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Osadchuk I, Luts HE, Zahharova A, Tamm T, Borovkov V. Controlling Chirogenic Effects in Porphyrin Based Supramolecular Systems: Theoretical Analysis Versus Experimental Observations. Chemphyschem 2024; 25:e202400104. [PMID: 38693766 DOI: 10.1002/cphc.202400104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Indexed: 05/03/2024]
Abstract
Electronic circular dichroism (ECD) spectroscopy is a widely employed method for studying chiral analysis, requiring the presence of a chromophore close to a chiral centre. Porphyrinoids are found to be one of the best chromophoric systems serving for this purpose and enabling the application of ECD spectroscopy for chirality determination across diverse classes of organic compounds. Consequently, it is crucial to understand the induction mechanisms of ECD in the porphyrin-based complexes. The present study explores systematically the influence of secondary chromophores, bonded to an achiral zinc porphyrin or to chiral guest molecules, on the B-region of ECD spectra using the time-dependent density functional theory (TD-DFT) calculations. The study analyses the impact of change in both the conformation of achiral porphyrin (host) and change in position and conformation of chiral organic molecule (guest) on the B-band of ECD spectra (energy, intensity, sign of Cotton effect). Finally, conclusions made on model complexes are applied to published experimental data, contributing to a deeper understanding of various factors influencing ECD spectra in chiral systems. In addition, a computer program aimed to help rationalise ECD spectra by visualizing corresponding orbital energies, rotatory strengths, electric and magnetic transition moments, and angles between them, is presented.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Aleksandra Zahharova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Toomas Tamm
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
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2
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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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3
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Osadchuk I, Luts HE, Norvaiša K, Borovkov V, Senge MO. Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis. Chemistry 2023; 29:e202301408. [PMID: 37227167 DOI: 10.1002/chem.202301408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/26/2023]
Abstract
The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Karolis Norvaiša
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Lichtenberg Str. 2a, 85748, Garching, Germany
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4
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Domes R, Frosch T. Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy. Anal Chem 2023; 95:12719-12731. [PMID: 37586701 PMCID: PMC10469332 DOI: 10.1021/acs.analchem.3c01415] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.
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Affiliation(s)
- Robert Domes
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
| | - Torsten Frosch
- Biophotonics and
Biomedical Engineering Group, Technical
University Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
- Leibniz
Institute of Photonic Technology, Albert Einstein Strasse 9, D-07745 Jena, Germany
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5
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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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6
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Johnson KL, Graves AB, Eckhert K, Liptak MD. Second-sphere tuning of analogues for the ferric-hydroperoxoheme form of Mycobacterium tuberculosis MhuD. J Inorg Biochem 2023; 246:112300. [PMID: 37364353 DOI: 10.1016/j.jinorgbio.2023.112300] [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: 04/03/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Mycobacterium tuberculosis MhuD catalyzes the oxygenation of heme to mycobilin; experimental data presented here elucidates the novel hydroxylation reaction catalyzed by this enzyme. Analogues for the critical ferric-hydroperoxoheme (MhuD-heme-OOH) intermediate of this enzyme were characterized using UV/Vis absorption (Abs), circular dichroism (CD), and magnetic CD (MCD) spectroscopies. In order to extract electronic transition energies from these spectroscopic data, a novel global fitting model was developed for analysis of UV/Vis Abs, CD, and MCD data. A variant of MhuD was prepared, N7S, which weakens the affinity of heme-bound enzyme for a hydroperoxo analogue, azide, without significantly altering the protein secondary structure. Global fitting of spectroscopic data acquired in this study revealed that the second-sphere N7S substitution perturbs the electronic structure of two analogues for MhuD-heme-OOH: azide-inhibited MhuD (MhuD-heme-N3) and cyanide-inhibited MhuD (MhuD-heme-CN). The ground state electronic structures of MhuD-heme-N3 and MhuD-heme-CN were assessed using variable-temperature, variable-field MCD. Altogether, these data strongly suggest that there is a hydrogen bond between the Asn7 side-chain and the terminal oxygen of the hydroperoxo ligand in MhuD-heme-OOH. As discussed herein, this finding supports a novel hydroxylation reaction mechanism where the Asn7 side-chain guides a transient hydroxyl radical derived from homolysis of the OO bond in MhuD-heme-OOH to the β- or δ-meso carbon of the porphyrin ligand yielding β- or δ-meso-hydroxyheme, respectively.
