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5ytl

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Current revision (10:25, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5ytl' size='340' side='right'caption='[[5ytl]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='5ytl' size='340' side='right'caption='[[5ytl]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ytl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YTL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ytl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YTL FirstGlance]. <br>
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</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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.401&#8491;</td></tr>
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<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>
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<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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ytl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytl OCA], [http://pdbe.org/5ytl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytl RCSB], [http://www.ebi.ac.uk/pdbsum/5ytl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytl ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ytl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytl OCA], [https://pdbe.org/5ytl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ytl RCSB], [https://www.ebi.ac.uk/pdbsum/5ytl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytl ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A1W6VP04_GEOTD A0A1W6VP04_GEOTD]
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Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO2(-)) to nitric oxide (NO) and the two-electron reduction of dioxygen (O2) to hydrogen peroxide (H2O2). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.
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Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.,Fukuda Y, Matsusaki T, Tse KM, Mizohata E, Murphy MEP, Inoue T Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):769-777. doi:, 10.1107/S2059798318010082. Epub 2018 Jul 24. PMID:30082512<ref>PMID:30082512</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5ytl" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Geobacillus thermodenitrificans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fukuda, Y]]
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[[Category: Fukuda Y]]
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[[Category: Inoue, T]]
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[[Category: Inoue T]]
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[[Category: Matsusaki, T]]
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[[Category: Matsusaki T]]
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[[Category: Mizohata, E]]
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[[Category: Mizohata E]]
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[[Category: Murphy, M E.P]]
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[[Category: Murphy MEP]]
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[[Category: Tse, K M]]
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[[Category: Tse KM]]
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[[Category: Copper]]
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[[Category: Nitrite reductase]]
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[[Category: Oxidoreductase]]
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Current revision

Crystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal

PDB ID 5ytl

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