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New page: left|200px<br /><applet load="1sda" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sda, resolution 2.5Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1sda.gif|left|200px]]<br /><applet load="1sda" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1sda, resolution 2.5&Aring;" />
'''CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE'''<br />


==Overview==
==CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE==
The crystal structure of bovine Cu,Zn superoxide dismutase modified with, peroxynitrite (ONOO-) was determined by X-ray diffraction, utilizing the, existing three-dimensional model of the native structure deposited in the, Brookhaven Protein Data Bank (J. A. Tainer et al., J. Mol. Biol. 160, 181-217, 1982). The native structure and the modified derivative were, refined to R factors of 19.0 and 18.7% respectively using diffraction data, from 6.0 to 2.5 A. The major result after reaction with peroxynitrite was, the appearance of electron density 1.45 A from a single epsilon carbon of, Tyr-108, the only tyrosine residue in the sequence. Tyr-108 is a, solvent-exposed residue 18 A from the copper atom in the active site. The, electron density was consistent with nitration of Tyr-108 at one of the, epsilon carbons to form 3-nitrotyrosine. We propose that the nitration, occurs in solution by transfer of a nitronium-like species from the active, site on one superoxide dismutase dimer to the Tyr-108 of a second dimer.
<StructureSection load='1sda' size='340' side='right'caption='[[1sda]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1sda]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SDA 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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1sda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sda OCA], [https://pdbe.org/1sda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sda RCSB], [https://www.ebi.ac.uk/pdbsum/1sda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sda ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SODC_BOVIN SODC_BOVIN] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
== 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/sd/1sda_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1sda ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of bovine Cu,Zn superoxide dismutase modified with peroxynitrite (ONOO-) was determined by X-ray diffraction, utilizing the existing three-dimensional model of the native structure deposited in the Brookhaven Protein Data Bank (J. A. Tainer et al., J. Mol. Biol. 160, 181-217, 1982). The native structure and the modified derivative were refined to R factors of 19.0 and 18.7% respectively using diffraction data from 6.0 to 2.5 A. The major result after reaction with peroxynitrite was the appearance of electron density 1.45 A from a single epsilon carbon of Tyr-108, the only tyrosine residue in the sequence. Tyr-108 is a solvent-exposed residue 18 A from the copper atom in the active site. The electron density was consistent with nitration of Tyr-108 at one of the epsilon carbons to form 3-nitrotyrosine. We propose that the nitration occurs in solution by transfer of a nitronium-like species from the active site on one superoxide dismutase dimer to the Tyr-108 of a second dimer.


==About this Structure==
Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase.,Smith CD, Carson M, van der Woerd M, Chen J, Ischiropoulos H, Beckman JS Arch Biochem Biophys. 1992 Dec;299(2):350-5. PMID:1444476<ref>PMID:1444476</ref>
1SDA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with NO2, CU, ZN and ACE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SDA OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase., Smith CD, Carson M, van der Woerd M, Chen J, Ischiropoulos H, Beckman JS, Arch Biochem Biophys. 1992 Dec;299(2):350-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1444476 1444476]
</div>
<div class="pdbe-citations 1sda" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Superoxide dismutase]]
[[Category: Beckman JS]]
[[Category: Beckman, J.S.]]
[[Category: Carson M]]
[[Category: Carson, M.]]
[[Category: Chen J]]
[[Category: Chen, J.]]
[[Category: Ischiropoulos H]]
[[Category: Ischiropoulos, H.]]
[[Category: Smith CD]]
[[Category: Smith, C.D.]]
[[Category: Van Der Woerd M]]
[[Category: Woerd, M.Van.Der.]]
[[Category: ACE]]
[[Category: CU]]
[[Category: NO2]]
[[Category: ZN]]
[[Category: oxidoreductase(copper)]]
 
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Latest revision as of 22:13, 26 March 2025

CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE

1sda, resolution 2.50Å

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