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Affiliation(s)
- Kayla L Johnson
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Amanda B Graves
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Kaitlyn Eckhert
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, United States of America.
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7
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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8
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Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. SCIENCE ADVANCES 2022; 8:eabm7193. [PMID: 35544567 PMCID: PMC9094664 DOI: 10.1126/sciadv.abm7193] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/28/2022] [Indexed: 06/10/2023]
Abstract
Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.
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Affiliation(s)
- Peter J. Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sophia M. Yi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - J. Patrick O’Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | | | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
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9
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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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10
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Morris JA, Lickey BS, Liptak MD. Insertion of cobalt into tetrapyrroles. VITAMINS AND HORMONES 2022; 119:1-22. [PMID: 35337616 DOI: 10.1016/bs.vh.2022.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Vitamin B12 is one of the most complex cofactors known, and this chapter will discuss current understanding with regards to the cobalt insertion step of its syntheses. Two total syntheses of vitamin B12 were reported in the 1970s, which remain two of the most exceptional achievements of natural product synthesis. In subsequent years, two distinct biosynthetic pathways were identified in aerobic and anaerobic organisms. For these biosynthetic pathways, selectivity for Co(II) over other divalent metal ions with similar ionic radii and coordination chemistry remains an open question with three competing hypotheses proposed: metal affinity, tetrapyrrole distortion, and product inhibition. A 20 step biosynthetic route to convert 5-aminolevulinic acid (ALA) to vitamin B12 was elucidated in aerobic organisms in the 1990s, where cobalt is inserted relatively late in the pathway by the CobNST multi-protein complex. This chapter includes a mechanistic proposal for this reaction, but the majority of the proposal is based upon analogy to the ChlDHI magnesium chelatase complex as critical data for the cobalt chelatase is lacking. Later, in the 2010s, a distinct 21 step pathway from ALA to vitamin B12 was reported in anaerobic organisms, where cobalt is inserted early in the pathway by the enzyme CbiK. A recent study strongly suggests that the cobalt affinity of CbiK is the origin of cobalt selectivity for CbiK, but several important mechanistic questions remain unanswered. In general, it is expected that significant insight into the cobalt insertion mechanisms of CobNST and CbiK could be derived from additional structural, spectroscopic, and computational data.
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Affiliation(s)
- J A Morris
- Department of Chemistry, University of Vermont, Burlington, VT, United States
| | - B S Lickey
- Department of Chemistry, University of Vermont, Burlington, VT, United States
| | - M D Liptak
- Department of Chemistry, University of Vermont, Burlington, VT, United States.
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11
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Schuelke-Sanchez AE, Cornetta AR, Kocian TA, Conger MA, Liptak MD. Ruffling is essential for Staphylococcus aureus IsdG-catalyzed degradation of heme to staphylobilin. J Inorg Biochem 2022; 230:111775. [PMID: 35247855 PMCID: PMC8930504 DOI: 10.1016/j.jinorgbio.2022.111775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/31/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2022]
Abstract
Non-canonical heme oxygenases are enzymes that degrade heme to non-biliverdin products within bacterial heme iron acquisition pathways. These enzymes all contain a conserved second-sphere Trp residue that is essential for enzymatic turnover. Here, UV/Vis absorption (Abs) and circular dichroism (CD) spectroscopies were employed to show that the W67F variant of IsdG perturbs the heme substrate conformation. In general, a dynamic equilibrium between "planar" and "ruffled" substrate conformations exists within non-canonical heme oxygenases, and that the second-sphere Trp favors population of the "ruffled" substrate conformation. 1H nuclear magnetic resonance and magnetic CD spectroscopies were used to characterize the electronic structures of IsdG and IsdI variants with different substrate conformational distributions. These data revealed that the "ruffled" substrate conformation promotes partial porphyrin-to‑iron electron transfer, which makes the meso carbons of the porphyrin ring susceptible to radical attack. Finally, UV/Vis Abs spectroscopy was utilized to quantify the enzymatic rates, and electrospray ionization mass spectrometry was used to identify the product distributions, for variants of IsdG with altered substrate conformational distributions. In general, the rate of heme oxygenation by non-canonical heme oxygenases depends upon the population of the "ruffled" substrate conformation. Also, the production of staphylobilin or mycobilin by these enzymes is correlated with the population of the "ruffled" substrate conformation, since variants that favor population of the "planar" substrate conformation yield significant amounts of biliverdin. These data can be understood within the framework of a concerted rearrangement mechanism for the monooxygenation of heme to meso-hydroxyheme by non-canonical heme oxygenases.
