How nitrous oxide is decomposed: Researchers identify structure of enzyme that breaks down potent greenhouse gas

Nitrous oxide (N2O) is a harmful climate gas. Its effect as a greenhouse gas is 300 times stronger than that of carbon dioxide. Nitrous oxide destroys the ozone layer. In industrial agriculture, it is generated on excessively fertilized fields when microorganisms decompose nitrate fertilizers. Decomposition of nitrous oxide frequently is incomplete and strongly depends on environmental conditions. Researchers from Freiburg, Constance, and KIT have now identified the structure of the enzyme that decomposes nitrous oxide and the decomposition mechanism.

Their results are published in the journal Nature.

The study demonstrated that the N2O-reductase enzyme possesses active centers made up of four copper atoms and two sulfur atoms. "Surprisingly, we found that microbiologists all over the world have assumed an incorrect structure so far," explains Professor Oliver Einsle, group leader at the Institute of Organic Chemistry and Biochemistry of the University of Freiburg. Scientists have assumed a single sulfur atom only and have not been able to completely identify the nitrous oxide decomposition mechanism. Based on the new data, the reaction sequence of the enzyme can be modeled much better. Future investigations are to provide further details and help understand which influence environmental conditions have on the process.

"It was of decisive importance that all steps of our investigation were executed in the absence of air oxygen," emphasizes Walter G. Zumft, retired professor of Karlsruher Institute of Technology. In contact with oxygen, parts of the enzyme react and the enzyme changes its structure. Together with Dr. Anja Pomowski from the University of Freiburg, the bacteria were cultivated under an oxygen-free atmosphere, the enzymes were isolated on a large scale, crystallized, and the structure was analyzed using X-rays. The team of four authors was completed by Professor Peter Kroneck from the University of Constance.

"The current study provides interesting and complementary insight into the nitrogen cycle," says Dr. Ralf Kiese from the KIT Institute of Meteorology and Climate Research. Nitrous oxide and nitrogen production on fields, pastures, and in forests depends on a multitude of often opposing effects. Last year, a KIT study demonstrated that animal husbandry may lead to less nitrous oxide unter certain conditions (doi:10.1038/nature08931). Detailed knowledge of microbial processes and their dependence on environmental conditions might help to better model the nitrous oxide contribution to the climate. In the long term, it might even be feasible to use the knowledge in order to prevent nitrous oxide from being released into the atmosphere, for example, by additives in fertilizers that preserve the functioning of N2O-reductase or by optimized processes in sewage treatment plants.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by Karlsruhe Institute of Technology.

Journal References:

Anja Pomowski, Walter G. Zumft, Peter M. H. Kroneck, Oliver Einsle. N2O binding at a [4Cu:2S] copper–sulphur cluster in nitrous oxide reductase. Nature, 2011; DOI: 10.1038/nature10332Benjamin Wolf, Xunhua Zheng, Nicolas Brüggemann, Weiwei Chen, Michael Dannenmann, Xingguo Han, Mark A. Sutton, Honghui Wu, Zhisheng Yao, Klaus Butterbach-Bahl. Grazing-induced reduction of natural nitrous oxide release from continental steppe. Nature, 2010; 464 (7290): 881 DOI: 10.1038/nature08931

Evonik has reduced its specific energy-related greenhouse gas emissions by sixteen percent compared to 2004

Evonik Industries has significantly improved its CO2 efficiency. The Group has been able to reduce its specific energy-related greenhouse gas emissions in chemical production by sixteen percent; compared to the previous year, the improvement in 2010 was a full three percent. This is highlighted in the company’s 2010 Corporate Responsibility Report, which was recently presented in Brussels. This success means that Evonik has moved another step closer to its self-imposed goal of reducing the specific energy-related greenhouse gases of its chemical activities to twenty percent below the level of 2004 by 2014.

60 percent of CO2 emissions in 2010 were energy-related and 40 percent related to chemical processes. Absolute emissions of greenhouse gases increased to 9.14 million metric tons CO2 equivalents in 2010, a rise of 11 percent over the previous year (2009: 8.23). At the same time, specific emissions, i.e. emissions relative to output, declined by 3 percent. Accordingly, Evonik has successfully detached its production growth from rising emissions. “Our significantly increased energy efficiency is making an important contribution to climate protection" says Klaus Engel, the Chairman of the Evonik Executive Board.

With the global economy regaining momentum, the Group returned to operating its chemical production facilities at full capacity in 2010, in many cases with optimized efficiency. A number of efficiency enhancement measures contributed to the reduction of specific greenhouse gas emissions.  These included the start-up of a new cogeneration power plant in Antwerp (Belgium) and a more efficient installation for thermal incineration of exhaust gases from the production of the feed additive methionine. In addition, Evonik initiated selective energy-saving programs at its site in Rheinfelden (Germany). During the 2010 financial year, Evonik invested a total of 36 million Euro in environmental protection for its chemical business activities.

“We want to be successful as a supplier of competitive products and technologies that also make a contribution to sustainability. At the same time, we want to be a responsible, reliable and fair partner for our customers, employees and society and meet the demands made by our shareholders,” noted CEO Klaus Engel.

