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| | <StructureSection load='6p73' size='340' side='right'caption='[[6p73]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='6p73' size='340' side='right'caption='[[6p73]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p73]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P73 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P73 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p73]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P73 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ubr|3ubr]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </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=6p73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p73 OCA], [https://pdbe.org/6p73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p73 RCSB], [https://www.ebi.ac.uk/pdbsum/6p73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p73 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=6p73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p73 OCA], [http://pdbe.org/6p73 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p73 RCSB], [http://www.ebi.ac.uk/pdbsum/6p73 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p73 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NRFA_SHEON NRFA_SHEON]] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182] | + | [https://www.uniprot.org/uniprot/NRFA_SHEON NRFA_SHEON] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6p73" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6p73" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pacheco, A]] | + | [[Category: Shewanella oneidensis]] |
| - | [[Category: Schmidt, M]] | + | [[Category: Pacheco A]] |
| - | [[Category: Nitrite reduction]] | + | [[Category: Schmidt M]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
NRFA_SHEON Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
Publication Abstract from PubMed
Cytochrome c nitrite reductase (ccNiR) is a periplasmic, decaheme homodimeric enzyme that catalyzes the six-electron reduction of nitrite to ammonia. Under standard assay conditions catalysis proceeds without detected intermediates, and it has been assumed that this is also true in vivo. However, this report demonstrates that it is possible to trap a putative intermediate by controlling the electrochemical potential at which reduction takes place. UV/vis spectropotentiometry showed that nitrite-loaded Shewanella oneidensis ccNiR is reduced in a concerted two-electron step to generate an {FeNO}(7) moiety at the active site, with an associated midpoint potential of +246 mV vs SHE at pH 7. By contrast, cyanide-bound active site reduction is a one-electron process with a midpoint potential of +20 mV, and without a strong-field ligand the active site midpoint potential shifts 70 mV lower still. EPR analysis subsequently revealed that the {FeNO}(7) moiety possesses an unusual spectral signature, different from those normally observed for {FeNO}(7) hemes, that may indicate magnetic interaction of the active site with nearby hemes. Protein film voltammetry experiments previously showed that catalytic nitrite reduction to ammonia by S. oneidensis ccNiR requires an applied potential of at least -120 mV, well below the midpoint potential for {FeNO}(7) formation. Thus, it appears that an {FeNO}(7) active site is a catalytic intermediate in the ccNiR-mediated reduction of nitrite to ammonia, whose degree of accumulation depends exclusively on the applied potential. At low potentials the species is rapidly reduced and does not accumulate, while at higher potentials it is trapped, thus preventing catalytic ammonia formation.
Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism.,Ali M, Stein N, Mao Y, Shahid S, Schmidt M, Bennett B, Pacheco AA J Am Chem Soc. 2019 Aug 28;141(34):13358-13371. doi: 10.1021/jacs.9b03036. Epub, 2019 Aug 19. PMID:31381304[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ali M, Stein N, Mao Y, Shahid S, Schmidt M, Bennett B, Pacheco AA. Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism. J Am Chem Soc. 2019 Aug 28;141(34):13358-13371. doi: 10.1021/jacs.9b03036. Epub, 2019 Aug 19. PMID:31381304 doi:http://dx.doi.org/10.1021/jacs.9b03036
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