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12
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Structure-function characterization of the mono- and diheme forms of MhuD, a noncanonical heme oxygenase from Mycobacterium tuberculosis. J Biol Chem 2021; 298:101475. [PMID: 34883099 PMCID: PMC8801480 DOI: 10.1016/j.jbc.2021.101475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022] Open
Abstract
MhuD is a noncanonical heme oxygenase (HO) from Mycobacterium tuberculosis (Mtb) that catalyzes unique heme degradation chemistry distinct from canonical HOs, generating mycobilin products without releasing carbon monoxide. Its crucial role in the Mtb heme uptake pathway has identified MhuD as an auspicious drug target. MhuD is capable of binding either one or two hemes within a single active site, but only the monoheme form was previously reported to be enzymatically active. Here we employed resonance Raman (rR) spectroscopy to examine several factors proposed to impact the reactivity of mono- and diheme MhuD, including heme ruffling, heme pocket hydrophobicity, and amino acid–heme interactions. We determined that the distal heme in the diheme MhuD active site has negligible effects on both the planarity of the His-coordinated heme macrocycle and the strength of the Fe-NHis linkage relative to the monoheme form. Our rR studies using isotopically labeled hemes unveiled unexpected biomolecular dynamics for the process of heme binding that converts MhuD from mono- to diheme form, where the second incoming heme replaces the first as the His75-coordinated heme. Ferrous CO-ligated diheme MhuD was found to exhibit multiple Fe-C-O conformers, one of which contains catalytically predisposed H-bonding interactions with the distal Asn7 residue identical to those in the monoheme form, implying that it is also enzymatically active. This was substantiated by activity assays and MS product analysis that confirmed the diheme form also degrades heme to mycobilins, redefining MhuD’s functional paradigm and further expanding our understanding of its role in Mtb physiology.
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13
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Osadchuk I, Aav R, Borovkov V, Clot E. Chirogenesis in Zinc Porphyrins: Theoretical Evaluation of Electronic Transitions, Controlling Structural Factors and Axial Ligation. Chemphyschem 2021; 22:1817-1833. [PMID: 34213815 PMCID: PMC8457158 DOI: 10.1002/cphc.202100345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/24/2021] [Indexed: 12/15/2022]
Abstract
In the present work, sixteen different zinc porphyrins (possessing different meso substituents) with and without a chiral guest were modelled using DFT and TD-DFT approaches in order to understand the influence of various controlling factors on electronic circular dichroism (ECD) spectra. Two major aspects are influenced by these factors: excitation energy of the electronic transitions and their intensity. In the case of excitation energy, the influence increases in the following order: orientation of the peripheral substituents
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
- ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
| | - Riina Aav
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
| | - Victor Borovkov
- Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
| | - Eric Clot
- ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
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14
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Yuan C, Ouyang Q, Wang X, Li X, Tan H, Chen G. Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation. Inorg Chem 2021; 60:6433-6445. [PMID: 33861573 DOI: 10.1021/acs.inorgchem.1c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two distinct sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C14. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C20-H or aliphatic C14-H pointing toward the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C14 site was 9.6 kcal/mol more favorable than that on the aromatic C20 site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C14 site formed hydrogen bonds with Ser280 and Thr385, which induced the l-Phe moiety to rotate around the Cβ-Cγ bond of the 4-nitrotryptophan moiety. Thus, it adopted an energetically favorable conformation with aromatic C20 adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B toward the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.
