• Number 355  |
• January 30, 2012

Key atom could be secret behind nitrogenase

If we could make plant food from nitrogen the way nature does, we’d have a much greener method for manufacturing fertilizer – a process that requires such high temperatures and pressures that it consumes about 1.5 percent of the world’s energy.

Scientist working at DOE's SLAC National Accelerator Laboratory have taken an important step towards understanding how nature performs this feat by identifying a single atom that plays a key role in the process.

The atom lies at the heart of an enzyme called nitrogenase, which helps convert nitrogen in the air into a form that living things can use. Scientists have been trying to figure out its structure for a long time.   Among other things, they hope to eventually reverse-engineer it and mimic nature’s gentle version of the reaction.

“The fascination with this enzyme is the fact that it enables this reaction to take place at room temperature and atmospheric pressure,” said chemist Serena DeBeer of Cornell University and the Max Planck Institute for Bioinorganic Chemistry, who led the team that performed crucial experiments at SLAC. So hot was the race to identify the mystery atom that it ended in a photo finish: in the Nov. 18 issue of Science, two independent teams, using different approaches, identified the atom as carbon.

The atom’s location inside a cage-like cluster of metal atoms made it hard to get at, so the scientists would need a trick.  They used an intense beam of X-rays from the Stanford Synchrotron Radiation Lightsource to knock the innermost electrons out of iron atoms in the cage. Normally other electrons from iron would fill this hole; but there was a tiny chance, much less than one in a thousand, that the hole would be filled by an electron belonging to the central mystery atom.  That’s what happened.  When it did, the process emitted X-rays that revealed that the mystery atom was carbon.   This technique, known as X-ray emission spectroscopy or XES, had been developed by SLAC’s Uwe Bergmann over the past decade.

“This was a simple but important question and we were able to give a straightforward answer,” said Bergmann, who was a co-author of the paper.   “I think this will have a big impact not only on the understanding of nitrogenase but on the use of X-ray emission spectroscopy.”

Why is this one atom so important? This particular metal cluster is where nitrogen molecules from the air, N2, are broken down and converted to ammonia and other useful compounds by microbes in the soil. Plants take up these nitrogen compounds and spread them through the food chain. This is how we get roughly half of the nitrogen in our bodies; the rest comes from artificial fertilizers made via the Haber-Bosch reaction, the resource-intensive method widely used to convert atmospheric nitrogen to ammonia.  Put another way: If not for the nitrogen provided by manufactured fertilizer, roughly half the world’s current population would not be alive today. 

Researchers knew a decade ago that the central atom in the metal cluster must be nitrogen, oxygen or carbon. Each would affect the reaction differently. But how to identify this one atom among the 20,545 total carbon atoms, 11,026 oxygen atoms and 5,431 nitrogen atoms in the enzyme?

“Because it’s sequestered in the middle of a bunch of metal atoms and you’ve got no way to get your hands on it, it’s a really hard problem,” said chemist Brian Hoffman of Northwestern University, who has investigated nitrogenase for 30 years but was not involved in these studies. “What the team has done would appear to be a classic case where new technology leads to new science.”

[Glennda Chui, 650.926.4897,
glennda@slac.stanford.edu]