1
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Das A, Gao S, Lal RG, Hicks MH, Oyala PH, Arnold FH. Reaction Discovery Using Spectroscopic Insights from an Enzymatic C-H Amination Intermediate. J Am Chem Soc 2024. [PMID: 39037870 DOI: 10.1021/jacs.4c05761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Engineered hemoproteins can selectively incorporate nitrogen from nitrene precursors like hydroxylamine, O-substituted hydroxylamines, and organic azides into organic molecules. Although iron-nitrenoids are often invoked as the reactive intermediates in these reactions, their innate reactivity and transient nature have made their characterization challenging. Here we characterize an iron-nitrosyl intermediate generated from NH2OH within a protoglobin active site that can undergo nitrogen-group transfer catalysis, using UV-vis, electron paramagnetic resonance (EPR) spectroscopy, and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) techniques. The mechanistic insights gained led to the discovery of aminating reagents─nitrite (NO2-), nitric oxide (NO), and nitroxyl (HNO)─that are new to both nature and synthetic chemistry. Based on the findings, we propose a catalytic cycle for C-H amination inspired by the nitrite reductase pathway. This study highlights the potential of engineered hemoproteins to access natural nitrogen sources for sustainable chemical synthesis and offers a new perspective on the use of biological nitrogen cycle intermediates in biocatalysis.
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Affiliation(s)
- Anuvab Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Shilong Gao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ravi G Lal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Madeline H Hicks
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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2
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Alvarez-Hernandez JL, Salamatian AA, Sopchak AE, Bren KL. Hydrogen evolution catalysis by a cobalt porphyrin peptide: A proposed role for porphyrin propionic acid groups. J Inorg Biochem 2023; 249:112390. [PMID: 37801884 DOI: 10.1016/j.jinorgbio.2023.112390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
Cobalt microperoxidase-11 (CoMP11-Ac) is a cobalt porphyrin-peptide catalyst for hydrogen (H2) evolution from water. Herein, we assess electrocatalytic activity of CoMP11-Ac from pH 1.0-10.0. This catalyst remains intact and active under highly acidic conditions (pH 1.0) that are desirable for maximizing H2 evolution activity. Analysis of electrochemical data indicate that H2 evolution takes place by two pH-dependent mechanisms. At pH < 4.3, a proton transfer mechanism involving the propionic acid groups of the porphyrin is proposed, decreasing the catalytic overpotential by 280 mV.
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Affiliation(s)
| | - Alison A Salamatian
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
| | - Andrew E Sopchak
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
| | - Kara L Bren
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
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3
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Londoño-Salazar J, Ayala M, Powell DR, Shao Y, Richter-Addo GB. Interactions of arylhydroxylamines and alkylaldoximes with a rhodium porphyrin. J Inorg Biochem 2023; 247:112337. [PMID: 37517330 DOI: 10.1016/j.jinorgbio.2023.112337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Heme enzymes are involved in the binding and metabolism of hydroxylamine (RNHOH) and aldoxime (RCH=NOH) compounds (R = H, alkyl, aryl). We report the synthesis and X-ray crystal structure of a metalloporphyrin in complex with an arylhydroxylamine, namely that of (TPP)Rh(PhNHOH)(C6H4Cl) (TPP = tetraphenylpophryinato dianion). The crystal structure reveals, in addition to N-binding of PhNHOH to Rh, the presence of an intramolecular H-bond between the hydroxylamine -OH proton and a porphyrin N-atom. Results from density functional theory (DFT) calculations support the presence of this intramolecular H-bond in this global minimum structure, and a natural bond order (NBO) analysis reveals that this H-bond comprises a donor π N=C (porphyrin) to acceptor σ* O-H (hydroxylamine) interaction of 2.32 kcal/mol. While DFT calculations predict the presence of similar intramolecular H-bond interactions in the related aldoxime complexes (TPP)Rh(RCH=NOH)(C6H4Cl) in their global minima structures, the X-ray crystal structure obtained for the (TPP)Rh(CH3(CH2)2CH=NOH)(C6H4Cl) complex is consistent with the local (non-global) minima conformation that does not have this intramolecular H-bond interaction.
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Affiliation(s)
| | - Megan Ayala
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Douglas R Powell
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.
| | - George B Richter-Addo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.