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Affiliation(s)
- Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
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15
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Thakuri B, O'Rourke BD, Graves AB, Liptak MD. A Dynamic Substrate is Required for MhuD-Catalyzed Degradation of Heme to Mycobilin. Biochemistry 2021; 60:918-928. [PMID: 33729746 DOI: 10.1021/acs.biochem.0c00892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The noncanonical heme oxygenase MhuD from Mycobacterium tuberculosis binds a heme substrate that adopts a dynamic equilibrium between planar and out-of-plane ruffled conformations. MhuD degrades this substrate to an unusual mycobilin product via successive monooxygenation and dioxygenation reactions. This article establishes a causal relationship between heme substrate dynamics and MhuD-catalyzed heme degradation, resulting in a refined enzymatic mechanism. UV/vis absorption (Abs) and electrospray ionization mass spectrometry (ESI-MS) data demonstrated that a second-sphere substitution favoring the population of the ruffled heme conformation changed the rate-limiting step of the reaction, resulting in a measurable buildup of the monooxygenated meso-hydroxyheme intermediate. In addition, UV/vis Abs and ESI-MS data for a second-sphere variant that favored the planar substrate conformation showed that this change altered the enzymatic mechanism resulting in an α-biliverdin product. Single-turnover kinetic analyses for three MhuD variants revealed that the rate of heme monooxygenation depends upon the population of the ruffled substrate conformation. These kinetic analyses also revealed that the rate of meso-hydroxyheme dioxygenation by MhuD depends upon the population of the planar substrate conformation. Thus, the ruffled heme conformation supports rapid heme monooxygenation by MhuD, but further oxygenation to the mycobilin product is inhibited. In contrast, the planar substrate conformation exhibits altered heme monooxygenation regiospecificity followed by rapid oxygenation of meso-hydroxyheme. Altogether, these data yielded a refined enzymatic mechanism for MhuD where access to both substrate conformations is needed for rapid incorporation of three oxygen atoms into heme yielding mycobilin.
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Affiliation(s)
- Biswash Thakuri
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Bruce D O'Rourke
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Amanda B Graves
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
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16
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Ferousi C, Schmitz RA, Maalcke WJ, Lindhoud S, Versantvoort W, Jetten MSM, Reimann J, Kartal B. Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link. J Biol Chem 2021; 296:100476. [PMID: 33652023 PMCID: PMC8042395 DOI: 10.1016/j.jbc.2021.100476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.
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Affiliation(s)
- Christina Ferousi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter J Maalcke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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17
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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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18
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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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19
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20
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Yuan C, Zhang Y, Tan H, Li X, Chen G, Jia Z. ONIOM investigations of the heme degradation mechanism by MhuD: the critical function of heme ruffling. Phys Chem Chem Phys 2020; 22:8817-8826. [DOI: 10.1039/c9cp05868k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A unique ruffling conformation of hydroxyheme in MhuD inhibits its “on-site” monooxygenation but induces “remote-site” dioxygenation.
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Affiliation(s)
- Chang Yuan
- College of Chemistry
- Key Laboratories of Theoretical and Computational Photochemistry
- Ministry of Education
- Beijing Normal University
- Beijing
| | - Ying Zhang
- College of Chemistry
- Key Laboratories of Theoretical and Computational Photochemistry
- Ministry of Education
- Beijing Normal University
- Beijing
| | - Hongwei Tan
- College of Chemistry
- Key Laboratories of Theoretical and Computational Photochemistry
- Ministry of Education
- Beijing Normal University
- Beijing
| | - Xichen Li
- College of Chemistry
- Key Laboratories of Theoretical and Computational Photochemistry
- Ministry of Education
- Beijing Normal University
- Beijing
| | - Guangju Chen
- College of Chemistry
- Key Laboratories of Theoretical and Computational Photochemistry
- Ministry of Education
- Beijing Normal University
- Beijing
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences
- Queen's University
- Kingston
- Ontario
- Canada
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21
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Zhang Y, Wang J, Yuan C, Liu W, Tan H, Li X, Chen G. Ruffling drives coproheme decarboxylation by facilitating PCET: a theoretical investigation of ChdC. Phys Chem Chem Phys 2020; 22:16117-16124. [DOI: 10.1039/d0cp02690e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coproheme decarboxylase (ChdC) is an essential enzyme in the coproporphyrin-dependent heme synthesis pathway, which catalyzes oxidative decarboxylation of coproheme at the positions p2 and p4 to generate heme b under the action of hydrogen peroxide.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
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22
