Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography

Yohta Fukuda, Ka Man Tse, Mamoru Suzuki, Kay Diederichs, Kunio Hirata, Takanori Nakane, Michihiro Sugahara, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Changyong Song, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Hiroyoshi Matsumura, Tsuyoshi Inoue, So Iwata, Eiichi Mizohata

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 Å resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR.

Original languageEnglish
Pages (from-to)527-538
Number of pages12
JournalJournal of biochemistry
Volume159
Issue number5
DOIs
Publication statusPublished - 2016 May 1

Keywords

  • X-ray free-electron laser
  • copper
  • electron transfer
  • enzyme
  • serial femtosecond crystallography

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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  • Cite this

    Fukuda, Y., Tse, K. M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., & Mizohata, E. (2016). Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography. Journal of biochemistry, 159(5), 527-538. https://doi.org/10.1093/jb/mvv133