Evonik invested some €338 million in research and development in 2010. The Group pursued about 500 different projects, of which approximately 100 focused on resource efficiency.

The Corporate Responsibility (CR) efforts of Evonik provide answers for challenges of the future, such as resource efficiency. Says Christine Anders, Head of CR at Evonik: “Corporate Responsibility is an integral part of our business and we plan to keep fine-tuning our CR strategy in 2011.” With its three dimensions of Business, Employees, and Processes, the CR strategy is a fixed component of the corporate strategy, providing support and new impulses.  In 2010, the Group identified important sustainability topics as part of so-called materiality analyses and intensified its dialog with stakeholders.

The Evonik Corporate Responsibility Report 2010 for the first time met the requirements for the highest application level A+ of the Global Reporting Initiative (GRI). GRI is the internationally recognized standard for comprehensive sustainability reporting and confirmed the A+ reporting level for Evonik. Large parts of the report underwent a business audit by an auditing firm.

 

Supermarkets Try to Clean Up Another Spill: Greenhouse Gases

 WARMING FROM COOLING: Leaks from grocery store refrigerators are a big source of potent greenhouse gases. Image: Flickr/Copyright daveynin

On top of the usual "spills in aisle five," grocery stores have another mess they're hoping to clean up: greenhouse gas leaks.

U.S. EPA announced yesterday that its partnership to cut greenhouse gas emissions from grocery stores has reached 50 states. The partnership, called GreenChill, now has 7,000 members, about a fifth of all supermarkets in the United States.

Much of their carbon footprint comes from the electricity that powers their lights, soda fountains, meat slicers and other equipment. But there's a subtler, sometimes bigger source of greenhouse gases: the massive refrigerators and the systems that keep them frosty.

Grocery stores use a network of pipes and pumps to get coolant to the refrigerators. The coolants are typically greenhouse gases that, if they escape, have a global warming effect hundreds or thousands of times greater than carbon dioxide's.

"If you have a lot of piping, if you have a lot of joints, the probability of leaking is greater," said Karim Amrane, vice president of regulatory and research at the Air-Conditioning, Heating and Refrigeration Institute, a trade group representing equipment manufacturers.

EPA doesn't directly regulate these emissions, so it set up GreenChill in 2007 to encourage supermarkets to act on the issue voluntarily. The agency has offered Silver, Gold and Platinum awards to grocery stores that prevent the gases from seeping.

One Platinum awardee, Star Market in Newton, Mass., used to need 4,000 pounds of refrigerant; now it needs 275. According to the manufacturers of the new equipment, just a pound of this refrigerant has the same effect as 3,800 pounds of CO2.

Big opportunities for reductions
On top of that, the store believes it has plugged up many of the common leaks. Where it would normally store refrigerant in 2,000-pound cisterns, now it uses dozens of 11-pound cells. If any of them springs a leak, the total emissions are far smaller.

A store doesn't have to be state-of-the-art, like Star Market, to benefit the climate. If every grocery store in the United States were just at the level of the average GreenChill member, EPA claims, it would save the equivalent of 22 million tons of CO2 a year.

That's roughly the annual emissions of 4.3 million cars. It would also save the stores $100 million -- cash they wouldn't have to pay for replacing their elusive coolants.

Cindy Newberg, a branch chief at EPA's Stratospheric Protection Division, said GreenChill's 7,000 members will benchmark their refrigerants to see how much they're losing and where. The companies can also share information about best practices.

Greenpeace wants to take the issue even further. The group yesterday won a Harvard University award for pushing green refrigeration with major world retailers, including Safeway, Wal-Mart and Kroger.

Debate over 'natural refrigerants'
In November, 400 such retailers committed to stop using hydrofluorocarbons -- coolants that affect the climate far more than CO2 -- by 2015.

HFCs, as they're known, are the main refrigerant in use today. But Amy Larkin, a solutions director for Greenpeace, said Greenpeace has long been wary of them.

"When HFCs were introduced in the early 1990s, Greenpeace said, 'Whoa. This is a horrible substitution for CFCs, because they may not carve a hole in the ozone, but they will kill us with global warming,'" she said.

Larkin and these companies believe the technology for "natural refrigerants," such as ammonia, CO2 and even some fossil fuels, isn't far away. These coolants have far weaker effects on the climate than HFCs.

Amrane, of AHRI, the air-conditioning trade group, was more skeptical.

He said there are coolants with low global warming effects, but even if they keep the food cold, they may pose safety hazards. "There's always a trade-off," he said.

A tiny bit of propane or butane in a household refrigerator poses little risk, he said, but a large system, such as the one in a grocery store, is a different beast. "From a safety standpoint, having hundreds of pounds of propane might not be a safe thing to have," he said.

EPA is still evaluating whether the compromise on the federal budget for 2011 will affect the GreenChill program.

