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Unusual monooxygenase mechanism adds oxygen to molecules without oxidizing them

Aminoperoxide adduct on the enzyme’s cofactor leads to these nonoxidative oxygenation reactions

by Celia Henry Arnaud
February 19, 2020 | A version of this story appeared in Volume 98, Issue 8


Crystal structure of the flavin monooxygenase RutA with a blow-up of the active site containing the flavin cofactor, molecular oxygen, and uracil.
Credit: Nat. Chem. Biol.
A crystal structure of the flavin monooxygenase showing the locations of the flavin cofactor, oxygen, and the uracil substrate. For inset, red = O; blue = N; white, yellow, and orange = C.

Cells use flavin monooxygenases to break down foreign molecules by adding oxygen atoms to them. Biochemists have long assumed that the enzymes use a particular cofactor adduct to add the oxygen. A new study suggests that some of these enzymes use a different adduct—one that significantly changes the reaction mechanism.

A team led by Robin Teufel of the University of Freiburg reports that some flavin monooxygenases use a flavin cofactor with a peroxide attached to a nitrogen on the molecule called N5 (Nat. Chem. Biol. 2020, DOI: 10.1038/s41589-020-0476-2). Most known monooxygenases instead have a peroxide attached to a carbon C4a on the flavin cofactor.

The change in where the peroxide forms leads to unexpected reactions. A peroxide oxygen nucleophilically attacks the substrate, which gets oxygenated but not oxidized. “It allows the enzymes to attack rather unreactive substrates such as modified aromatic rings and cleave these relatively stable bonds,” Teufel says.

Reaction scheme showing an aminoperoxide-containing flavin cofactor transforming hexachlorobenzene to pentachlorophenol.
An aminoperoxide-containing flavin cofactor transforms hexachlorobenzene to pentachlorophenol.

To figure out that the enzyme was using a flavin N5-peroxide adduct, Teufel and his team used O2-pressurized X-ray crystallography to capture structures of a monooxygenase called RutA with its cofactor and substrates. The structures show that an O2 molecule sits right next to the N5 position. “Just by looking at the geometry of approach to the flavin, you can directly see that reaction with the N5 is much more likely than reaction with C4a,” Teufel says.

The enzyme forms a pocket that keeps the oxygen and substrate on opposite sides of the cofactor. “The O2 has a protected environment to react with the flavin-N5,” Teufel says. After reacting with O2 to form N5-peroxide, the nitrogen flips so that the peroxide faces the substrate.

The novel mechanism applies to at least three flavin monooxygenases. RutA from Escherichia coli catalyzes carbon-nitrogen bond cleavage in uracil. DszA from Rhodococcus erythropolis catalyzes carbon-sulfur bond cleavage in dibenzothiophene sulfone. And HcbA1 from a Nocardioides strain catalyzes carbon-chlorine bond cleavage in hexachlorobenzene.

Hexachlorobenzene and dibenzothiophene sulfone are persistent pollutants. “There’s the potential to further optimize these enzymes and apply them in the bioremediation of these pollutants,” Teufel says. But he notes that such applications are still a long way off.

“This is the first time that an N-peroxide species was clearly identified and described in a flavoprotein reaction mechanism while interacting with a substrate,” says Dirk Tischler, an expert on monooxygenases at Ruhr University Bochum. The team could identify this novel adduct only through “the combination of relevant protein candidates together with a special X-ray crystallography method.”

Teufel suspects that more enzymes using the N5-peroxide remain to be found, because bioinformatic analyses suggest that the structural motif for aminoperoxide formation is widespread in nature.



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