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1q0d

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[[Image:1q0d.gif|left|200px]]<br /><applet load="1q0d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1q0d, resolution 2.20&Aring;" />
 
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'''Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state'''<br />
 
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==Overview==
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==Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state==
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Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.
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<StructureSection load='1q0d' size='340' side='right'caption='[[1q0d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1q0d]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis]. The October 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Superoxide Dismutase'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_10 10.2210/rcsb_pdb/mom_2007_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0D FirstGlance]. <br>
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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]] 2.2&#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=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=1q0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0d OCA], [https://pdbe.org/1q0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0d RCSB], [https://www.ebi.ac.uk/pdbsum/1q0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SODN_STRSO SODN_STRSO]
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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/q0/1q0d_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=1q0d ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1Q0D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=3NI:'>3NI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 1Q0D with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb94_1.html Superoxide Dismutase]]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0D OCA].
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*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of nickel-containing superoxide dismutase reveals another type of active site., Wuerges J, Lee JW, Yim YI, Yim HS, Kang SO, Djinovic Carugo K, Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8569-74. Epub 2004 Jun 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15173586 15173586]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: RCSB PDB Molecule of the Month]]
[[Category: Streptomyces seoulensis]]
[[Category: Streptomyces seoulensis]]
[[Category: Superoxide Dismutase]]
[[Category: Superoxide Dismutase]]
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[[Category: Superoxide dismutase]]
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[[Category: Djinovic Carugo K]]
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[[Category: Carugo, K Djinovic.]]
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[[Category: Kang S-O]]
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[[Category: Kang, S O.]]
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[[Category: Lee J-W]]
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[[Category: Lee, J W.]]
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[[Category: Wuerges J]]
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[[Category: Wuerges, J.]]
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[[Category: Yim H-S]]
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[[Category: Yim, H S.]]
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[[Category: Yim Y-I]]
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[[Category: Yim, Y I.]]
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[[Category: 3NI]]
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[[Category: SO4]]
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[[Category: homohexamer of four-helix bundles]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:34:32 2008''
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Current revision

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state

PDB ID 1q0d

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