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1q0d
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<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> | <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> | ||
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id=' | + | <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> |
| - | + | ||
<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> | <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> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/SODN_STRSO SODN_STRSO] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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]. | </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]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | 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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| - | 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:15173586<ref>PMID:15173586</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1q0d" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] | *[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
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[[Category: Streptomyces seoulensis]] | [[Category: Streptomyces seoulensis]] | ||
[[Category: Superoxide Dismutase]] | [[Category: Superoxide Dismutase]] | ||
| - | [[Category: | + | [[Category: Djinovic Carugo K]] |
| - | + | [[Category: Kang S-O]] | |
| - | [[Category: Kang | + | [[Category: Lee J-W]] |
| - | [[Category: Lee | + | [[Category: Wuerges J]] |
| - | [[Category: Wuerges | + | [[Category: Yim H-S]] |
| - | [[Category: Yim | + | [[Category: Yim Y-I]] |
| - | [[Category: Yim | + | |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state
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