Celebrating the International Year of Crystallography with methylation of Nod Factor


Each year, ~150 million tonnes of atmospheric nitrogen are converted to plant nutrients (reducing the load of artificial fertilizers) by soil bacteria, called rhizobia, that live in symbiosis with legume plants, such as lupine. The association is highly specific and before it starts, the symbionts must recognize each other via exchange of precise chemical signals. The plant's root produces characteristic flavonoids, while the bacterial 'business card', called nodulation factor (NF), is an oligosaccharide molecule with a unique pattern of strange chemical decorations. The nodulation factor is named very adequately: once recognized, it will induce formation of root nodules, to be colonized by the bacterial partner. Rhizobia have unique biosynthetic pathways to produce NF, involving about a dozen of specialized proteins. One of them is NodS, an enzyme that decorates the Nod factor with a methyl group (CH3), transferred from a donor molecule called SAM. Dr. Ozgur Cakici, working at the Center for Biocrystallographic Research in Poznan (Poland), discovered the crystal structure of NodS and was able to elucidate its enzymatic mechanism, so elegantly shown in the movie. The enzyme starts with an open conformation, which allows docking of the SAM molecule. Upon SAM binding, the protein conformation changes dramatically, burying the donor molecule and forming a docking platform for the NF acceptor. When the NF molecule completes the tripartite complex, the methyl group gets transferred, and the products can depart the enzyme. The last component to leave is SAH, a molecule generated from SAM by methyl group removal. The open NodS molecule is ready to start a new catalytic cycle.

To solve the structure of NodS and of its complex with SAH, Ozgur first genetically modified bacterial cells for production of the protein in a variant containing selenium (Se) atoms. Crystals of that protein were taken for diffraction experiments to a synchrotron center that provided an extremely powerful X-ray beam with tunable wavelength. The experimental data were the basis for structure determination, which utilized the method of multiwavelength anomalous diffraction (MAD).

Dr. Cakici's results were published in Acta Crystallographica (Acta Cryst. F64, 1149-1152, 2008) and in the Journal of Molecular Biology (J. Mol. Biol. 404, 874-889, 2010).


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Last update: April 14, 2014 (MJ)