1ndt

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[[Image:1ndt.jpg|left|200px]]
 
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==NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS==
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The line below this paragraph, containing "STRUCTURE_1ndt", creates the "Structure Box" on the page.
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<StructureSection load='1ndt' size='340' side='right'caption='[[1ndt]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ndt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.1&#8491;</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
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{{STRUCTURE_1ndt| PDB=1ndt | SCENE= }}
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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=1ndt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndt OCA], [https://pdbe.org/1ndt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndt RCSB], [https://www.ebi.ac.uk/pdbsum/1ndt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O68601_ALCXX O68601_ALCXX]
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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/nd/1ndt_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=1ndt 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 ==
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Denitrification is one of the main steps of the global nitrogen cycle that is sustained by prokaryotic organisms. Denitrifying bacteria use two entirely different enzymes in this process, one based on haem cd1 prosthetic groups and the other on type 1-type 2 Cu centres. Copper-containing nitrite reductases (NiRs) are sub-divided into blue and green NiRs, which are respectively thought to be redox partners of azurins and pseudo-azurins. Crystallographic structures of the blue nitrite reductase from Alcaligenes xylosoxidans (AxNiR) are presented in the oxidised hexagonal form and the substrate-bound orthorhombic form to 2.1 A and 2.8 A resolution, respectively. The complete amino acid sequence of AxNiR has been determined by conventional chemical analysis. A 3 A structure of AxNiR has been published where the modelling was based on the sequence of another blue NiR. The higher resolution of the hexagonal form together with the correct sequence allows a detailed comparison with the crystallographic structures of the green NiRs. There is a striking difference in the overall surface charge distribution between the two sub-groups, providing a neat structural explanation for their different reactivities to pseudoazurin or azurin and supporting the view that electron transfer proceeds via complex formation. A detailed examination of the type-1 Cu site, the site responsible for the colour, reveals several subtle differences, including a lateral displacement of 0.7 A for Smet. The structure of the type-2 Cu site, and changes that occur upon substrate binding are discussed in terms of the catalytic mechanism. The similarity of the type 2 Cu site to the catalytic Zn site in carbonic anhydrase and the catalytic Cu site of superoxide dismutase is re-examined in view of the high-resolution (2.1 A) structure.
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'''NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS'''
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X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner.,Dodd FE, Van Beeumen J, Eady RR, Hasnain SS J Mol Biol. 1998 Sep 18;282(2):369-82. PMID:9735294<ref>PMID:9735294</ref>
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==Overview==
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Denitrification is one of the main steps of the global nitrogen cycle that is sustained by prokaryotic organisms. Denitrifying bacteria use two entirely different enzymes in this process, one based on haem cd1 prosthetic groups and the other on type 1-type 2 Cu centres. Copper-containing nitrite reductases (NiRs) are sub-divided into blue and green NiRs, which are respectively thought to be redox partners of azurins and pseudo-azurins. Crystallographic structures of the blue nitrite reductase from Alcaligenes xylosoxidans (AxNiR) are presented in the oxidised hexagonal form and the substrate-bound orthorhombic form to 2.1 A and 2.8 A resolution, respectively. The complete amino acid sequence of AxNiR has been determined by conventional chemical analysis. A 3 A structure of AxNiR has been published where the modelling was based on the sequence of another blue NiR. The higher resolution of the hexagonal form together with the correct sequence allows a detailed comparison with the crystallographic structures of the green NiRs. There is a striking difference in the overall surface charge distribution between the two sub-groups, providing a neat structural explanation for their different reactivities to pseudoazurin or azurin and supporting the view that electron transfer proceeds via complex formation. A detailed examination of the type-1 Cu site, the site responsible for the colour, reveals several subtle differences, including a lateral displacement of 0.7 A for Smet. The structure of the type-2 Cu site, and changes that occur upon substrate binding are discussed in terms of the catalytic mechanism. The similarity of the type 2 Cu site to the catalytic Zn site in carbonic anhydrase and the catalytic Cu site of superoxide dismutase is re-examined in view of the high-resolution (2.1 A) structure.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1NDT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDT OCA].
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</div>
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<div class="pdbe-citations 1ndt" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner., Dodd FE, Van Beeumen J, Eady RR, Hasnain SS, J Mol Biol. 1998 Sep 18;282(2):369-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9735294 9735294]
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*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Achromobacter xylosoxidans]]
[[Category: Achromobacter xylosoxidans]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dodd, F E.]]
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[[Category: Dodd FE]]
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[[Category: Eady, R R.]]
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[[Category: Eady RR]]
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[[Category: Hasnain, S S.]]
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[[Category: Hasnain SS]]
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[[Category: Vanbeeumen, J.]]
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[[Category: Vanbeeumen J]]
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[[Category: Blue copper]]
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[[Category: Copper]]
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[[Category: Nitrite reductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:24:59 2008''
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Current revision

NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

PDB ID 1ndt

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