4ysc: Difference between revisions
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==Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis== | |||
<StructureSection load='4ysc' size='340' side='right'caption='[[4ysc]], [[Resolution|resolution]] 2.03Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ysc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ysc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysc OCA], [https://pdbe.org/4ysc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysc RCSB], [https://www.ebi.ac.uk/pdbsum/4ysc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysc ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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-A resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-A 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. | |||
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.,Fukuda Y, Tse KM, 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 ME, Inoue T, Iwata S, Mizohata E Proc Natl Acad Sci U S A. 2016 Feb 29. pii: 201517770. PMID:26929369<ref>PMID:26929369</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 4ysc" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Alcaligenes faecalis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Nakane | [[Category: Diederichs K]] | ||
[[Category: | [[Category: Fukuda Y]] | ||
[[Category: | [[Category: Hatsui T]] | ||
[[Category: | [[Category: Hirata K]] | ||
[[Category: | [[Category: Inoue T]] | ||
[[Category: | [[Category: Iwata S]] | ||
[[Category: | [[Category: Joti Y]] | ||
[[Category: | [[Category: Kameshima T]] | ||
[[Category: | [[Category: Matsumura H]] | ||
[[Category: Mizohata E]] | |||
[[Category: Nakane T]] | |||
[[Category: Nango E]] | |||
[[Category: Nureki O]] | |||
[[Category: Song C]] | |||
[[Category: Sugahara M]] | |||
[[Category: Suzuki M]] | |||
[[Category: Tono K]] | |||
[[Category: Tse KM]] | |||
[[Category: Yabashi M]] | |||
Latest revision as of 13:02, 6 September 2023
Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalisCompletely oxidized structure of copper nitrite reductase from Alcaligenes faecalis
Structural highlights
FunctionPublication Abstract from PubMedProton-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-A resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-A 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. Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.,Fukuda Y, Tse KM, 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 ME, Inoue T, Iwata S, Mizohata E Proc Natl Acad Sci U S A. 2016 Feb 29. pii: 201517770. PMID:26929369[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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