1ndr: Difference between revisions

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[[Image:1ndr.png|left|200px]]


{{STRUCTURE_1ndr| PDB=1ndr | SCENE= }}
==CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS==
<StructureSection load='1ndr' size='340' side='right'caption='[[1ndr]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIR_ALCXX NIR_ALCXX]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS===
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>


{{ABSTRACT_PUBMED_15299906}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 1ndr" style="background-color:#fffaf0;"></div>
[[1ndr]] is a 3 chain structure of [[Nitric reductase]] with 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].


==See Also==
==See Also==
*[[Nitric reductase|Nitric reductase]]
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:015299906</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Achromobacter xylosoxidans]]
[[Category: Achromobacter xylosoxidans]]
[[Category: Abraham, Z H.L.]]
[[Category: Large Structures]]
[[Category: Dodd, F E.]]
[[Category: Abraham ZHL]]
[[Category: Eady, R R.]]
[[Category: Dodd FE]]
[[Category: Hasnain, S S.]]
[[Category: Eady RR]]
[[Category: Smith, B E.]]
[[Category: Hasnain SS]]
[[Category: Blue copper nitrite reductase]]
[[Category: Smith BE]]
[[Category: Copper protein]]
[[Category: Nitrite reduction]]
[[Category: Reductase]]

Latest revision as of 09:30, 9 August 2023

CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANSCRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Structural highlights

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

Function

NIR_ALCXX

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Dodd FE, Hasnain SS, Abraham ZH, Eady RR, Smith BE. Structures of a blue-copper nitrite reductase and its substrate-bound complex. Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):406-18. PMID:15299906 doi:10.1107/S0907444997002667

1ndr, resolution 3.00Å

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