Institut de Biologie StructuraleGrenoble / France


Radical chemistry : how radical SAM enzymes control it

Radical chemistry uses high-energy intermediates to carry out difficult reactions or even ones impossible to perform by the so-called polar chemistry. In nature, these reactions are fine-tuned by the structural environment within dedicated enzymes. Radical SAM proteins use an iron-sulfur cluster and S-adenosyl-L-methionine to initiate several radical reactions. These metalloproteins are notably involved in the biosynthesis of numerous cofactors and in the modification of peptides with antibiotic properties. The crystal structure of ThiH, involved in the anaerobic synthesis of vitamin B1, allowed us, by combining structural analysis and theoretical calculations, to understand how the substrate is recognized by the protein and how it is activated. In particular, hydrogen atom transfer is facilitated by a tunnel effect which allows the lowering of the activation barrier.
In conclusion, this work showed how a sum of small changes allowed to modify both the substrate selectivity and the specificity of a chemical reaction within this important family of proteins, thus paving the way to future molecular engineering approaches for more extensive use of these proteins as a biotechnological tool.

L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases. Amara P, Saragaglia C, Mouesca JM, Martin L, Nicolet Y. Nature Communications ; 13(1):2284

Contact : Yvain Nicolet( IBS/Metalloproteins group)

How an enzyme makes room for its substrates

In enzymes the "1st coordination sphere" describes the binding of substrate(s) to the active site whereas protein ligands that serve to correctly orient substrate(s) are generally defined as belonging to the "2nd coordination sphere". Protein elements that are found beyond that point, and still can affect catalysis, are part of the "outer coordination sphere". Quinolinate synthase is a good example of this classification because, besides having an active site and residues that accommodates its substrates, it modulates its catalytic site volume through remarkable internal conformational changes.

Quinolinate synthase : an example of the roles of the second and outer coordination spheres in enzyme catalysis. Juan C. Fontecilla-Camps* and Anne Volbeda. Chem Rev. (2022) doi : 10.1021/acs.chemrev.1c00869.

Contact : Juan Carlos Fontecilla-Camps (IBS/Metalloproteins group)

Extracellular endosulfatase HSulf-2 harbours a polysaccharide chain that muzzles its pro-tumoral activity

Polysaccharides of the Glycosaminoglycans (GAGs) family are essential components of cell surfaces and interstitial matrices. Among them, heparan sulfates (HS) are involved in a large number of biological functions, thanks to their ability to bind and regulate a wide array of signaling proteins. These mechanisms are tightly controlled by extracellular enzymes such as HSulf-2 endosulfatase, which modify the structure of HS and their interaction properties.
Researchers from IBS (Structure and activity of Glycosaminoglycans, Vivès team) and CEA-Biosanté (IMAC team, Odile Filhol-Cochet) have shown that HSulf-2 itself carries a GAG chain that acts as a modulator of its activity. As such, its removal (by mutation or enzymatic digestion) significantly increases the activity of the enzyme in vitro, and overexpression of Sulf-2 without a GAG chain in breast cancer cells promotes cell proliferation, migration and invasion, but also tumor growth and lung metastasis in vivo (figure).
This work sheds new light on the regulation of HS by HSulf-2, and for the development of antitumor strategies targeting these enzymes.

Extracellular endosulfatase Sulf-2 harbors a chondroitin/dermatan sulfate chain that modulates its enzyme activity. El Masri R, Seffouh A, Roelants C, Seffouh I, Gout E, Pérard J, Dalonneau F, Nishitsuji K, Noborn F, Nikpour M, Larson G, Crétinon Y, Friedel-Arboleas M, Uchimura K, Daniel R, Lortat-Jacob H, Filhol O, Vivès RR. Cell Reports ; 38(11):110516

Contact : Romain Vivès (IBS/Structure and Activity of Glycosaminoglycans Group)