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1qnn

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[[Image:1qnn.gif|left|200px]]<br />
 
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<applet load="1qnn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qnn, resolution 1.80&Aring;" />
 
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'''CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PORPHYROMONAS GINGIVALIS'''<br />
 
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==Overview==
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==Cambialistic superoxide dismutase from Porphyromonas gingivalis==
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The crystal structure of cambialistic superoxide dismutase (SOD) from, Porphyromonas gingivalis, which exhibits full activity with either Fe or, Mn at the active site, has been determined at 1.8-A resolution by, molecular replacement and refined to a crystallographic R factor of 17.9%, (Rfree 22.3%). The crystals belong to the space group P212121 (a = 75.5 A, b = 102.7 A, c = 99.6 A) with four identical subunits in the asymmetric, unit. Each pair of subunits forms a compact dimer, but not a tetramer, with 222 point symmetry. Each subunit has 191 amino-acid residues most of, which are visible in electron density maps, and consists of seven alpha, helices and one three-stranded antiparallel beta sheet. The metal ion, a 3, : 1 mixture of Fe and Mn, is coordinated with five ligands (His27, His74, His161, Asp157, and water) arranged at the vertices of a trigonal, bipyramid. Although the overall structural features, including the metal, coordination geometry, are similar to those found in other single-metal, containing SODs, P. gingivalis SOD more closely resembles the dimeric, Fe-SODs from Escherichia coli rather than another cambialistic SOD from, Propionibacterium shermanii, which itself is rather similar to other, tetrameric SODs.
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<StructureSection load='1qnn' size='340' side='right'caption='[[1qnn]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qnn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QNN 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]] 1.8&#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=FE:FE+(III)+ION'>FE</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=1qnn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnn OCA], [https://pdbe.org/1qnn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qnn RCSB], [https://www.ebi.ac.uk/pdbsum/1qnn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SODF_PORGI SODF_PORGI] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
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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/qn/1qnn_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=1qnn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of cambialistic superoxide dismutase (SOD) from Porphyromonas gingivalis, which exhibits full activity with either Fe or Mn at the active site, has been determined at 1.8-A resolution by molecular replacement and refined to a crystallographic R factor of 17.9% (Rfree 22.3%). The crystals belong to the space group P212121 (a = 75.5 A, b = 102.7 A, c = 99.6 A) with four identical subunits in the asymmetric unit. Each pair of subunits forms a compact dimer, but not a tetramer, with 222 point symmetry. Each subunit has 191 amino-acid residues most of which are visible in electron density maps, and consists of seven alpha helices and one three-stranded antiparallel beta sheet. The metal ion, a 3 : 1 mixture of Fe and Mn, is coordinated with five ligands (His27, His74, His161, Asp157, and water) arranged at the vertices of a trigonal bipyramid. Although the overall structural features, including the metal coordination geometry, are similar to those found in other single-metal containing SODs, P. gingivalis SOD more closely resembles the dimeric Fe-SODs from Escherichia coli rather than another cambialistic SOD from Propionibacterium shermanii, which itself is rather similar to other tetrameric SODs.
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==About this Structure==
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Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.,Sugio S, Hiraoka BY, Yamakura F Eur J Biochem. 2000 Jun;267(12):3487-95. PMID:10848964<ref>PMID:10848964</ref>
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1QNN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis] with FE as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Structure known Active Sites: FE1, FE2, FE3 and FE4. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QNN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis., Sugio S, Hiraoka BY, Yamakura F, Eur J Biochem. 2000 Jun;267(12):3487-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10848964 10848964]
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</div>
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[[Category: Porphyromonas gingivalis]]
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<div class="pdbe-citations 1qnn" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Superoxide dismutase]]
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[[Category: Hiraoka, B.Y.]]
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[[Category: Sugio, S.]]
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[[Category: Yamakura, F.]]
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[[Category: FE]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 15:34:35 2007''
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==See Also==
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*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Porphyromonas gingivalis]]
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[[Category: Hiraoka BY]]
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[[Category: Sugio S]]
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[[Category: Yamakura F]]

Current revision

Cambialistic superoxide dismutase from Porphyromonas gingivalis

PDB ID 1qnn

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