1j9r: Difference between revisions

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<StructureSection load='1j9r' size='340' side='right'caption='[[1j9r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1j9r' size='340' side='right'caption='[[1j9r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1j9r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9R FirstGlance]. <br>
<table><tr><td colspan='2'>[[1j9r]] 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=1J9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9R FirstGlance]. <br>
</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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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]] 2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j9q|1j9q]], [[1j9s|1j9s]], [[1j9t|1j9t]]</div></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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=1j9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9r OCA], [https://pdbe.org/1j9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9r RCSB], [https://www.ebi.ac.uk/pdbsum/1j9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9r ProSAT]</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=1j9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9r OCA], [https://pdbe.org/1j9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9r RCSB], [https://www.ebi.ac.uk/pdbsum/1j9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9r ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1j9r ConSurf].
</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=1j9r ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:11478880<ref>PMID:11478880</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1j9r" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alcfa]]
[[Category: Alcaligenes faecalis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Boulanger, M J]]
[[Category: Boulanger MJ]]
[[Category: Murphy, M E]]
[[Category: Murphy ME]]
[[Category: Curpredoxin fold copper nitrite]]
[[Category: Oxidoreductase]]

Latest revision as of 10:38, 7 February 2024

Crystal structure of nitrite soaked reduced D98N AFNIRCrystal structure of nitrite soaked reduced D98N AFNIR

Structural highlights

1j9r is a 3 chain structure with sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIR_ALCFA

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1j9r, resolution 2.00Å

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