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4
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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5
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Bollmeyer MM, Majer SH, Coleman RE, Lancaster KM. Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460. Chem Sci 2023; 14:8295-8304. [PMID: 37564409 PMCID: PMC10411619 DOI: 10.1039/d3sc02288a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/22/2023] [Indexed: 08/12/2023] Open
Abstract
Product selectivity of ammonia oxidation by ammonia-oxidizing bacteria (AOB) is tightly controlled by metalloenzymes. Hydroxylamine oxidoreductase (HAO) is responsible for the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO). The non-metabolic enzyme cytochrome (cyt) P460 also oxidizes NH2OH, but instead produces nitrous oxide (N2O). While both enzymes use a heme P460 cofactor, they selectively oxidize NH2OH to different products. Previously reported structures of Nitrosomonas sp. AL212 cyt P460 show that a capping phenylalanine residue rotates upon ligand binding, suggesting that this Phe may influence substrate and/or product binding. Here, we show via substitutions of the capping Phe in Nitrosomonas europaea cyt P460 that the bulky phenyl side-chain promotes the heme-lysine cross-link forming reaction operative in maturing the cofactor. Additionally, the Phe side-chain plays an important role in modulating product selectivity between N2O and NO during NH2OH oxidation under aerobic conditions. A picture emerges where the sterics and electrostatics of the side-chain in this capping position control the kinetics of N2O formation and NO binding affinity. This demonstrates how the outer coordination sphere of cyt P460 is tuned not only for selective NH2OH oxidation, but also for the autocatalytic cross-link forming reaction that imbues activity to an otherwise inactive protein.
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Affiliation(s)
- Melissa M Bollmeyer
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Sean H Majer
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Rachael E Coleman
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Kyle M Lancaster
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
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6
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Bollmeyer MM, Coleman RE, Majer SH, Ferrao SD, Lancaster KM. Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc 2023; 145:14404-14416. [PMID: 37338957 PMCID: PMC10431212 DOI: 10.1021/jacs.3c03608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli. When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c'β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.
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Affiliation(s)
- Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Rachael E. Coleman
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Sean H. Majer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Silas D. Ferrao
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
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7
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Adams HR, Svistunenko DA, Wilson MT, Fujii S, Strange RW, Hardy ZA, Vazquez PA, Dabritz T, Streblow GJ, Andrew CR, Hough MA. A Heme Pocket Aromatic Quadrupole Modulates Gas Binding to Cytochrome c'-β: Implications for NO Sensors. J Biol Chem 2023:104742. [PMID: 37100286 DOI: 10.1016/j.jbc.2023.104742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023] Open
Abstract
The structural basis by which gas-binding heme proteins control their interactions with NO, CO, and O2, is fundamental to enzymology, biotechnology and human health. Cytochromes c´ (cyts c´) are a group of putative NO-binding heme proteins that fall into two families: the well characterised four alpha helix bundle fold (cyts c´-α) and an unrelated family with a largely beta sheet fold (cyts c´-β) resembling that of cytochromes P460. A recent structure of cyt c´-β from Methylococcus capsulatus Bath (McCP-β) revealed two heme pocket phenylalanine residues (Phe 32 and Phe 61) positioned near the distal gas binding site. This feature, dubbed the "Phe cap", is highly conserved within the sequences of other cyts c´-β, but is absent in their close homologues, the hydroxylamine oxidizing cytochromes P460, although some do contain a single Phe residue. Here we report an integrated structural, spectroscopic, and kinetic characterization of McCP-β complexes with diatomic gases, focusing on the interaction of the Phe cap with NO and CO. Significantly, crystallographic and resonance Raman data show that orientation of the electron rich aromatic ring face of Phe 32 towards distally-bound NO or CO is associated with weakened backbonding and higher off rates. Moreover, we propose that an aromatic quadrupole also contributes to the unusually weak backbonding reported for some heme-based gas sensors, including the mammalian NO-sensor, soluble guanylate cyclase (sGC). Collectively, this study sheds light on the influence of highly conserved distal Phe residues on heme-gas complexes of cytochrome c'-β, including the potential for aromatic quadrupoles to modulate NO and CO binding in other heme proteins.
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Affiliation(s)
- Hannah R Adams
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima, Hiroshima, 739-8528, Japan; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard W Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Zoe A Hardy
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Priscilla A Vazquez
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Tyler Dabritz
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Gabriel J Streblow
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA
| | - Colin R Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande OR 97850, USA.
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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8
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Abendroth J, Buchko GW, Liew FN, Nguyen JN, Kim HJ. Structural Characterization of Cytochrome c'β-Met from an Ammonia-Oxidizing Bacterium. Biochemistry 2022; 61:563-574. [PMID: 35315646 DOI: 10.1021/acs.biochem.1c00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'β-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'β-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'β-Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c'β-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'β-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,UCB Biosciences, Bainbridge Island, Washington 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 98354, United States.,School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Fong Ning Liew
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
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9
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Interactions of N-hydroxyamphetamine with an iron porphyrin: A unique intramolecular H-bond probed by DFT calculations. J Inorg Biochem 2022; 231:111779. [DOI: 10.1016/j.jinorgbio.2022.111779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 11/18/2022]
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10
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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11
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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12
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Chen L, Deng Z, Zhao C. Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis. ACS Chem Biol 2021; 16:559-570. [PMID: 33721494 DOI: 10.1021/acschembio.1c00052] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO2-, NO+, and N2O3 in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.
