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Institut de Biologie StructuraleGrenoble / France

Highlights

’Green’ chemistry and biofuels : Observing a photoenzyme at work

An international consortium* of scientists, including researchers from the IBS/DYNAMOP and IBS/SYN groups, has deciphered the mechanism and dynamics of the fatty acid photodecarboxylase (FAP) enzyme, a discovery published in Science on 08/04/2021. This photoenzyme is naturally present in many microscopic algae and uses light energy to catalyse the generation of hydrocarbons from fatty acids.
To elucidate the mechanism of this unique enzyme, the research teams have combined multi-faceted experimental and theoretical approaches comprising site-directed mutagenesis, time-resolved vibrational and electronic optical spectroscopies or cryotrapping of reaction intermediates, static and kinetic crystallography at synchrotrons and an X-ray free electron laser (XFEL) and quantum chemical calculations. The elucidation of the FAP catalytic mechanism and the identification of reaction intermediates and structural elements indispensable to its activity constitute a key basis for the optimization of the enzyme for the production of ‘green’ hydrocarbon fuels and chemicals that can be easily modulated by light. Press release.

* In France, this study mobilized researchers from the Institut de Biosciences et Biotechnologies Aix-Marseille in Cadarache, the Institut de Biologie Intégrative de la Cellule in Gif-sur-Yvette, the Institut Polytechnique de Paris in Palaiseau, the Institut de Biologie Structurale in Grenoble, the Universities of Lille and Rennes, the European Synchrotron Radiation Facility and the Institut Laue-Langevin. Abroad, researchers from the Max-Planck Institute in Heidelberg, Moscow State University and the SLAC National Accelerator Laboratory in Stanford are involved.

Mechanism and dynamics of fatty acid photodecarboxylase. 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 RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin S, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier J-P, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Science 2021 ; 372:eabd5687 (https://science.sciencemag.org/content/372/6538/eabd5687/tab-pdf)

IBS Contact : Martin Weik

An Unexpected P-Cluster like Intermediate En Route to the Nitrogenase FeMo-co

Nitrogenase is a key metalloprotein that catalyzes the reduction of nitrogen to ammonia at room temperature and ambient pressure. It thus plays a major role in the global nitrogen cycle. It uses two metal centers : the P-cluster, an atypical [Fe8S7] center, which allows electron transfer to the active site itself, which is an organometallic [MoFe7S9C-(R)-homocitrate] center. Its biosynthesis requires the action of a dozen accessory proteins that constitute the NIF (for NItrogen Fixation) assembly machinery. The NifB protein is the key enzyme in this mechanism because it is responsible for the fusion of two [Fe4S4] centers combined with a carbide ion insertion and the addition of a sulfide ion to produce a [Fe8S9C] precursor termed NifB-co. Recently, American colleagues published a crystal structure of the NifB protein with all its metal centers. Unfortunately, they did not model their crystallographic data well and missed the identity of cluster bound to the active site. By reusing these data, we were able to highlight the presence of a unique [Fe8S8] center resulting from the fusion of [Fe4S4] centers. This crystal structure allowed us to redefine the order of the reaction steps showing that the FeS center fusion must take place before the carbide ion insertion. The particular coordination of this intermediate highlights the role of the protein matrix in the organization of the NifB-co biosynthetic steps, thus revealing the mechanism of the enzyme.

An unexpected P-cluster like intermediate en route to the nitrogenase FeMo-co. Leon P. Jenner, Mickael V. Cherrier, Patricia Amara, Luis M. Rubio and Yvain Nicolet. Chemical Science DOI : 10.1039/D1SC00289A

New issue for the IBS Newsletter

Find the March 2021 issue (in french only).