Reprinted from Climatewire with permission from Environment & Energy Publishing, LLC. www.eenews.net, 202-628-6500

 

Greenhouse gas-producing enzyme may yield insights into earliest oxygen-breathing ancestor evolution

 Every year, nitrogen-metabolizing bacteria in the soil and seas churn out more than ten billion kilograms of nitrous oxide (N2O) gas as they respire in these oxygen-deficient environments.

Nitric oxide reductase (NOR) enzymes are the powerhouse underlying production of this gas, taking pairs of nitric oxide (NO) molecules and transforming them into N2O and water via a chemical reaction known as ‘reduction’. These enzymes also help pathogenic bacteria to evade destruction by the immune system, as some T cells use NO as a chemical weapon against infectious agents.

More generally, scientists are interested in the potential to employ these enzymes as a tool for synthesizing useful, customized molecules for a variety of applications. “The nitrogen-oxygen bond cleavage and nitrogen–nitrogen bond formation reactions executed by these enzymes are the essence of chemistry,” says Yoshitsugu Shiro of the RIKEN SPring-8 Center in Harima.

Although a great deal is known about the biochemical properties of these proteins, scientists have found it challenging to determine the structure of bacterial NOR in fine detail. Now, after seven years of hard work, Shiro and colleagues have finally obtained the first such structure for NOR from Pseudomonas aeruginosa, a pathogenic bacterium associated with opportunistic infections in immune-compromised patients (Fig. 1).

Not-so-distant relations

Although all NOR enzymes execute essentially the same chemical reaction to produce N2O, they can be subdivided into three major classes: cNOR, qNOR and qCuNOR. The enzyme crystallized by Shiro and colleagues (Fig. 2) belongs to the cNOR family, and contains a subunit known as cytochrome c that also enables bacteria to engage in aerobic (oxygen-driven) respiration. This ability to switch from oxygen-based to nitrogen-based respiration is highly beneficial for survival in the oxygen-poor conditions deep in the soil or beneath the waves.

 

Accordingly, cNORs are thought to be closely related to the cytochrome oxidases (COX), enzymes that play a central role in aerobic respiration, and these new findings have revealed a number of structural parallels between the two. “There is a long history of research into these respiratory enzymes, COX and NOR, and a lot of knowledge on NOR has been accumulated by biochemical, chemical, molecular biology and microbiological studies,” says Shiro. “From these points of view, our NOR structure is not surprising, but seeing is believing!”

The reduction process is dependent on the directional transport of electrons and protons, and COX and cNOR appear to closely resemble one another in terms of the structure of their electron-transfer networks. Both enzymes depend on precisely positioned metal ions to enable electron transport, and the four iron atoms contained within cNOR are arranged in a configuration that closely resembles COX, maintained via interactions between these positively charged iron atoms and a set of evolutionarily conserved, negatively charged histidine and glutamate amino acids.

On the other hand, the researchers observed some notable differences with regard to the movement of protons. Both COX and cNOR are bound within membranes, but COX contains channels that are believed to direct the flow of protons across the membrane from the interior of the cell. This flow helps generate electrical potential that subsequently powers a variety of cellular motors. However, cNOR lacks such membrane-spanning channels, and protons entering the enzyme from the exterior of the cell only make it as far as the membrane interior, where the reductase catalytic site is located.

Back to the beginning

Even with a structure in hand for this well-studied enzyme, a number of mysteries remain to be addressed. For example, these data are insufficient to resolve an ongoing debate over the fine details of the N2O production mechanism. Shiro and colleagues were readily able to identify the two iron atoms involved in catalysis, but their structure reveals insufficient space at this ‘active site’ to accommodate the two molecules of NO believed to be required for this reaction.

“The NOR active site is tightly packed and very crowded,” says Shiro. “This observation suggests that some conformational change [is] needed to achieve catalytic turnover, but no one knows of any such conformational change so far.” Resolving this issue will require the acquisition of additional, high-resolution structures that might offer clear snapshots of the enzyme at intermediate stages in the catalytic process.

This structure offers tentative support for the hypothesis that the COX aerobic respiratory machinery originally evolved from NOR enzymes, although additional work will clearly be required to confirm this. Unlike NOR, which exclusively employs iron ions, COX makes use of both copper and iron for catalysis, and the researchers have tentatively identified a few amino acid changes that might have enabled this transition to take place. In addition, although NOR lacks the ‘K-channel’ that allows COX to deliver protons from the cytoplasm, Shiro’s team has identified some structural elements that could potentially represent early evolutionary precursors in the formation of this channel.

In future studies, Shiro plans to develop experimental tests for some of these still-speculative models. “We want to follow the molecular evolution of the respiratory enzymes from anaerobic to aerobic conditions on Earth, from NOR to COX,” he says. “Using mutagenesis, based on our structural comparisons, we are hoping to convert NO-reducing NOR into oxygen-reducing COX.” For the present, though, he is optimistic that this structure will give a boost to researchers seeking to understand and manipulate this enzymatic process. “Scientists worldwide who are interested in NO reduction can enter a new stage of NOR research with this structure,” he says.

More information: Hino, T., et al. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330, 1666–1670 (2010). http://www.science … 666.abstract

Provided by RIKEN (news : web)