Models for Molybdenum Coordination during the Catalytic Cycle of Periplasmic Nitrate Reductase from Paracoccus denitrificans Derived from EPR and EXAFS Spectroscopy
Abstract
The periplasmic nitrate reductase from Paracoccus denitrificans is a soluble two-subunit enzyme which binds two hemes (c-type), a [4Fe-4S] center, and a bis molybdopterin guanine dinucleotide cofactor (bis-MGD). A catalytic cycle for this enzyme is presented based on a study of these redox centers using electron paramagnetic resonance (EPR) and extended X-ray absorption fine structure (EXAFS) spectroscopies. The Mo(V) EPR signal of resting NAP (High g [resting]) has g(av) = 1.9898 is rhombic, exhibits low anisotropy, and is split by two weakly interacting protons which are not solvent-exchangeable. Addition of exogenous ligands to this resting state (e.g., nitrate, nitrite, azide) did not change the form of the signal. A distinct form of the High g Mo(V) signal, which has slightly lower anisotropy and higher rhombicity, was trapped during turnover of nitrate and may represent a catalytically relevant Mo(V) intermediate (High g [nitrate]). Mo K-edge EXAFS analysis was undertaken on the ferricyanide oxidized enzyme, a reduced sample frozen within 10 min of dithionite addition, and a nitrate-reoxidized form of the enzyme. The oxidized enzyme was fitted best as a di-oxo Mo(VI) species with 5 sulfur ligands (4 at 2. 43 A and 1 at 2.82 A), and the reduced form was fitted best as a mono-oxo Mo(IV) species with 3 sulfur ligands at 2.35 A. The addition of nitrate to the reduced enzyme resulted in reoxidation to a di-oxo Mo(VI) species similar to the resting enzyme. Prolonged incubation of NAP with dithionite in the absence of nitrate (i.e., nonturnover conditions) resulted in the formation of a species with a Mo(V) EPR signal that is quite distinct from the High g family and which has a g(av) = 1.973 (Low g [unsplit]). This signal resembles those of the mono-MGD xanthine oxidase family and is proposed to arise from an inactive form of the nitrate reductase in which the Mo(V) form is only coordinated by the dithiolene of one MGD. In samples of NAP that had been reduced with dithionite, treated with azide or cyanide, and then reoxidized with ferricyanide, two Mo(V) signals were detected with g(av) elevated compared to the High g signals. Kinetic analysis demonstrated that azide and cyanide displayed competitive and noncompetitive inhibition, respectively. EXAFS analysis of azide-treated samples show improvement to the fit when two nitrogens are included in the molybdenum coordination sphere at 2.52 A, suggesting that azide binds directly to Mo(IV). Based on these spectroscopic and kinetic data, models for Mo coordination during turnover have been proposed.
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NapA from Paracoccus pantotrophus is competitively inhibited by azide and thiocyanate with a Ki of 11.0 mM and 4.0 mM, respectively.
“NapA from Paracoccus pantotrophus is competitively inhibited by azide212 and thiocyanate206 with a Ki 11.0 mM and 4.0 mM, respectively.”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [212]
Cyanide inhibits Paracoccus pantotrophus NapA noncompetitively, with a distinct change in Vmax but no significant change in Km.
“Cyanide also inhibits this enzyme but noncompetitively, with a distinct change in Vmax but no significant change in Km,212”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [212]
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EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes
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Electrocatalytic reduction of nitrate and selenate by NapAB
Gates, A. J., Butler, C. S., Richardson, D. J., & Butt, J. N. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390236 · Cited by 10 · see citing works
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McGarry, J. M., Mintmier, B., Metzger, M. C., Giri, N. C., Britt, N., Basu, P., & Wilcoxen, J. (2024) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-024-02087-5 · Cited by 9 · see citing works
The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions
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Ridley, H., Watts, C. A., Richardson, D. J., & Butler, C. S. (2006) · Analytical Biochemistry · doi:10.1016/j.ab.2006.08.028 · Cited by 7 · see citing works
Self-citationIsolated molybdenum-based microporous POMs for selective adsorption of gases
Deng, L. Q., Lin, R.-Y., & Zhou, Z. (2022) · Dalton Transactions · doi:10.1039/d2dt00134a · Cited by 6 · see citing works
Kinetic Studies of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase
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The Inhibition of Engineered Nano-ZnO in the Biological Nitrogen Removal Process: A Review
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The Metabolism of Nitrogen and Amino Acids
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Active Site Structure and Mechanism of a Molybdenum Catechol Dehydroxylase
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Dissimilatory Nitrate Reductase
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Characterization of molybdenum and tungsten formate dehydrogenases from sulfate reducing bacteria
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- Authors
- Butler, C. S., Charnock, J. M., Bennett, B., Sears, H. J., Reilly, A. J., Ferguson, S. J., Garner, C. D., Lowe, D. J., Thomson, A. J., Berks, B. C., & Richardson, D. J.
- Affiliations
- John Innes Centre (GB)
- Corresponding author
- Richardson, David J.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1999-06-22
- Volume
- 38
- Issue
- 28
- Pages
- 9000-9012
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2049948155
- Cited by
- 99
- References
- 19
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 3 · 2023: 3 · 2022: 5 · 2021: 4 · 2020: 3 · 2019: 1 · 2018: 2 · 2017: 1 · 2016: 1 · 2015: 1 · 2014: 6 · 2013: 5 · 2012: 3
- FWCI
- 6.15
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Topics
- Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
- Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- periplasmic nitrate reductase, Paracoccus denitrificans, molybdenum coordination, catalytic cycle, [4Fe-4S] cluster
- MeSH terms
- Azides, Catalysis, Cyanides, Electron Spin Resonance Spectroscopy, Kinetics, Models, Chemical, Molybdenum, Nitrate Reductases, Oxidation-Reduction, Paracoccus denitrificans, Potentiometry, Spectrometry, Fluorescence, X-Rays, Periplasm, Nitrate Reductase
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