5f7b: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-'''Unreleased structure'''
-The entry 5f7b is ON HOLD
+==Resting state structure of CuNiR form Alcaligenes faecalis determined at 293 K==
+<StructureSection load='5f7b' size='340' side='right'caption='[[5f7b]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5f7b]] 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=5F7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F7B 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]] 1.56&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f7b OCA], [https://pdbe.org/5f7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f7b RCSB], [https://www.ebi.ac.uk/pdbsum/5f7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f7b 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.
-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.
+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>
-Description: Resting state structure of CuNiR form Alcaligenes faecalis determined at 293 K
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Nureki, O]]
+<div class="pdbe-citations 5f7b" style="background-color:#fffaf0;"></div>
-[[Category: Tse, K.M]]
-[[Category: Inoue, T]]
+==See Also==
-[[Category: Inoue, S]]
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-[[Category: Yumoto, F]]
+== References ==
-[[Category: Murphy, M.E.P]]
+<references/>
-[[Category: Suzuki, M]]
+__TOC__
-[[Category: Iwata, S]]
+</StructureSection>
-[[Category: Sugahara, M]]
+[[Category: Alcaligenes faecalis]]
-[[Category: Mizohata, E]]
+[[Category: Large Structures]]
-[[Category: Nango, E]]
+[[Category: Fukuda Y]]
-[[Category: Fukuda, Y]]
+[[Category: Hatsui T]]
-[[Category: Song, C]]
+[[Category: Inoue S]]
-[[Category: Hatsui, T]]
+[[Category: Inoue T]]
-[[Category: Tono, K]]
+[[Category: Iwata S]]
-[[Category: Nakane, T]]
+[[Category: Joti Y]]
-[[Category: Yabashi, M]]
+[[Category: Kameshima T]]
-[[Category: Nakatsu, T]]
+[[Category: Masuda T]]
-[[Category: Joti, Y]]
+[[Category: Matsugaki N]]
-[[Category: Masuda, T]]
+[[Category: Mizohata E]]
-[[Category: Kameshima, T]]
+[[Category: Murphy MEP]]
-[[Category: Matsugaki, N]]
+[[Category: Nakane T]]
+[[Category: Nakatsu 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]]
+[[Category: Yumoto F]]