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‘Molecular films’ shed light on enzyme involved in greenhouse gas production

2DNiR crystal. (A) The T2Cu site after the first exposure to 0.8-MGy X-rays (DS1) with full occupancy of a single-sided nitrite coordinated with T2Cu, Asp92 in proximal position and dual channel waters (W4 and W5). Ile252 and His250 show no changes. (B) The T2Cu site in DS8 (6.4 MGy) with equal occupations of nitrite and NO. No other changes can be seen. (C) The T2Cu site in DS17 (13.6 MGy) with full occupancy of a unilateral NO coordinated to T2Cu. W4 is now gone. (D) The T2Cu site in DS25 (20 MGy) with equal occupations of NO and water (Wa). W4 is now back. (E) The T2Cu site in DS38 (30.4 MGy) with full occupancy of a single water coordinated with T2Cu, mimicking the oxidized T2CuII site in other prototypical CuNiRs. No other changes can be seen. (F) The T2Cu site in the final dataset of the nitrite-bound MSOX series (DS65), after a total of 50 MGy, with the single water (Wa) still coordinated with T2Cu. Asp92 shows signs of burning off due to exceeding the dose limit in the crystal where a loss of density is observed. W4 and W5 are also almost completely gone. 2Fo − Fc electron density maps of residues are contoured at 1σ level. 2Fo − Fc electron density maps of ligands are contoured at the 0.9σ level. T2Cu is shown as a blue sphere. Credit: Procedures of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2205664119″ width=”800″ height=”508″/>

T2Cu site during the MSOX series of a nitrite infused Br2DNiR crystal. (A) The T2Cu site after the first exposure to 0.8-MGy X-rays (DS1) with full occupancy of a single-sided nitrite coordinated with T2Cu, Asp92 in proximal position and dual channel waters (W4 and W5). Ile252 and His250 show no changes. (B) The T2Cu site in DS8 (6.4 MGy) with equal occupations of nitrite and NO. No other changes can be seen. (C) The T2Cu site in DS17 (13.6 MGy) with full occupancy of a unilateral NO coordinated to T2Cu. W4 is now gone. (D) The T2Cu site in DS25 (20 MGy) with equal occupations of NO and water (Wa). W4 is now back. (E) The T2Cu site in DS38 (30.4 MGy) with full occupancy of a single water coordinated with T2Cu, mimicking the oxidized T2CuII site in other prototypical CuNiRs. No other changes can be seen. (F) The T2Cu site in the final dataset of the nitrite-bound MSOX series (DS65), after a total of 50 MGy, with the single water (Wa) still coordinated with T2Cu. Asp92 shows signs of burning off due to exceeding the dose limit in the crystal where a loss of density is observed. W4 and W5 are also almost completely gone. 2Fo − Fc electron density maps of residues are contoured at 1σ level. 2Fo − Fc electron density maps of ligands are contoured at the 0.9σ level. T2Cu is shown as a blue sphere. Credit: Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2205664119

An international team of scientists, led by the University of Liverpool, has created structural films of an important enzyme involved in a biological pathway of greenhouse gas production that provides new insight into its catalytic activity.

A major cause of global warming is the greenhouse gas nitrous oxide, which is 300 times more harmful to the ozone layer than carbon dioxide. Nitrous oxide is a by-product of the denitrification pathway, which occurs when special species of microorganisms remove excess nitrate or nitrite from ecosystems and convert it back to nitrogen gas.

The first step of this process involves an enzyme called copper nitrite reductase (CuNiR), which converts nitrite into nitric oxide gas, using an electron and a proton. Recently, a CuNiR from a Rhizobia species has been discovered with significantly lower catalytic activity. This species is abundant in agriculture and is an important contributor to the denitrification pathway and thus to nitrous oxide.

CuNiR is a metalloprotein, meaning it contains metal ions to function properly. In this case, it contains two copper sites, one where catalysis takes place and another that receives and donates an electron needed for catalysis. Metalloproteins are widespread in biology and make up at least 30% of all proteins.

Researchers from the UK and Japan used single crystal spectroscopy and an X-ray crystallography approach known as MSOX (multiple structures of one crystal) to produce a molecular film of the enzyme to understand why the activity in this CuNiR is much lower. X-ray crystallography is an important technique that allows to visualize the atomic details of biological molecules in three dimensions, helping to understand how they are composed, how they function and how they interact. MSOX is an advancement in this area as catalysis can be visualized in real time.

First author, Ph.D. student Samuel Rose said: “This research is important for two reasons. First, it helps us understand why the activity in this CuNiR is lower compared to others, which could help future bioengineering to combat global warming.” Second, it shows that the MSOX approach along with single crystal spectroscopy is an exciting combination that can help dissect complex redox reactions in other fundamental metalloenzymes.”

Professor Samar Hasnain, who led the research at the University of Liverpool, said: “Only by understanding basic biological and chemical processes will we be able to tackle major environmental problems. Those involved in the production of hydrogen (hydrogenase ), nitrogen utilization (nitrogenases), and photosynthesis (Photosystem II).”

The research was published in Proceedings of the National Academy of Sciences.


Study reveals insights into enzyme that fights a common greenhouse gas


More information:
Samuel L. Rose et al, Single crystal spectroscopy and multiple single crystal structures (MSOX) define catalysis in copper nitrite reductases, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2205664119

Provided by the University of Liverpool

Quote: ‘Molecular movies’ shed light on enzyme involved in greenhouse gas production (2022, Aug. 18) retrieved Aug. 18, 2022 from https://phys.org/news/2022-08-molecular-movies-enzyme-involved -greenhouse.html

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