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Title: Mechanism and dynamics of fatty acid photodecarboxylase

Abstract

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning ofmore » the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1FAD* (~300 ps in WT FAP) to form FAD∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H2O and D2O buffers indicated that back electron transfer from FAD∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD∙– reoxidation (to a red-shifted form FADRS) in 100 ns, most of the CO2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FADRS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [4];  [5]; ORCiD logo [6]; ORCiD logo [4]; ORCiD logo [4];  [4]; ORCiD logo [7]; ORCiD logo [2]; ORCiD logo [8]; ORCiD logo [7]; ORCiD logo [1];  [9];  [9]; ORCiD logo [9];  [9];  [9] more »; ORCiD logo [1]; ORCiD logo [9];  [10]; ORCiD logo [7]; ORCiD logo [1]; ORCiD logo [11]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [1];  [2]; ORCiD logo [9];  [12]; ORCiD logo [4]; ORCiD logo [13]; ORCiD logo [9]; ORCiD logo [2]; ORCiD logo [4]; ORCiD logo [14]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [15]; ORCiD logo [16]; ORCiD logo [4]; ORCiD logo [9]; ORCiD logo [1]; ORCiD logo [16]; ORCiD logo [1] « less
+ Show Author Affiliations
  1. Aix-Marseille Univ., Saint-Paul-lez-Durance, (France)
  2. Univ. Grenoble Alpes (France)
  3. European Synchrotron Radiation Facility, Grenoble (France)
  4. Ecole Polytechnique, Palaiseau (France)
  5. Inst. Laue Langevin, Grenoble (France)
  6. Aix-Marseille Univ., Saint-Paul-lez-Durance, (France); Univ. Paris-Saclay, Gif-sur-Yvette (France)
  7. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  8. Univ. of Rennes (France); European Synchrotron Radiation Facility (ESRF), Grenoble (France)
  9. Max-Planck-Institut für medizinische Forschung, Heidelberg (Germany)
  10. Max-Planck-Institut für medizinische Forschung, Heidelberg (Germany); Sample Environment and Characterization European XFEL, Schenefeld (Germany)
  11. Synchrotron SOLEIL, Gif-sur-Yvette (France)
  12. Univ. Lille (France)
  13. Ecole Polytechnique, Palaiseau (France); Univ. Paris-Saclay, Gif-sur-Yvette (France)
  14. Univ. Grenoble Alpes (France); European Synchrotron Radiation Facility, Grenoble (France)
  15. Max-Planck-Institut für medizinische Forschung, Heidelberg (Germany); Lomonosov Moscow States Univ. (Russia)
  16. Univ. Paris-Saclay, Gif-sur-Yvette (France)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
OSTI Identifier:
1810562
Grant/Contract Number:  
AC02-76SF00515; P41GM103393
Resource Type:
Accepted Manuscript
Journal Name:
Science
Additional Journal Information:
Journal Volume: 372; Journal Issue: 6538; Journal ID: ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Sorigué, D., Hadjidemetriou, K., Blangy, S., Gotthard, G., Bonvalet, A., Coquelle, N., Samire, P., Aleksandrov, A., Antonucci, L., Benachir, A., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Cuiné, S., Doak, R. B., Foucar, L., Gorel, A., Grünbein, M., Hartmann, E., Hienerwadel, R., Hilpert, M., Kloos, M., Lane, T. J., Légeret, B., Legrand, P., Li-Beisson, Y., Moulin, S. Y., Nurizzo, D., Peltier, G., Schirò, G., Shoeman, R. L., Sliwa, M., Solinas, X., Zhuang, B., Barends, T. M., Colletier, J. -P., Joffre, M., Royant, A., Berthomieu, C., Weik, M., Domratcheva, T., Brettel, K., Vos, M. H., Schlichting, I., Arnoux, P., Müller, P., and Beisson, F. Mechanism and dynamics of fatty acid photodecarboxylase. United States: N. p., 2021. Web. doi:10.1126/science.abd5687.
