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Structural Biology

Bacterial enzyme packs its catalysis into one tiny chamber

The structure is the smallest known biological reaction chamber found

by Celia Arnaud
October 31, 2018 | APPEARED IN VOLUME 96, ISSUE 44

09644-scicon3-enzyme.jpg
Credit: Tobias Erb/Max Planck Society
The ligase (pink), dehydratase (yellow), and reductase (blue) domains of propionyl-CoA synthase are arranged around a shared reaction chamber.

Enzymes that catalyze multiple reactions from a reactant to a product often have evolved a way to get intermediates from one active site to another. Researchers report that one bacterial enzyme uses a tiny chamber to sequester all of its chemistry in one place. The structure is the smallest compartment for biological reactions yet observed.

Tobias J. Erb, a researcher at the Max Planck Institute for Terrestrial Microbiology and a member of C&EN’s Talented 12 Class of 2015, and coworkers found the compartment when they solved a crystal structure of the enzyme propionyl-CoA synthase (PCS) from Erythrobacter sp. NAP1 (Nat. Chem. Biol. 2018, DOI: 10.1038/s41589-018-0153-x). The enzyme catalyzes the conversion of 3-hydroxypropionate to propionyl-CoA as part of the microbe’s carbon dioxide fixation pathway.

The 400-kilodalton protein is a dimer of identical subunits, each of which contains three catalytic domains fused together. The first domain is a ligase that attaches the biomolecule coenzyme A to 3-hydroxypropionate. Then a dehydratase domain removes water, forming the toxic intermediate acrylyl-CoA. Finally, a reductase domain converts the intermediate to the final product.

“It’s not simply three enzymes fused to each other,” Erb says. “They are fused to each other in a way that they form a compartment.”

Other compartments for biological reactions exist in cells, such as protein shells called micro- and nanocompartments in bacteria and archaea. This enzyme chamber is a mere 33 nm3, which is significantly smaller than bacterial microcompartments and known nanocompartments.

With its central reaction chamber, PCS also differs from other known fusion enzymes, in which the individual active sites are usually connected by nanoscale tunnels.

The researchers found that the three domains work together in a concerted fashion. The enzyme undergoes synchronized conformational changes that let substrates and products in and out of the reaction chamber.

This kind of coordination also allows the enzyme to sequester the reaction pathway’s toxic intermediate. Acrylyl-CoA is almost “too hot to handle,” for a cell, says Andrew D. Hanson, a biochemist at the University of Florida. “This triple fusion provides the oven glove.”

This new structure will give synthetic biologists inspiration for designing biological systems involving synchronized reactions, says Cheryl Kerfeld, an expert on bacterial microcompartments and carbon fixation at Lawrence Berkeley National Laboratory and Michigan State University.

Erb hopes to find more examples of enzymes with similar reaction chambers. “I’m pretty sure that nature has built other fusion enzymes that look similar,” he says. “The question is where to look for them. We should carefully look into enzymes that seem to have three or four domains fused to each other.”

In the meantime, his team is working to incorporate the enzyme into artificial CO2 fixation pathways and artificial chloroplasts.

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