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

Journal of Biochemistry
Yohta FukudaEiichi Mizohata

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.

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Citations

Mar 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Yohta FukudaEiichi Mizohata
Nov 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Takanori NakaneEiichi Mizohata
Mar 16, 2017·Acta Crystallographica. Section F, Structural Biology Communications·Yohta FukudaTsuyoshi Inoue
Apr 1, 2017·Scientific Reports·Tetsuya MasudaMichihiro Sugahara
Jul 14, 2017·Metallomics : Integrated Biometal Science·Sam HorrellMichael A Hough
Mar 16, 2018·Metallomics : Integrated Biometal Science·Masami Lintuluoto, Juha Mikael Lintuluoto
Aug 8, 2018·Acta Crystallographica. Section D, Structural Biology·Yohta FukudaTsuyoshi Inoue
Apr 8, 2017·Scientific Reports·Michihiro SugaharaSo Iwata
Mar 15, 2019·IUCrJ·Diederik Johannes OppermanFelix Martín Ferroni
Feb 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yohta FukudaTaro Tamada
Oct 5, 2021·Acta Crystallographica. Section D, Structural Biology·Gabriela C Schröder, Flora Meilleur

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