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Affiliation(s)
- Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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13
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Abstract
Ammonia-oxidizing bacteria (AOB) convert ammonia (NH3) to nitrite (NO2-) as their primary metabolism and thus provide a blueprint for the use of NH3 as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH2OH) to NO2-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH2OH and were both originally reported to produce NO2-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH2OH oxidation. Under aerobic conditions substoichiometric production of NO2- was observed along with production of nitrous oxide (N2O). Under anaerobic conditions, however, N2O was the exclusive product of NH2OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O2, thus producing NO2- abiotically. Because N2O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO2- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO2- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH2OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH2OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.
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Affiliation(s)
- Rachael E. Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M. Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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14
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Zsombor-Pindera J, Effaty F, Escomel L, Patrick B, Kennepohl P, Ottenwaelder X. Five Nitrogen Oxidation States from Nitro to Amine: Stabilization and Reactivity of a Metastable Arylhydroxylamine Complex. J Am Chem Soc 2020; 142:19023-19028. [PMID: 33124796 DOI: 10.1021/jacs.0c09300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Redox noninnocent ligands enhance the reactivity of the metal they complex, a strategy used by metalloenzymes and in catalysis. Herein, we report a series of copper complexes with the same ligand framework, but with a pendant nitrogen group that spans five different redox states between nitro and amine. Of particular interest is the synthesis of a unprecedented copper(I)-arylhydroxylamine complex. While hydroxylamines typically disproportionate or decompose in the presence of transition metal ions, the reactivity of this metastable species is arrested by the presence of an intramolecular hydrogen bond. Two-electron oxidation yields a copper(II)-(arylnitrosyl radical) complex that can dissociate to a copper(I) species with uncoordinated arylnitroso. This combination of ligand redox noninnocence and hemilability provides opportunities in catalysis for two-electron chemistry via a one-electron copper(I/II) shuttle, as exemplified with an aerobic alcohol oxidation.
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Affiliation(s)
- Joseph Zsombor-Pindera
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada.,Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Farshid Effaty
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Léon Escomel
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Brian Patrick
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Pierre Kennepohl
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Xavier Ottenwaelder
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
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15
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Brown BN, Robinson KJ, Durfee QC, Kekilli D, Hough MA, Andrew CR. Hydroxylamine Complexes of Cytochrome c': Influence of Heme Iron Redox State on Kinetic and Spectroscopic Properties. Inorg Chem 2020; 59:14162-14170. [PMID: 32970420 DOI: 10.1021/acs.inorgchem.0c01925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylamine (NH2OH or HA) is a redox-active nitrogen oxide that occurs as a toxic intermediate in the oxidation of ammonium by nitrifying and methanotrophic bacteria. Within ammonium containing environments, HA is generated by ammonia monooxygenase (nitrifiers) or methane monooxygenase (methanotrophs). Subsequent oxidation of HA is catalyzed by heme proteins, including cytochromes P460 and multiheme hydroxylamine oxidoreductases, the former contributing to emissions of N2O, an ozone-depleting greenhouse gas. A heme-HA complex is also a proposed intermediate in the reduction of nitrite to ammonia by cytochrome c nitrite reductase. Despite the importance of heme-HA complexes within the biogeochemical nitrogen cycle, fundamental aspects of their coordination chemistry remain unknown, including the effect of the Fe redox state on heme-HA affinity, kinetics, and spectroscopy. Using stopped-flow UV-vis and resonance Raman spectroscopy, we investigated HA complexes of the L16G distal pocket variant of Alcaligenes xylosoxidans cytochrome c'-α (L16G AxCP-α), a pentacoordinate c-type cytochrome that we show binds HA in its Fe(III) (Kd ∼ 2.5 mM) and Fe(II) (Kd = 0.0345 mM) states. The ∼70-fold higher HA affinity of the Fe(II) state is due mostly to its lower koff value (0.0994 s-1 vs 11 s-1), whereas kon values for Fe(II) (2880 M-1 s-1) and Fe(III) (4300 M-1 s-1) redox states are relatively similar. A comparison of the HA and imidazole affinities of L16G AxCP-α was also used to predict the influence of Fe redox state on HA binding to other proteins. Although HA complexes of L16G AxCP-α decompose via redox reactions, the lifetime of the Fe(II)HA complex was prolonged in the presence of excess reductant. Spectroscopic parameters determined for the Fe(II)HA complex include the N-O stretching vibration of the NH2OH ligand, ν(N-O) = 906 cm-1. Overall, the kinetic trends and spectroscopic benchmarks from this study provide a foundation for future investigations of heme-HA reaction mechanisms.
