REDUCTIVE DEHALOGENASE STRUCTURES STRUCTURAL BIOLOGY: Enzymes use
vitamin B-12 in an unusual way
I
N RECENT WEEKS, two independent teams have
reported long-sought X-ray crystal structures of two enzymes that remove halides from molecules with help from vitamin B-12. These so-called reductive dehalogenase enzymes enable some bacteria to breathe organohalides like other organisms breathe oxygen. A better understanding of these enzymes could lead to improved bioremediation of pollutants such as halogenated solvents. In one study, structural biologist Holger Dobbek of Humboldt University of Berlin; microbiologist Gabriele Diekert of Friedrich Schiller University, in Jena, Germany; and coworkers report crystal structures of a reductive dehalogenase from the bacterium Sulfurospirillum multivorans alone and in the presence of its substrate trichloroethylene (Science 2014, DOI: 10.1126/ science.1258118). In the other study, structural biologist David Leys and coworkers at the University of Manchester, in England, report a crystal structure and propose two possible catalytic mechanisms of a reductive dehalogenase from the bacterium Nitratireductor pacificus (Nature 2014, DOI: 10.1038/nature13901). These structures represent the first detailed pictures of a specific class of B-12-dependent enzymes. Vitamin B-12, also known as cobalamin, is a cofactor that consists of cobalt coordinated to a tetrapyrrole ring. In other classes of B-12-dependent enzymes, the cobalt bonds to carbon on the substrate molecule. But
in this class of enzymes, cobalt bonds with a halide atom on the substrate, the new structures reveal. Dobbek and coworkers were surprised by the size of the substratebinding pocket. “We only realized once we had the substrate inside how tight this active site is,” Dobbek says. The trichloroethylene substrate fit in the space “like a hand in a glove.” Leys and coworkers weren’t able to get a structure of the N. pacificus enzyme with its substrate. Instead, they performed electron paramagnetic resonance (EPR) experiments with the enzyme and 2,6-dibromophenol as a substrate to narrow down potential reaction CLOSE-UP A view mechanisms. They propose two possibilities that of the active site of a are consistent with their data. reductive dehalogenase In one mechanism, the reaction includes nufrom N. pacificus, cleophilic attack of Co(I) on the halogen and transhown docked with sient formation of a halogen-Co(III) species with a 3,5-dibromo-4subsequent reduction to Co(II). The other possihydroxybenzoic acid bility involves cleavage of the carbon-halogen bond substrate. following formation of an aryl radical. “Guided by structural and elegant EPR spectroscopic data, Leys and colleagues propose a provocative mechanism for cobalamin-dependent reductive dehalogenases, which have been notoriously difficult to study,” says Ruma V. Banerjee, a professor of biological chemistry at the University of Michigan Medical School who is an expert on B-12-dependent enzymes. The researchers hope that organisms that use enzymes like the ones reported could be used in bioremediation. According to Leys, “Clearly, some of these bacteria have made it their business to survive entirely on mopping up whatever chlorinated entities are in the environment.”—CELIA ARNAUD
CLEAN TECHNOLOGY Start-up Skyonic opens CO2-to-chemicals plant In San Antonio last week, the start-up firm Skyonic opened what it claims to be an industrial first: a commercial-scale facility that captures carbon dioxide emissions and converts them into salable chemicals. Built at a cost of $125 million, the facility will consume up to 75,000 metric tons per year of CO2 generated as a by-product at an adjacent cement plant. The company expects to log $48 million in sales and $28 million in earnings annually by marketing the resulting sodium bicarbonate and hydrochloric acid. The chemicals are made in a process
patented by Skyonic founder Joe Jones. The firm uses conventional electrolysis to turn sodium chloride into sodium hydroxide, chlorine, and hydrogen. It then reacts sodium hydroxide with CO2 to form sodium bicarbonate. The chlorine and hydrogen that remain are converted into hydrochloric acid. In a report generated for the Department of Energy, which put $28 million into the project, Skyonic acknowledges that the energy-intensive electrolysis process does subtract from the plant’s CO2 reduction benefit. But the firm still calculates a net CO2 savings, especially
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when the chemical sales are considered. John Thompson, director of the fossil transition program at the Clean Air Task Force, a nonprofit that has been following Skyonic’s progress, agrees that the project should turn a profit. “That’s a good thing,” he says. Thompson points out that the bicarbonate and HCl markets aren’t big enough to support multiple plants of this type, but he notes that Skyonic plans to apply its technology to the production of limestone and other raw materials for the huge concrete industry.—MICHAEL MCCOY
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