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Sorigué, D., Hadjidemetriou, K., Blangy, S., Gotthard, G., Bonvalet, A., Coquelle, N., Samire, P., Aleksandrov, A., Antonucci, L., Benachir, A., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Cuiné, S., Doak, R. B., Foucar, L., Gorel, A., Grünbein, M., Hartmann, E., Hienerwadel, R., Hilpert, M., Kloos, M., Lane, T. J., Légeret, B., Legrand, P., Li-Beisson, Y., Moulin, S. Y., Nurizzo, D., Peltier, G., Schirò, G., Shoeman, R. L., Sliwa, M., Solinas, X., Zhuang, B., Barends, T. M., Colletier, J. -P., Joffre, M., Royant, A., Berthomieu, C., Weik, M., Domratcheva, T., Brettel, K., Vos, M. H., Schlichting, I., Arnoux, P., Müller, P., & Beisson, F. Mechanism and dynamics of fatty acid photodecarboxylase. United States. https://doi.org/10.1126/science.abd5687
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Sorigué, D., Hadjidemetriou, K., Blangy, S., Gotthard, G., Bonvalet, A., Coquelle, N., Samire, P., Aleksandrov, A., Antonucci, L., Benachir, A., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Cuiné, S., Doak, R. B., Foucar, L., Gorel, A., Grünbein, M., Hartmann, E., Hienerwadel, R., Hilpert, M., Kloos, M., Lane, T. J., Légeret, B., Legrand, P., Li-Beisson, Y., Moulin, S. Y., Nurizzo, D., Peltier, G., Schirò, G., Shoeman, R. L., Sliwa, M., Solinas, X., Zhuang, B., Barends, T. M., Colletier, J. -P., Joffre, M., Royant, A., Berthomieu, C., Weik, M., Domratcheva, T., Brettel, K., Vos, M. H., Schlichting, I., Arnoux, P., Müller, P., and Beisson, F. Fri . "Mechanism and dynamics of fatty acid photodecarboxylase". United States. https://doi.org/10.1126/science.abd5687. https://www.osti.gov/servlets/purl/1810562.
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@article{osti_1810562,
title = {Mechanism and dynamics of fatty acid photodecarboxylase},
author = {Sorigué, D. and Hadjidemetriou, K. and Blangy, S. and Gotthard, G. and Bonvalet, A. and Coquelle, N. and Samire, P. and Aleksandrov, A. and Antonucci, L. and Benachir, A. and Boutet, S. and Byrdin, M. and Cammarata, M. and Carbajo, S. and Cuiné, S. and Doak, R. B. and Foucar, L. and Gorel, A. and Grünbein, M. and Hartmann, E. and Hienerwadel, R. and Hilpert, M. and Kloos, M. and Lane, T. J. and Légeret, B. and Legrand, P. and Li-Beisson, Y. and Moulin, S. Y. and Nurizzo, D. and Peltier, G. and Schirò, G. and Shoeman, R. L. and Sliwa, M. and Solinas, X. and Zhuang, B. and Barends, T. M. and Colletier, J. -P. and Joffre, M. and Royant, A. and Berthomieu, C. and Weik, M. and Domratcheva, T. and Brettel, K. and Vos, M. H. and Schlichting, I. and Arnoux, P. and Müller, P. and Beisson, F.},
abstractNote = {Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1FAD* (~300 ps in WT FAP) to form FAD∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H2O and D2O buffers indicated that back electron transfer from FAD∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD∙– reoxidation (to a red-shifted form FADRS) in 100 ns, most of the CO2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FADRS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.},
doi = {10.1126/science.abd5687},
journal = {Science},
number = 6538,
volume = 372,
place = {United States},
year = {Fri Apr 09 00:00:00 EDT 2021},
month = {Fri Apr 09 00:00:00 EDT 2021}
}
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A Preference for Edgewise Interactions between Aromatic Rings and Carboxylate Anions:  The Biological Relevance of Anion−Quadrupole Interactions
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Photochemical Mechanism of Light-Driven Fatty Acid Photodecarboxylase
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Crystal Structure of a Photolyase Bound to a CPD-Like DNA Lesion After in Situ Repair
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The photophysical and photochemical properties of flavins (isoalloxazines)
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Ultrafast catalytic processes in enzymes
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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions
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Estimation of amino acid residue side-chain absorption in the infrared spectra of protein solutions in heavy water
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RADDOSE-3D : time- and space-resolved modelling of dose in macromolecular crystallography
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Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction
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Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and QM/MM Calculations
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Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
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Intruder state avoidance multireference Møller-Plesset perturbation theory: Multireference Møller-Plesset Perturbation Theory
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FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments
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Hydrocarbon Synthesis via Photoenzymatic Decarboxylation of Carboxylic Acids
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Light‐Driven Kinetic Resolution of α‐Functionalized Carboxylic Acids Enabled by an Engineered Fatty Acid Photodecarboxylase
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Modeling Vibrational Spectra of Amino Acid Side Chains in Proteins:  Effects of Protonation State, Counterion, and Solvent on Arginine C−N Stretch Frequencies
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Multiscale control and rapid scanning of time delays ranging from picosecond to millisecond
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Structure and insights into the function of a Ca2+-activated Cl− channel
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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
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Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy
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Arbitrary-detuning asynchronous optical sampling with amplified laser systems
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Accessing non-natural reactivity by irradiating nicotinamide-dependent enzymes with light
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A vibrational-spectroscopic study of the species present in the CO2?H2O system
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ID29: a high-intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering
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Membrane Inlet Mass Spectrometry: A Powerful Tool for Algal Research
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Improved Estimation of Structure-Factor Difference Amplitudesfrom Poorly Accurate Data
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Kinetics and Mechanism of Carbamate Formation from CO 2 (aq), Carbonate Species, and Monoethanolamine in Aqueous Solution
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An anti-settling sample delivery instrument for serial femtosecond crystallography
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Excited state dynamics and catalytic mechanism of the light-driven enzyme protochlorophyllide oxidoreductase
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Phaser crystallographic software
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