Etude structurale et fonctionnelle de la protéine à radical SAM Hyde

Abstract : Radical S-adenosyl-L-methionine (SAM) proteins use a reduced [Fe4S4] cluster to initiate homolytic reductive cleavage of SAM, which leads to the formation of highly reactive 5'-deoxyadenosyl radical species or 5'-dA•. In almost all cases this alkyl radical will abstract a hydrogen atom from the substrate and thus trigger its conversion into product. These enzymes are found in key steps of the synthesis of certain vitamins, antibiotics, DNA precursors or protein cofactors. They are often involved in the cleavage or formation of C-C, C-N, C-S or C-P bonds. The present thesis work has been focused on the structural and functional study of HydE protein; a radical SAM enzyme, involved in the biosynthesis of the organometallic active site of [FeFe]-hydrogenase. The main goal was to identify the substrate of HydE and to study details of how radical SAM proteins control the highly oxidizing 5'-dA• species. We managed to identify a group of molecules, derived from cysteine, containing a thiazolidine ring with one or two carboxylate groups, which have a very good affinity for the active site of HydE. We have demonstrated some of these ligands are non-physiological substrates of the enzyme. With these substrates we could highlight a new radical attack mechanism in radical SAM proteins. Indeed, in HydE we observed a direct attack on the 5'-dA • radical on the sulfur atom of the thioether belonging to the thiazolidine ring. This is an unprecedented reaction that contrasts with sulfur (or selenium) atom insertion reactions catalysed by some radical SAM enzymes. This is also the first observation of a radical reaction in the protein crystal of a radical SAM enzyme and also the first real-time monitoring by 1H- & 13C-NMR spectroscopy of the accumulation of products of the reaction catalysed by these enzymes. Theoretical calculations based on our high-resolution crystal structures suggest that in the case of this protein superfamily the 5'-dA• radical, which triggers the reaction in radical SAM enzymes, is a transition state and therefore not an isolable intermediate species.
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Roman Rohac. Etude structurale et fonctionnelle de la protéine à radical SAM Hyde. Biologie structurale [q-bio.BM]. Université Grenoble Alpes, 2016. Français. ⟨NNT : 2016GREAV010⟩. ⟨tel-01524860⟩

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