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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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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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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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Weitz AC, Biswas S, Rizzolo K, Elliott S, Bominaar EL, Hendrich MP. Electronic State of the His/Tyr-Ligated Heme of BthA by Mössbauer and DFT Analysis. Inorg Chem 2020; 59:10223-10233. [PMID: 32602712 DOI: 10.1021/acs.inorgchem.0c01349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The BthA protein from the microorganism Burkholderia thailandensis contains two hemes with axial His/OH2 and His/Tyr coordinations separated by the closest interheme distance of 14 Å. BthA has a similar structure and belongs to the same family of multiheme cytochrome c peroxidases as MauG, which performs long-range oxidation of the partner protein methylamine dehydrogenase. Magnetic Mössbauer spectroscopy of the diferric state of BthA corroborates previous structural work identifying a high-spin (His/OH2) peroxidatic heme and a low-spin (His/Tyr) electron transfer heme. Unlike MauG, addition of H2O2 fully converts the diferric form of BthA to a stable 2e- oxidized state, allowing a new assessment of this state. The peroxidatic heme is found to be oxidized to a canonical compound II, S = 1 oxoiron(IV) heme. In contrast, the electronic properties of the oxidized His/Tyr heme are puzzling. The isomer shift of the His/Tyr heme (0.17 mm/s) is close to that of the precursor S = 1/2 Fe3+ heme (0.21 mm/s) which suggests oxidation of the Tyr. However, the spin-dipolar hyperfine coupling constants are found here to be the same as those for the ferryl peroxidatic heme, indicating that the His/Tyr heme is also a compound II, S = 1 Fe4+ heme and ruling out oxidation of the Tyr. DFT calculations indicate that the unusually high isomer shift is not attributable to the rare axial His/Tyr heme coordination. The calculations are only compatible with spectroscopy for an unusually long Fe4+-OTyr distance, which is presumably under the influence of the protein environment of the His/Tyr heme moiety in the H2O2 oxidized state of the protein. The results offer new insights into how high valence intermediates can be tuned by the protein environment for performing long-range oxidation.
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Affiliation(s)
- Andrew C Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kim Rizzolo
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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