1ndr

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[[Image:1ndr.gif|left|200px]]
 
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{{Structure
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==CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS==
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|PDB= 1ndr |SIZE=350|CAPTION= <scene name='initialview01'>1ndr</scene>, resolution 3.0&Aring;
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<StructureSection load='1ndr' size='340' side='right'caption='[[1ndr]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Monomer+A+Type+1+Cu+Site'>AC1</scene>, <scene name='pdbsite=AC2:Monomer+A+Type+2+Cu+Site'>AC2</scene>, <scene name='pdbsite=BC1:Monomer+B+Type+1+Cu+Site'>BC1</scene>, <scene name='pdbsite=BC2:Monomer+B+Type+2+Cu+Site'>BC2</scene>, <scene name='pdbsite=CC1:Monomer+C+Type+1+Cu+Site'>CC1</scene> and <scene name='pdbsite=CC2:Monomer+C+Type+2+Cu+Site'>CC2</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>
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<table><tr><td colspan='2'>[[1ndr]] is a 3 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=1NDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDR 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]] 3&#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></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=1ndr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndr OCA], [https://pdbe.org/1ndr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndr RCSB], [https://www.ebi.ac.uk/pdbsum/1ndr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndr ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ndr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndr OCA], [http://www.ebi.ac.uk/pdbsum/1ndr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ndr RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/NIR_ALCXX NIR_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/1ndr_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=1ndr 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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Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been determined. Alcaligenes xylosoxidans has been shown to have a blue-copper nitrite reductase (AxNiR) and two azurins with 67% homology both of which donate electrons to it effectively. The first crystal structure of a blue NiR (AxNiR) in its oxidized and nitrite-bound forms, with particular emphasis to the Cu sites, is presented. The Cu-Smet distance is the same as those in the green NiR's. Thus, the length of this interaction is unlikely to be responsible for differences in colour. Crystallographic data presented here taken together with structural data of other single Cu type-1 proteins and their mutants suggest that the displacement of Cu from the strong ligand plane is perhaps the cause for the differences in colour observed for otherwise 'classical' blue Cu centre. Nitrite is observed binding to the catalytic Cu in a bidentate fashion displacing the water molecule, offering a neat rationalization for the XAFS observation that the type-2 Cu-ligand distances increase on nitrite binding as a result of increased coordination. These results are discussed in terms of enzyme mechanism.
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'''CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS'''
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Structures of a blue-copper nitrite reductase and its substrate-bound complex.,Dodd FE, Hasnain SS, Abraham ZH, Eady RR, Smith BE Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):406-18. PMID:15299906<ref>PMID:15299906</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1ndr" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been determined. Alcaligenes xylosoxidans has been shown to have a blue-copper nitrite reductase (AxNiR) and two azurins with 67% homology both of which donate electrons to it effectively. The first crystal structure of a blue NiR (AxNiR) in its oxidized and nitrite-bound forms, with particular emphasis to the Cu sites, is presented. The Cu-Smet distance is the same as those in the green NiR's. Thus, the length of this interaction is unlikely to be responsible for differences in colour. Crystallographic data presented here taken together with structural data of other single Cu type-1 proteins and their mutants suggest that the displacement of Cu from the strong ligand plane is perhaps the cause for the differences in colour observed for otherwise 'classical' blue Cu centre. Nitrite is observed binding to the catalytic Cu in a bidentate fashion displacing the water molecule, offering a neat rationalization for the XAFS observation that the type-2 Cu-ligand distances increase on nitrite binding as a result of increased coordination. These results are discussed in terms of enzyme mechanism.
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*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1NDR 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=1NDR OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structures of a blue-copper nitrite reductase and its substrate-bound complex., Dodd FE, Hasnain SS, Abraham ZH, Eady RR, Smith BE, Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):406-18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299906 15299906]
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[[Category: Achromobacter xylosoxidans]]
[[Category: Achromobacter xylosoxidans]]
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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: Abraham ZHL]]
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[[Category: Abraham, Z H.L.]]
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[[Category: Dodd FE]]
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[[Category: Dodd, F E.]]
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[[Category: Eady RR]]
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[[Category: Eady, R R.]]
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[[Category: Hasnain SS]]
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[[Category: Hasnain, S S.]]
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[[Category: Smith BE]]
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[[Category: Smith, B E.]]
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[[Category: blue copper nitrite reductase]]
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[[Category: copper protein]]
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[[Category: nitrite reduction]]
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[[Category: reductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:28:58 2008''
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Current revision

CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

PDB ID 1ndr

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