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Schuelke-Sanchez AE, Stone AA, Liptak MD. CfbA promotes insertion of cobalt and nickel into ruffled tetrapyrroles in vitro. Dalton Trans 2019; 49:1065-1076. [PMID: 31868194 DOI: 10.1039/c9dt03601f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The nickel chelatase CfbA is the smallest member of the chelatase family, but the mechanism by which this enzyme inserts nickel into sirohydrochlorin is unknown. In order to gain mechanistic insight, metal binding, tetrapyrrole binding, and enzyme activity were characterized for a variety of substrates using several spectroscopic and computational approaches. Mass spectrometery and magnetic circular dichroism experiments revealed that CfbA binds an octahedral, high-spin metal substrate. UV/Vis absorption spectroscopy demonstrated that the enzyme binds a wide range of tetrapyrrole substrates and perturbs their electronic structures. Based upon activity assays, CfbA promotes insertion of cobalt and nickel into several tetrapyrroles, including cobalt insertion into protopophyrin IX. Finally, density functional theory models were developed which strongly suggest that observed spectral changes upon binding to the enzyme can be explained by tetrapyrrole ruffling, but not deprotonation or saddling. The observation of an octahedral, high-spin metal bound to CfbA leads to a generalization for all class II chelatases: these enzymes bind labile metal substrates and metal desolvation is not a rate-limiting step. The conclusion that CfbA ruffles its tetrapyrrole substrate reveals that the CfbA mechanism is different from that currently proposed for ferrochelatase, and identifies an intriguing correlation between metal substrate specificity and tetrapyrrole distortion mode in chelatases.
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Affiliation(s)
| | - Alissa A Stone
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA.
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA.
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23
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Matthews SJ, Pacholarz KJ, France AP, Jowitt TA, Hay S, Barran PE, Munro AW. MhuD from Mycobacterium tuberculosis: Probing a Dual Role in Heme Storage and Degradation. ACS Infect Dis 2019; 5:1855-1866. [PMID: 31480841 DOI: 10.1021/acsinfecdis.9b00181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Mycobacterium tuberculosis (Mtb) heme oxygenase MhuD liberates free iron by degrading heme to the linear tetrapyrrole mycobilin. The MhuD dimer binds up to two hemes within the active site of each monomer. Binding the first solvent-exposed heme allows heme degradation and releases free iron. Binding a second heme renders MhuD inactive, allowing heme storage. Native-mass spectrometry revealed little difference in binding affinity between solvent-exposed and solvent-protected hemes. Hence, diheme-MhuD is formed even when a large proportion of the MhuD population is in the apo form. Apomyoglobin heme transfer assays showed MhuD-diheme dissociation is far slower than monoheme dissociation at ∼0.12 min-1 and ∼0.25 s-1, respectively, indicating that MhuD has a strong affinity for diheme. MhuD has not evolved to preferentially occupy the monoheme form and, through formation of a diheme complex, it functions as part of a larger network to tightly regulate both heme and iron levels in Mtb.
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Affiliation(s)
- Sarah J. Matthews
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kamila J. Pacholarz
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Aidan P. France
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Thomas A. Jowitt
- The Biomolecular Analysis Facility, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E. Barran
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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24
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Conger MA, Cornetta AR, Liptak MD. Spectroscopic Evidence for Electronic Control of Heme Hydroxylation by IsdG. Inorg Chem 2019; 58:15455-15465. [PMID: 31693363 DOI: 10.1021/acs.inorgchem.9b02530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus IsdG catalyzes a unique trioxygenation of heme to staphylobilin, and the data presented in this article elucidate the mechanism of the novel chemical transformation. More specifically, the roles of the second-sphere Asn and Trp residues in the monooxygenation of ferric-peroxoheme have been clarified via spectroscopic characterization of the ferric-azidoheme analogue. Analysis of UV/vis absorption data quantified the strength of the hydrogen bond that exists between the Asn7 side chain and the azide moiety of ferric-azidoheme. X-band electron paramagnetic resonance data were acquired and analyzed, which revealed that this hydrogen bond weakens the π-donor strength of the azide, resulting in perturbations of the Fe 3d based orbitals. Finally, nuclear magnetic resonance characterization of 13C-enriched samples demonstrated that the Asn7···N3 hydrogen bond triggers partial porphyrin to iron electron transfer, resulting in spin density delocalization onto the heme meso carbons. These spectroscopic experiments were complemented by combined quantum mechanics/molecular mechanics computational modeling, which strongly suggested that the electronic structure changes observed for the N7A variant arose from loss of the Asn7···N3 hydrogen bond as opposed to a decrease in porphyrin ruffling. From these data a fascinating picture emerges where an Asn7···N3 hydrogen bond is communicated through four bonds, resulting in meso carbons with partial cationic radical character that are poised for hydroxylation. This chemistry is not observed in other heme proteins because Asn7 and Trp67 must work in concert to trigger the requisite electronic structure change.
