (1) 6-HNA binding; (2) NADH binding and FAD reduction; and (3) O2 binding with C4a-adduct formation, substrate hydroxylation, and FAD regeneration. Global kinetic simulations by numeric integration were used to supplement analytical fitting of time-resolved data and establish a kinetic mechanism. Results indicate that 6-HNA binding is a two-step process that substantially increases the affinity of NicC for NADH and enables the formation of a charge-transfer-complex intermediate to enhance the rate of flavin reduction. Singular value decomposition of the time-resolved spectra during the reaction of the substrate-bound, reduced enzyme with dioxygen provides evidence for the involvement of C4a-hydroperoxy-flavin and C4a-hydroxy-flavin intermediates in NicC catalysis. Global analysis of the full kinetic mechanism suggests that steady-state catalytic turnover is partially limited by substrate hydroxylation and C4a-hydroxy-flavin dehydration to regenerate the flavoenzyme. Insights gleaned from the kinetic model and determined microscopic rate constants provide a fundamental basis for understanding NicC's substrate specificity and reactivity.
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Affiliation(s)
- Scott W Perkins
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - May Z Hlaing
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, The State University of New York College at Cortland, Cortland, New York 13045, United States
| | - Lauren J Rajakovich
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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Westphal AH, Tischler D, van Berkel WJH. Natural diversity of FAD-dependent 4-hydroxybenzoate hydroxylases. Arch Biochem Biophys 2021; 702:108820. [PMID: 33684360 DOI: 10.1016/j.abb.2021.108820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 01/05/2023]
Abstract
4-Hydroxybenzoate 3-hydroxylase (PHBH) is the most extensively studied group A flavoprotein monooxygenase (FPMO). PHBH is almost exclusively found in prokaryotes, where its induction, usually as a consequence of lignin degradation, results in the regioselective formation of protocatechuate, one of the central intermediates in the global carbon cycle. In this contribution we introduce several less known FAD-dependent 4-hydroxybenzoate hydroxylases. Phylogenetic analysis showed that the enzymes discussed here reside in distinct clades of the group A FPMO family, indicating their separate divergence from a common ancestor. Protein homology modelling revealed that the fungal 4-hydroxybenzoate 3-hydroxylase PhhA is structurally related to phenol hydroxylase (PHHY) and 3-hydroxybenzoate 4-hydroxylase (3HB4H). 4-Hydroxybenzoate 1-hydroxylase (4HB1H) from yeast catalyzes an oxidative decarboxylation reaction and is structurally similar to 3-hydroxybenzoate 6-hydroxylase (3HB6H), salicylate hydroxylase (SALH) and 6-hydroxynicotinate 3-monooxygenase (6HNMO). Genome mining suggests that the 4HB1H activity is widespread in the fungal kingdom and might be responsible for the oxidative decarboxylation of vanillate, an import intermediate in lignin degradation. 4-Hydroxybenzoyl-CoA 1-hydroxylase (PhgA) catalyzes an intramolecular migration reaction (NIH shift) during the three-step conversion of 4-hydroxybenzoate to gentisate in certain Bacillus species. PhgA is phylogenetically related to 4-hydroxyphenylacetate 1-hydroxylase (4HPA1H). In summary, this paper shines light on the natural diversity of group A FPMOs that are involved in the aerobic microbial catabolism of 4-hydroxybenzoate.
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Affiliation(s)
- Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands.
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Germany.
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands.
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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