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1j9q

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[[Image:1j9q.gif|left|200px]]
 
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{{Structure
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==Crystal structure of nitrite soaked oxidized D98N AFNIR==
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|PDB= 1j9q |SIZE=350|CAPTION= <scene name='initialview01'>1j9q</scene>, resolution 1.65&Aring;
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<StructureSection load='1j9q' size='340' side='right'caption='[[1j9q]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>
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<table><tr><td colspan='2'>[[1j9q]] 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=1J9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9Q FirstGlance]. <br>
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|ACTIVITY= <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>
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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]] 1.65&#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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
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|DOMAIN=
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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=1j9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9q OCA], [https://pdbe.org/1j9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9q RCSB], [https://www.ebi.ac.uk/pdbsum/1j9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9q ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1j9r|1J9R]], [[1j9s|1J9S]], [[1j9t|1J9T]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9q OCA], [http://www.ebi.ac.uk/pdbsum/1j9q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j9q RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
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== Evolutionary Conservation ==
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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/j9/1j9q_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1j9q ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of nitrite soaked oxidized D98N AFNIR'''
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==See Also==
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*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.
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==About this Structure==
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1J9Q is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9Q OCA].
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==Reference==
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Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate., Boulanger MJ, Murphy ME, Biochemistry. 2001 Aug 7;40(31):9132-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11478880 11478880]
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[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
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[[Category: Nitrite reductase (NO-forming)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Boulanger MJ]]
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[[Category: Boulanger, M J.]]
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[[Category: Murphy ME]]
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[[Category: Murphy, M E.]]
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[[Category: cupredoxin fold copper nitrite]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:30:31 2008''
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Current revision

Crystal structure of nitrite soaked oxidized D98N AFNIR

PDB ID 1j9q

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