2e81

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[[Image:2e81.jpg|left|200px]]
 
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{{Structure
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==Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine==
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|PDB= 2e81 |SIZE=350|CAPTION= <scene name='initialview01'>2e81</scene>, resolution 2.0&Aring;
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<StructureSection load='2e81' size='340' side='right'caption='[[2e81]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene> and <scene name='pdbligand=HOA:HYDROXYAMINE'>HOA</scene>
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<table><tr><td colspan='2'>[[2e81]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Wolinella_succinogenes_DSM_1740 Wolinella succinogenes DSM 1740]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E81 FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2&#8491;</td></tr>
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|GENE=
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<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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HOA:HYDROXYAMINE'>HOA</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene></td></tr>
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}}
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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=2e81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e81 OCA], [https://pdbe.org/2e81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e81 RCSB], [https://www.ebi.ac.uk/pdbsum/2e81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e81 ProSAT]</span></td></tr>
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</table>
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'''Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine'''
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== Function ==
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[https://www.uniprot.org/uniprot/NRFA_WOLSU NRFA_WOLSU] Plays a role in nitrite reduction.<ref>PMID:10672190</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/2e81_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2e81 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.
Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.
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==About this Structure==
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Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase.,Einsle O, Messerschmidt A, Huber R, Kroneck PM, Neese F J Am Chem Soc. 2002 Oct 2;124(39):11737-45. PMID:12296741<ref>PMID:12296741</ref>
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2E81 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Wolinella_succinogenes Wolinella succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E81 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase., Einsle O, Messerschmidt A, Huber R, Kroneck PM, Neese F, J Am Chem Soc. 2002 Oct 2;124(39):11737-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12296741 12296741]
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</div>
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[[Category: Nitrite reductase (cytochrome; ammonia-forming)]]
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<div class="pdbe-citations 2e81" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Wolinella succinogenes]]
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[[Category: Einsle, O.]]
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[[Category: Kroneck, P M.H.]]
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[[Category: CA]]
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[[Category: HEM]]
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[[Category: HOA]]
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[[Category: YT3]]
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[[Category: multiheme cytochrome]]
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[[Category: nitrite reductase]]
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[[Category: reaction intermediate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:36:35 2008''
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==See Also==
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*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Wolinella succinogenes DSM 1740]]
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[[Category: Einsle O]]
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[[Category: Kroneck PMH]]

Current revision

Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine

PDB ID 2e81

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