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Structural basis of inter-protein electron transfer for nitrite reduction in denitrification

Abstract

Recent earth science studies have pointed out that massive acceleration of the global nitrogen cycle by anthropogenic addition of bio-available nitrogen has led to a host of environmental problems1. Nitrous oxide (N2O) is a greenhouse gas that is an intermediate during the biological process known as denitrification2. Copper-containing nitrite reductase (CuNIR) is a key enzyme in the process; it produces a precursor for N2O by catalysing the one-electron reduction of nitrite () to nitric oxide (NO)3. The reduction step is performed by an efficient electron-transfer reaction with a redox-partner protein4,5,6. However, details of the mechanism during the electron-transfer reaction are still unknown. Here we show the high-resolution crystal structure of the electron-transfer complex for CuNIR with its cognate cytochrome c as the electron donor. The hydrophobic electron-transfer path is formed at the docking interface by desolvation owing to close contact between the two proteins. Structural analysis of the interface highlights an essential role for the loop region with a hydrophobic patch for protein–protein recognition; it also shows how interface construction allows the variation in atomic components to achieve diverse biological electron transfers.

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Figure 1: The electron-transfer complex between AxgNIR and Cyt c551.
Figure 2: The docking interface.
Figure 3: A dominant electron-transfer path in the AxgNIR:Cyt c 551 complex.
Figure 4: Packing of Met 135 at the interface by Cyt c 551 docking.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure are deposited in the Protein Data Bank under accession number 2ZON.

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Acknowledgements

We thank A. Nakagawa, M. Suzuki, M. Yoshimura and E. Yamashita (beamline 44XU at SPring-8) for their support in the collection of X-ray data (proposal numbers 2007A6918 and 2007B6918, to M.N.). This work was supported in part by Grants-in-Aids for Scientific Research 20350078 (to S.S.) and Encouragement of Young Scientists 20750137 (to M.N.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and a Grant for Basic Science Research Projects from the Sumitomo Foundation (to M.N.).

Author Contributions M.N., H.K. and S.S. conceived and designed the project; M.N., H.K., T.N. and K.Y. purified; M.N. and H.K. crystallized; M.N., H.K., K.K. and T.I. conducted experimental works including data collection and structure analysis; M.N. and H.K. performed stopped-flow kinetics and analysed; M.N. and S.S. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Masaki Nojiri or Shinnichiro Suzuki.

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Nojiri, M., Koteishi, H., Nakagami, T. et al. Structural basis of inter-protein electron transfer for nitrite reduction in denitrification . Nature 462, 117–120 (2009). https://doi.org/10.1038/nature08507

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