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Affiliation(s)
- Matthew A Conger
- Department of Chemistry , University of Vermont , Burlington , Vermont 05405 , United States
| | - Amanda R Cornetta
- Department of Chemistry , University of Vermont , Burlington , Vermont 05405 , United States
| | - Matthew D Liptak
- Department of Chemistry , University of Vermont , Burlington , Vermont 05405 , United States
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25
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Lei H, Bowler BE. Naturally Occurring A51V Variant of Human Cytochrome c Destabilizes the Native State and Enhances Peroxidase Activity. J Phys Chem B 2019; 123:8939-8953. [PMID: 31557440 DOI: 10.1021/acs.jpcb.9b05869] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The A51V variant of human cytochrome c is linked to thrombocytopenia 4 (THC4), a condition that causes decreased blood platelet counts. A 1.82 Å structure of the A51V variant shows only minor changes in tertiary structure relative to the wild-type (WT) protein. Guanidine hydrochloride denaturation demonstrates that the global stability of the A51V variant is 1.3 kcal/mol less than that of the WT protein. The midpoint pH, pH1/2, of the alkaline transition of the A51V variant is 1 unit less than that of the WT protein. Stopped-flow pH jump experiments show that the A51V substitution affects the triggering ionization for one of two kinetically distinguishable alkaline conformers and enhances the accessibility of a high-spin heme transient. The pH1/2 for acid unfolding of the A51V variant is 0.7 units higher than for that of the WT protein. Consistent with the greater accessibility of non-native conformers for the A51V variant, the kcat values for its peroxidase activity increase by 6- to 15-fold in the pH range of 5-8 versus those of the WT protein. These data along with previously reported data for the other THC4-linked variants, G41S and Y48H, underscore the role of Ω-loop C (residues 40-57) in modulating the peroxidase activity of cytochrome c early in apoptosis.
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Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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26
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Ehudin MA, Senft L, Franke A, Ivanović-Burmazović I, Karlin KD. Formation and Reactivity of New Isoporphyrins: Implications for Understanding the Tyr-His Cross-Link Cofactor Biogenesis in Cytochrome c Oxidase. J Am Chem Soc 2019; 141:10632-10643. [PMID: 31150209 DOI: 10.1021/jacs.9b01791] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of dioxygen to water utilizing a heterobinuclear active site composed of a heme moiety and a mononuclear copper center coordinated to three histidine residues, one of which is covalently cross-linked to a tyrosine residue via a post-translational modification (PTM). Although this tyrosine-histidine moiety has functional and structural importance, the pathway behind this net oxidative C-N bond coupling is still unknown. A novel route employing an iron(III) meso-substituted isoporphyrin derivative, isoelectronic with Cmpd-I ((Por•+)FeIV═O), is for the first time proposed to be a key intermediate in the Tyr-His cofactor biogenesis. Newly synthesized iron(III) meso-substituted isoporphyrins were prepared with azide, cyanide, and substituted imidazole functionalities, by adding nucleophiles to an iron(III) π-dication species formed via addition of trifluoroacetic acid to F8Cmpd-I (F8 = (tetrakis(2,6-difluorophenyl)porphyrinate)). Isoporphyrin derivatives were characterized at cryogenic temperatures via ESI-MS and UV-vis, 2H NMR, and EPR spectroscopies. Addition of 1,3,5-trimethoxybenzene or 4-methoxyphenol to the imidazole-substituted isoporphyrin led to formation of the organic product containing the imidazole coupled to aromatic substrate via a new C-N bond, as detected via cryo-ESI-MS. Experimental evidence for the formation of an imidazole-substituted isoporphyrin and its promising reactivity to form the imidazole-phenol coupled product yields viability to the herein proposed pathway behind the PTM (i.e., biogenesis) leading to the key covalent Tyr-His cross-link in CcO.
