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4YSE

High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis

Summary for 4YSE
Entry DOI10.2210/pdb4yse/pdb
Related4YSA 4YSC 4YSD 4YSO 4YSP 4YSQ 4YSR 4YSS 4YST 4YSU
DescriptorCopper-containing nitrite reductase, COPPER (II) ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
Functional Keywordsnitrite, copper, reductase, oxidoreductase
Biological sourceAlcaligenes faecalis
Total number of polymer chains3
Total formula weight112450.35
Authors
Primary citationFukuda, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.2 Å)
Structure validation

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