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Affiliation(s)
- Brianna N Brown
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Kelsey J Robinson
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Quentin C Durfee
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Demet Kekilli
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
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16
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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17
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Coleman RE, Vilbert AC, Lancaster KM. The Heme-Lys Cross-Link in Cytochrome P460 Promotes Catalysis by Enforcing Secondary Coordination Sphere Architecture. Biochemistry 2020; 59:2289-2298. [PMID: 32525655 DOI: 10.1021/acs.biochem.0c00261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome (cyt) P460 is a c-type monoheme enzyme found in ammonia-oxidizing bacteria (AOB) and methanotrophs; additionally, genes encoding it have been found in some pathogenic bacteria. Cyt P460 is defined by a unique post-translational modification to the heme macrocycle, where a lysine (Lys) residue covalently attaches to the 13' meso carbon of the porphyrin, modifying this heme macrocycle into the enzyme's eponymous P460 cofactor, similar to the cofactor found in the enzyme hydroxylamine oxidoreductase. This cross-link imbues the protein with unique spectroscopic properties, the most obvious of which is the enzyme's green color in solution. Cyt P460 from the AOB Nitrosomonas europaea is a homodimeric redox enzyme that produces nitrous oxide (N2O) from 2 equiv of hydroxylamine. Mutation of the Lys cross-link results in spectroscopic features that are more similar to those of standard cyt c' proteins and renders the enzyme catalytically incompetent for NH2OH oxidation. Recently, the necessity of a second-sphere glutamate (Glu) residue for redox catalysis was established; it plausibly serves as proton relay during the first oxidative half of the catalytic cycle. Herein, we report the first crystal structure of a cross-link deficient cyt P460. This structure shows that the positioning of the catalytically essential Glu changes by approximately 0.8 Å when compared to a cross-linked, catalytically competent cyt P460. It appears that the heme-Lys cross-link affects the relative position of the P460 cofactor with respect to the second-sphere Glu residue, therefore dictating the catalytic competency of the enzyme.
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Affiliation(s)
- Rachael E Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Avery C Vilbert
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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18
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Liew FN, Brandys MA, Biswas S, Nguyen JN, Rahmawati M, Nevala M, Elmore BO, Hendrich MP, Kim HJ. Cytochrome c' β-Met Is a Variant in the P460 Superfamily Lacking the Heme-Lysyl Cross-Link: A Peroxidase Mimic Generating a Ferryl Intermediate. Biochemistry 2020; 59:704-716. [PMID: 31887031 DOI: 10.1021/acs.biochem.9b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A defining characteristic of bacterial cytochromes (cyt's) in the P460 family is an unusual cross-link connecting the heme porphyrin to the side chain of a lysyl residue in the protein backbone. Here, via proteomics of the periplasmic fraction of the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea, we report the identification of a variant member of the P460 family that contains a methionyl residue in place of the cross-linking lysine. We formally designate this protein cytochrome "c'β-Met" to distinguish it from other members bearing different residues at this position (e.g., cyt c'β-Phe from the methane-oxidizing Methylococcus capsulatus Bath). As isolated, the monoheme cyt c'β-Met is high-spin (S = 5/2). Optical spectroscopy suggests that a cross-link is absent. Hydroxylamine, the substrate for the cross-linked cyt P460 from N. europaea, did not appreciably alter the optical spectrum of cyt c'β with up to 1000-fold excess at pH 7.5. Cyt c'β-Met did however bind 1 equiv of H2O2, and with a slight excess, Mössbauer spectroscopy indicated the formation of a semistable ferryl (FeIV═O) Compound II-like species. The corresponding electron paramagnetic resonance showed a very low intensity signal indicative of a radical at g = 2.0. Furthermore, cyt c'β-Met exhibited guaiacol-dependent peroxidase activity (kcat = 20.0 ± 1.2 s-1; KM = 2.6 ± 0.4 mM). Unlike cyt c'β-Met, cyt P460 showed evidence of heme inactivation in the presence of 2 equiv of H2O2 with no appreciable guaiacol-dependent peroxidase activity. Mutagenesis of the cross-linking lysyl residue to an alanine in cyt P460, however, reversed this lack of activity.
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Affiliation(s)
- Fong Ning Liew
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Marisa A Brandys
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Saborni Biswas
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Mustika Rahmawati
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Michael Nevala
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States.,Veolia Nuclear Solutions Federal Solutions , Richland , Washington 99354 , United States
| | - Bradley O Elmore
- Newport Laboratories , Worthington , Minnesota 56187 , United States
| | - Michael P Hendrich
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
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