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| | ==The X-ray structure of iron superoxide dismutase from Pseudoalteromonas haloplanktis (crystal form II)== | | ==The X-ray structure of iron superoxide dismutase from Pseudoalteromonas haloplanktis (crystal form II)== |
| - | <StructureSection load='3ljf' size='340' side='right' caption='[[3ljf]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3ljf' size='340' side='right'caption='[[3ljf]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ljf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseht Pseht]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LJF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ljf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_translucida_TAC125 Pseudoalteromonas translucida TAC125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LJF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lio|3lio]], [[3lj9|3lj9]]</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>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sodB, PSHAa1215 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=326442 PSEHT])</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=3ljf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ljf OCA], [https://pdbe.org/3ljf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ljf RCSB], [https://www.ebi.ac.uk/pdbsum/3ljf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ljf ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ljf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ljf OCA], [http://pdbe.org/3ljf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ljf RCSB], [http://www.ebi.ac.uk/pdbsum/3ljf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ljf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SODF_PSEHT SODF_PSEHT]] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.<ref>PMID:16713057</ref> | + | [https://www.uniprot.org/uniprot/SODF_PSET1 SODF_PSET1] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.<ref>PMID:16713057</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/3ljf_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/3ljf_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | ==See Also== | | ==See Also== |
| - | *[[Superoxide Dismutase|Superoxide Dismutase]] | + | *[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pseht]] | + | [[Category: Large Structures]] |
| - | [[Category: Superoxide dismutase]] | + | [[Category: Pseudoalteromonas translucida TAC125]] |
| - | [[Category: Conte, M]] | + | [[Category: Conte M]] |
| - | [[Category: Krauss, I Russo]] | + | [[Category: Merlino A]] |
| - | [[Category: Merlino, A]] | + | [[Category: Rossi B]] |
| - | [[Category: Rossi, B]] | + | [[Category: Russo Krauss I]] |
| - | [[Category: Sica, F]] | + | [[Category: Sica F]] |
| - | [[Category: Vergara, A]] | + | [[Category: Vergara A]] |
| - | [[Category: Cold adaptation]]
| + | |
| - | [[Category: Flexibility]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Psychrophilic protein]]
| + | |
| - | [[Category: Thermal stability]]
| + | |
| Structural highlights
Function
SODF_PSET1 Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Superoxide dismutases (SODs) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Here, we present the crystal structure of a cold-adapted Fe-SOD from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhSOD), and that of its complex with sodium azide. The structures were compared with those of the corresponding homologues having a high sequence identity with PhSOD, such as the mesophilic SOD from Escherichia coli (EcSOD) or Pseudomonas ovalis, and the psychrophilic SOD from Aliivibrio salmonicida (AsSOD). These enzymes shared a large structural similarity, such as a conserved tertiary structure and arrangement of the two monomers, an almost identical total number of inter- and intramolecular hydrogen bonds and salt bridges. However, the two cold-adapted SODs showed an increased flexibility of the active site residues with respect to their mesophilic homologues. Structural information was combined with a characterisation of the chemical and thermal stability performed by CD and fluorescence measurements. Despite of its psychrophilic origin, the denaturation temperature of PhSOD was comparable with that of the mesophilic EcSOD, whereas AsSOD showed a lower denaturation temperature. On the contrary, the values of the denaturant concentration at the transition midpoint were in line with the psychrophilic/mesophilic origin of the proteins. These data provide additional support to the hypothesis that cold-adapted enzymes achieve efficient catalysis at low temperature, by increasing the flexibility of their active site; moreover, our results underline how fine structural modifications can alter enzyme flexibility and/or stability without compromising the overall structure of typical rigid enzymes, such as SODs.
Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis.,Merlino A, Krauss IR, Castellano I, Vendittis ED, Rossi B, Conte M, Vergara A, Sica F J Struct Biol. 2010 Aug 21. PMID:20732427[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Castellano I, Di Maro A, Ruocco MR, Chambery A, Parente A, Di Martino MT, Parlato G, Masullo M, De Vendittis E. Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis: biochemical characterization and identification of a highly reactive cysteine residue. Biochimie. 2006 Oct;88(10):1377-89. Epub 2006 Apr 27. PMID:16713057 doi:http://dx.doi.org/S0300-9084(06)00055-1
- ↑ Merlino A, Krauss IR, Castellano I, Vendittis ED, Rossi B, Conte M, Vergara A, Sica F. Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis. J Struct Biol. 2010 Aug 21. PMID:20732427 doi:10.1016/j.jsb.2010.08.008
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