1dqi: Difference between revisions

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New page: left|200px<br /><applet load="1dqi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dqi, resolution 1.7Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1dqi.gif|left|200px]]<br /><applet load="1dqi" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dqi, resolution 1.7&Aring;" />
'''CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS RESOLUTION'''<br />


==Overview==
==CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS RESOLUTION==
Superoxide reductase (SOR) is a blue non-heme iron protein that functions, in anaerobic microbes as a defense mechanism against reactive oxygen, species by catalyzing the reduction of superoxide to hydrogen peroxide, [Jenney, F. E., Jr., Verhagen, M. F. J. M., Cui, X. , and Adams, M. W. W., (1999) Science 286, 306-309]. Crystal structures of SOR from the, hyperthermophilic archaeon Pyrococcus furiosus have been determined in the, oxidized and reduced forms to resolutions of 1.7 and 2.0 A, respectively., SOR forms a homotetramer, with each subunit adopting an, immunoglobulin-like beta-barrel fold that coordinates a mononuclear, non-heme iron center. The protein fold and metal center are similar to, those observed previously for the homologous protein desulfoferrodoxin, from Desulfovibrio desulfuricans [Coelho, A. V., Matias, P., Fulop, V., Thompson, A., Gonzalez, A., and Carrondo, M. A. (1997) J. Bioinorg. Chem., 2, 680-689]. Each iron is coordinated to imidazole nitrogens of four, histidines in a planar arrangement, with a cysteine ligand occupying an, axial position normal to this plane. In two of the subunits of the, oxidized structure, a glutamate carboxylate serves as the sixth ligand to, form an overall six-coordinate, octahedral coordinate environment. In the, remaining two subunits, the sixth coordination site is either vacant or, occupied by solvent molecules. The iron centers in all four subunits of, the reduced structure exhibit pentacoordination. The structures of the, oxidized and reduced forms of SOR suggest a mechanism by which superoxide, accessibility may be controlled and define a possible binding site for, rubredoxin, the likely physiological electron donor to SOR.
<StructureSection load='1dqi' size='340' side='right'caption='[[1dqi]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dqi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQI 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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1dqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqi OCA], [https://pdbe.org/1dqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqi RCSB], [https://www.ebi.ac.uk/pdbsum/1dqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqi ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SOR_PYRFU SOR_PYRFU] Uses electrons from reduced NADP, by way of rubredoxin and an oxidoreductase, to catalyze the reduction of superoxide to hydrogen peroxide.
== 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/dq/1dqi_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=1dqi ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DQI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with FE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DQI OCA].
*[[Superoxide Reductase|Superoxide Reductase]]
 
__TOC__
==Reference==
</StructureSection>
Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states., Yeh AP, Hu Y, Jenney FE Jr, Adams MW, Rees DC, Biochemistry. 2000 Mar 14;39(10):2499-508. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10704199 10704199]
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Single protein]]
[[Category: Adams MWW]]
[[Category: Adams, M.W.W.]]
[[Category: Hu Y]]
[[Category: Hu, Y.]]
[[Category: Jenney Jr FE]]
[[Category: Jr., F.E.Jenney.]]
[[Category: Rees DC]]
[[Category: Rees, D.C.]]
[[Category: Yeh AP]]
[[Category: Yeh, A.P.]]
[[Category: FE]]
[[Category: immunoglobulin-like (ig) beta barrel fold]]
[[Category: non-heme iron protein]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:29:55 2007''

Latest revision as of 09:57, 7 February 2024

CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS RESOLUTIONCRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS RESOLUTION

Structural highlights

1dqi is a 4 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SOR_PYRFU Uses electrons from reduced NADP, by way of rubredoxin and an oxidoreductase, to catalyze the reduction of superoxide to hydrogen peroxide.

Evolutionary Conservation

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

See Also

1dqi, resolution 1.70Å

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