Discovering a whole new family of copper-binding proteins

Discovering a whole new family of copper-binding proteins

While studying a class of copper-containing enzymes, a team of researchers discovered and characterised a new family of fungal proteins. Their study has now been published on Nature Chemical Biology, including analysis performed at BioMAX. The article is published together with a parallel study that sheds light on one of the potential biological roles of the proteins in this new family.

In contrast with a certain romanticised idea of research, scientific discoveries seldom come with a shouted “eureka!” as to mark the end of a linear intellectual endeavour. Much more frequently, new scientific findings emerge from observations where a scientist’s first reaction might sound like “that’s odd…”. Perhaps that was how the authors of this study reacted when they realised what they were looking at wasn’t what they were looking for.

In an article published this week on Nature Chemical Biology, a team of scientists from INRA, University of Copenhagen, Marseille Université, and University of York characterised a new family of proteins, named X325, found in various fungal lineages. The article is published together with a parallel study in which one protein of this new family, Bim1, is described as involved in fungal meningitis.

The authors were initially searching for new lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes specialised in the degradation of polysaccharides and widely used in the production of biofuels. The proteins of this new family seemed promising candidates since they share many structural features and a probable common ancestor with LPMOs. However, the researchers proved that the members of this LPMO-like protein family are not involved in polysaccharides degradation, but they more likely play a role in the regulation of copper ion content in the organisms where they are expressed.

Archive image of BioMAX endstation. BioMAX is the first X-ray macromolecular crystallography beamline of MAX IV Laboratory, in user operations since 2017.

“While investigating a family of proteins discovered by our co-workers in Marseille and Duke University, we discovered that their copper-binding site was similar to the one found in our favourite enzymes LPMOs”, says Leila Lo Leggio, Professor at University of Copenhagen and leader of one of the teams that authored this work. “However, the binding site in the new family of proteins was a little different, with an extra chemical group binding to the copper ion, and other structural features that just did not fit with this enzymatic role, which indeed has now been dismissed by our excellent co-workers who have looked at the biochemical features.”

Prof Lo Leggio’s team came to MAX IV and performed x-ray diffractions experiments at BioMAX beamline to characterise these new proteins. “At BioMAX we collected X-ray diffraction data on crystals grown at different conditions which turned out in three different space groups” explain Tobias Tandrup and Kristian Frandsen, respectively PhD student and Postdoc in Lo Leggio’s team and authors of the study. “The data converged and were very important in solving the structure of LaX325 and elucidating the active site configuration.” 

The results the team obtained at BioMAX on LaX325 not only were instrumental in order to illustrate the structural similarities and differences between proteins of the X325 family and LPMOs, but they also served as homology model for characterising Bim1, the X325 protein studied in the parallel article published this week on Nature Chemical Biology and co-authored by Prof Lo Leggio.

Header image: Copper binding site of two different proteins. Left: LaX325 protein belonging to the newly identified LPMO-like protein family X325. Right: cellulose cleaving LPMO enzyme TaAA9. Image developed by Tobias Tandrup, University of Copenhagen.

Read the full articles here

Labourel, A., Frandsen, K.E.H., Zhang, F. et al.
A fungal family of lytic polysaccharide monooxygenase-like copper proteins.
Nat Chem Biol (2020)

Garcia-Santamarina, S., Probst, C., Festa, R.A. et al.
A lytic polysaccharide monooxygenase-like protein functions in fungal copper import and meningitis.
Nat Chem Biol (2020)

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