Solving the puzzle of the extraordinary cofactor: It's now crystal clear

Published September 13, 2017

For the past several years, Michigan State University researchers have been working to solve a puzzle—one step at a time. Now, they have put another piece in place. And one part of the resulting picture is crystal clear.

The figure above depicts two views of the Hexameric quaternary structure of the LarE enzyme, highlighting its metal-binding site. MSU's Robert Hausinger and Jian Hu's labs combined sructural biology and enzymatic approaches to clarify the catalytic mechanism of an unusual enzyme that could ultimately have applications in human health and medicine.

“We now have a crystal structure that allows us to see how the electrons are pushed around and understand how the sulfur transfer reaction works,” said Robert Hausinger, a professor of microbiology and molecular genetics and of biochemistry and molecular biology, who is collaborating with Jian Hu, assistant professor of chemistry and of biochemistry and molecular biology.

This most recent work builds on the earlier discovery of a previously unknown cofactor—a nonprotein chemical compound containing nickel plus nicotinic acid (vitamin B3)—called an (SCS)Ni(II) pincer complex, where “SCS” means that the nickel ion is coordinated by two sulfur atoms and one carbon atom. Hausinger named it the “extraordinary cofactor.”

After this initial discovery, the researchers went back to the lab to figure out exactly how the cofactor was made, setting out to solve the puzzle of how several bacteria make this complex molecule. The results of that research showing the roles for LarB, LarE and LarC enzymes were published last spring in the Proceedings of the National Academy of Sciences (PNAS).

Now, the scientists have taken it a step further. Their current work was published in PNAS in August.

In their newest paper, the scientists’ laboratories combined structural biology and enzymatic approaches to clarify the catalytic mechanism of this unusual enzyme. Nine crystal structures of LarE were solved by postdoctoral researcher Matthias Fellner, who is a member of Hausinger’s lab.

“LarE is a newly identified enzyme that catalyzes an unusual sulfur-sacrificing reaction involving two substrates and several key residues,” Hu said. “In order to make the reaction happen, these components have to approach with proper orientations.

“By solving the crystal structures of LarE in distinct functional states, we are able to locate these key elements in the three-dimensional space and therefore provide a structural basis for how the substrates and the catalytic residues react in the highly ordered multiple-step sequential reaction,” Hu explained. “In addition, the structural work enabled us to propose a mechanism explaining the enigmatic sulfur-sacrificing process. The crystallographic work in this research represents an important advance in the clarification of the catalytic mechanism of this unusual enzyme.”

The earlier stages of this research project were carried out by Benoît Desguin, a postdoctoral scholar at MSU who has now returned to his home at Université Catholique de Louvain in Belgium.

“We still have the question we started with—why is the nickel there?” Hausinger said. “It’s not clear what the nickel is doing, and we still have the question of exactly how this co-factor is made in living cells; we know in general the pathway and now we know one enzyme, but we don’t know how some of the other enzymes work in the pathway. Furthermore, the idea that maybe this nickel pincer complex is being used for other purposes, or that it can somehow be designed for other purposes, that’s intriguing.”

The researchers intend to continue to develop better assays, and explore the enzyme mechanisms and how catalysis occurs in those proteins. Further discoveries could have applications in human health and medicine.