5D4I

Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography

Summary for 5D4I

• Entry DOI: 10.2210/pdb5d4i/pdb
• Related: 5D4H 5D4J
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, NITRITE ION, ... (4 entities in total)
• Functional Keywords: copper, oxidoreductase
• Biological source: Alcaligenes faecalis
• Cellular location: Periplasm: P38501
• Total number of polymer chains: 3
• Total formula weight: 111579.06

Authors

Fukuda, Y.,Tse, K.M.,Nakane, T.,Nakatsu, T.,Suzuki, M.,Sugahara, M.,Inoue, S.,Masuda, T.,Yumoto, F.,Matsugaki, N.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Murphy, M.E.P.,Inoue, T.,Iwata, S.,Mizohata, E. (deposition date: 2015-08-07, release date: 2016-03-09, Last modification date: 2023-09-06)

Primary citation

Fukuda, Y.,Tse, K.M.,Nakane, T.,Nakatsu, T.,Suzuki, M.,Sugahara, M.,Inoue, S.,Masuda, T.,Yumoto, F.,Matsugaki, N.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Murphy, M.E.,Inoue, T.,Iwata, S.,Mizohata, E.
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Proc.Natl.Acad.Sci.USA, 113:2928-2933, 2016

PubMed Abstract: Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.

PubMed: 26929369
DOI: 10.1073/pnas.1517770113

Experimental method

X-RAY DIFFRACTION (1.6 Å)