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Affiliation(s)
- Melanie A Ehudin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Laura Senft
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Alicja Franke
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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27
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Adams HR, Krewson C, Vardanega JE, Fujii S, Moreno-Chicano T, Moreno T, Chicano, Sambongi Y, Svistunenko D, Paps J, Andrew CR, Hough MA. One fold, two functions: cytochrome P460 and cytochrome c'-β from the methanotroph Methylococcus capsulatus (Bath). Chem Sci 2019; 10:3031-3041. [PMID: 30996884 PMCID: PMC6427953 DOI: 10.1039/c8sc05210g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/20/2019] [Indexed: 11/21/2022] Open
Abstract
Nature is adept at utilising highly similar protein folds to carry out very different functions, yet the mechanisms by which this functional divergence occurs remain poorly characterised. In certain methanotrophic bacteria, two homologous pentacoordinate c-type heme proteins have been identified: a cytochrome P460 (cyt P460) and a cytochrome c'-β (cyt cp-β). Cytochromes P460 are able to convert hydroxylamine to nitrous oxide (N2O), a potent greenhouse gas. This reactivity is similar to that of hydroxylamine oxidoreductase (HAO), which is a key enzyme in nitrifying and methanotrophic bacteria. Cyt P460 and HAO both have unusual protein-heme cross-links, formed by a Tyr residue in HAO and a Lys in cyt P460. In contrast, cyts cp-β (the only known cytochromes c' with a β-sheet fold) lack this crosslink and appears to be optimized for binding non-polar molecules (including NO and CO) without enzymatic conversion. Our bioinformatics analysis supports the proposal that cyt cp-β may have evolved from cyt P460 via a gene duplication event. Using high-resolution X-ray crystallography, UV-visible absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy, we have characterized the overall protein folding and active site structures of cyt cp-β and cyt P460 from the obligate methanotroph, Methylococcus capsulatus (Bath). These proteins display a similar β-sheet protein fold, together with a pattern of changes to the heme pocket regions and localised tertiary structure that have converted a hydroxylamine oxidizing enzyme into a gas-binding protein. Structural comparisons provide insights relevant to enzyme redesign for synthetic enzymology and engineering of gas sensor proteins. We also show the widespread occurrence of cyts cp-β and characterise their phylogeny.
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Affiliation(s)
- Hannah R Adams
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Callie Krewson
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Jenny E Vardanega
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Sotaro Fujii
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | | | - Tadeo Moreno
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Chicano
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | - Dimitri Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Jordi Paps
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Colin R Andrew
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Michael A Hough
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
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28
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Chao A, Sieminski PJ, Owens CP, Goulding CW. Iron Acquisition in Mycobacterium tuberculosis. Chem Rev 2018; 119:1193-1220. [PMID: 30474981 DOI: 10.1021/acs.chemrev.8b00285] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The highly contagious disease tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis (Mtb), which has been evolving drug resistance at an alarming rate. Like all human pathogens, Mtb requires iron for growth and virulence. Consequently, Mtb iron transport is an emerging drug target. However, the development of anti-TB drugs aimed at these metabolic pathways has been restricted by the dearth of information on Mtb iron acquisition. In this Review, we describe the multiple strategies utilized by Mtb to acquire ferric iron and heme iron. Mtb iron uptake is a complex process, requiring biosynthesis and subsequent export of Mtb siderophores, followed by ferric iron scavenging and ferric-siderophore import into Mtb. Additionally, Mtb possesses two possible heme uptake pathways and an Mtb-specific mechanism of heme degradation that yields iron and novel heme-degradation products. We conclude with perspectives for potential therapeutics that could directly target Mtb heme and iron uptake machineries. We also highlight how hijacking Mtb heme and iron acquisition pathways for drug import may facilitate drug transport through the notoriously impregnable Mtb cell wall.
