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Institut de Biologie StructuraleGrenoble / France

Highlights

Scientists uncover mechanism allowing bacteria to survive the human immune system

A team of scientists at the University of East Anglia (UEA) and the IBS (Metalloproteins Group) have uncovered molecular details of how pathogenic bacteria fight back against the human immune response to infection. Every step towards understanding this complex process paves the way to the possibility of developing intervention strategies that disable the response. Details

Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding. Anne Volbeda, Erin L. Dodd, Claudine Darnault, Jason C. Crack, Oriane Renoux, Matthew I. Hutchings, Nick E. Le Brun & Juan C. Fontecilla-Camps. Nature Com

Development of innovative strategies to monitor formation of biological structures

The spontaneous formation of biological higher order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. NMR spectroscopy possesses the unique ability to monitor structural changes in real-time, however its size limitation and time resolution constraints remain a challenge when studying the self-assembly of large biological particles.
In the framework of the ERC SeeNanoLifeInAction project, scientists from IBS groups report the application of methyl specific isotopic labeling combined with relaxation-optimized NMR spectroscopy to overcome both size- and time-scale limitations. They report for the first time the self-assembly process of a half-megadalton protein complex that was monitored at the structural level, including the characterization of intermediate states, using a mutagenesis free strategy. NMR was used to obtain individual kinetics data on the different transient intermediates and the formation of final native particle. In addition, complementary time-resolved electron microscopy and native mass spectrometry were used to characterize the low-resolution structures of oligomerization intermediates.

Unraveling Self-Assembly Pathways of the 468 kDa Proteolytic Machine TET2. Pavel Macek, Rime Kerfah, Elisabetta Boeri Erba, Elodie Crublet, Christine Moriscot, Guy Schoehn, Carlos Amero, Jerome Boisbouvier. Science Advances; vol3, n4, e1601601

The remarkable complexity of vitamin B6 biosynthesis

The main enzyme responsible for the biosynthesis of vitamin B6 is the dodecameric enzyme Pdx1, whose mechanism has long been enigmatic. Pdx1 catalyses the condensation of two phosphorylated carbohydrates and ammonia into an active form of vitamin B6. The complex reaction involves more than ten catalytic steps and two distant active sites. Among the numerous intermediates that are successively formed during the reaction, several are coloured, facilitating their detection in crystallo by optical spectroscopy at the IBS/ESRF Cryobench prior to structure determination on the Structural Biology beamlines. Of particular interest is the formation of the I320 intermediate, which strongly absorbs in the UV region, and forms after the first carbohydrate and ammonia have been added. The crystallographic structure shows formation of a double covalent adduct between two distant lysine residues, one from each active site. A reorientation of one lysine later in the mechanism displaces the product from the first to the second active site. The bridging position of the I320 intermediate is an elegant solution for intermediate transfer, and represents a novel example of substrate channelling, where the use of covalent tethers prevent the loss of intermediates to surrounding solvent and maintain a high local concentration of substrate.

Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Rodrigues M, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes J, Royant A, Evans G, Sinning I, Ealick S, Begley T & Tews I. Nat. Chem. Biol.;13(3):290-294.