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5d4j

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Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

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Retrieved from "http://52.214.119.220/wiki/index.php/5d4j"

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 ==Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals==
-<StructureSection load='5d4j' size='340' side='right' caption='[[5d4j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5d4j' size='340' side='right'caption='[[5d4j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5d4j]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D4J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5d4j]] 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=5D4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D4J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d4h|5d4h]], [[5d4i|5d4i]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></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=5d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4j OCA], [https://pdbe.org/5d4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d4j RCSB], [https://www.ebi.ac.uk/pdbsum/5d4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d4j ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5d4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d4j OCA], [http://pdbe.org/5d4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d4j RCSB], [http://www.ebi.ac.uk/pdbsum/5d4j PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
-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>
+==See Also==
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5d4j" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Fukuda, Y]]
+[[Category: Alcaligenes faecalis]]
-[[Category: Inoue, S]]
+[[Category: Large Structures]]
-[[Category: Inoue, T]]
+[[Category: Fukuda Y]]
-[[Category: Iwata, S]]
+[[Category: Inoue S]]
-[[Category: Joti, Y]]
+[[Category: Inoue T]]
-[[Category: Kameshima, T]]
+[[Category: Iwata S]]
-[[Category: Matsugaki, N]]
+[[Category: Joti Y]]
-[[Category: Mizohata, E]]
+[[Category: Kameshima T]]
-[[Category: Murphy, M E.P]]
+[[Category: Matsugaki N]]
-[[Category: Nakane, T]]
+[[Category: Mizohata E]]
-[[Category: Nakatsu, T]]
+[[Category: Murphy MEP]]
-[[Category: Nango, E]]
+[[Category: Nakane T]]
-[[Category: Nureki, O]]
+[[Category: Nakatsu T]]
-[[Category: Song, C]]
+[[Category: Nango E]]
-[[Category: Sugahara, M]]
+[[Category: Nureki O]]
-[[Category: Suzuki, M]]
+[[Category: Song C]]
-[[Category: Tono, K]]
+[[Category: Sugahara M]]
-[[Category: Tse, K M]]
+[[Category: Suzuki M]]
-[[Category: Yabashi, M]]
+[[Category: Tono K]]
-[[Category: Yumoto, F]]
+[[Category: Tse KM]]
-[[Category: Copper]]
+[[Category: Yabashi M]]
-[[Category: Oxidoreductase]]
+[[Category: Yumoto F]]

5d4j

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Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

Structural highlights

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