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Affiliation(s)
| | | | - Cedric P Owens
- Schmid College of Science and Technology , Chapman University , Orange , California 92866 , United States
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29
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Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem 2018; 57:14386-14395. [PMID: 30378421 DOI: 10.1021/acs.inorgchem.8b02584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O2 levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O2 binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O2 states, while the other dimer consists of the Fe(III)-H2O and Fe(II)-O2 states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O2 form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O2-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O2 sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Paul G Young
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Eric D Hoffer
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Gregory E Vansuch
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carmen L Metzler
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Christine M Dunham
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Emily E Weinert
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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30
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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31
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Lewis RD, Garcia-Borràs M, Chalkley MJ, Buller AR, Houk KN, Kan SBJ, Arnold FH. Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase. Proc Natl Acad Sci U S A 2018; 115:7308-7313. [PMID: 29946033 PMCID: PMC6048479 DOI: 10.1073/pnas.1807027115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, heme proteins have been discovered and engineered by directed evolution to catalyze chemical transformations that are biochemically unprecedented. Many of these nonnatural enzyme-catalyzed reactions are assumed to proceed through a catalytic iron porphyrin carbene (IPC) intermediate, although this intermediate has never been observed in a protein. Using crystallographic, spectroscopic, and computational methods, we have captured and studied a catalytic IPC intermediate in the active site of an enzyme derived from thermostable Rhodothermus marinus (Rma) cytochrome c High-resolution crystal structures and computational methods reveal how directed evolution created an active site for carbene transfer in an electron transfer protein and how the laboratory-evolved enzyme achieves perfect carbene transfer stereoselectivity by holding the catalytic IPC in a single orientation. We also discovered that the IPC in Rma cytochrome c has a singlet ground electronic state and that the protein environment uses geometrical constraints and noncovalent interactions to influence different IPC electronic states. This information helps us to understand the impressive reactivity and selectivity of carbene transfer enzymes and offers insights that will guide and inspire future engineering efforts.
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Affiliation(s)
- Russell D Lewis
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Matthew J Chalkley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - S B Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Frances H Arnold
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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32
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Smith MA, Lancaster KM. The Eponymous Cofactors in Cytochrome P460s from Ammonia-Oxidizing Bacteria Are Iron Porphyrinoids Whose Macrocycles Are Dibasic. Biochemistry 2018; 57:334-343. [PMID: 29211462 PMCID: PMC6361160 DOI: 10.1021/acs.biochem.7b00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear. Here we report the 1.45 Å crystal structure of cyt P460 from Nitrosomonas sp. AL212 and conclude that the cross-link does not lead to a change in hybridization of the heme carbon participating in the cross-link but rather enforces structural distortions to the macrocycle away from planarity. Time-dependent density functional theory coupled to experimental structural and spectroscopic analysis suggest that this geometric distortion is sufficient to define the spectroscopic properties of the heme P460 cofactor and provide clues toward establishing a relationship between heme P460 electronic structure and function.
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Affiliation(s)
- Meghan A Smith
- 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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33
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Kleingardner EC, Asher WB, Bren KL. Efficient and Flexible Preparation of Biosynthetic Microperoxidases. Biochemistry 2016; 56:143-148. [DOI: 10.1021/acs.biochem.6b00915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erin C. Kleingardner
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Wesley B. Asher
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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34
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McLean KJ, Munro AW. Drug targeting of heme proteins in Mycobacterium tuberculosis. Drug Discov Today 2016; 22:566-575. [PMID: 27856345 DOI: 10.1016/j.drudis.2016.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/28/2016] [Accepted: 11/02/2016] [Indexed: 01/08/2023]
Abstract
TB, caused by the human pathogen Mycobacterium tuberculosis (Mtb), causes more deaths than any other infectious disease. Iron is crucial for Mtb to infect the host and to sustain infection, with Mtb encoding large numbers of iron-binding proteins. Many of these are hemoproteins with key roles, including defense against oxidative stress, cellular signaling and regulation, host cholesterol metabolism, and respiratory processes. Various heme enzymes in Mtb are validated drug targets and/or products of genes essential for bacterial viability or survival in the host. Here, we review the structure, function, and druggability of key Mtb heme enzymes and strategies used for their inhibition.
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Affiliation(s)
- Kirsty J McLean
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew W Munro
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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35
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Graves AB, Horak EH, Liptak MD. Dynamic ruffling distortion of the heme substrate in non-canonical heme oxygenase enzymes. Dalton Trans 2016; 45:10058-67. [DOI: 10.1039/c6dt00702c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A double-well exists along the ruffling coordinate of cyanide-inhibited ferric heme, which explains the observation of “nested” VTVH MCD saturation magnetization curves.
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Affiliation(s)
| | - Erik H. Horak
- Department of Chemistry
- University of Vermont
- Burlington
- USA
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