3f7k

From Proteopedia

(Difference between revisions)

Current revision

X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Structural highlights

3f7k is a 1 chain structure with sequence from Alvinella pompejana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.35Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B6CHW7_9ANNE Destroys radicals which are normally produced within the cells and which are toxic to biological systems.[RuleBase:RU000393]

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

Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.

Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.,Shin DS, Didonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA J Mol Biol. 2009 Feb 6;385(5):1534-55. Epub 2008 Nov 25. PMID:19063897^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shin DS, Didonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol. 2009 Feb 6;385(5):1534-55. Epub 2008 Nov 25. PMID:19063897 doi:http://dx.doi.org/10.1016/j.jmb.2008.11.031

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f7k"

@@ Line 1: / Line 1: @@
 ==X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex==
-<StructureSection load='3f7k' size='340' side='right' caption='[[3f7k]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+<StructureSection load='3f7k' size='340' side='right'caption='[[3f7k]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f7k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alvinella_pompejana Alvinella pompejana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F7K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alvinella_pompejana Alvinella pompejana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F7K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f7l|3f7l]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=3f7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f7k OCA], [https://pdbe.org/3f7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f7k RCSB], [https://www.ebi.ac.uk/pdbsum/3f7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f7k ProSAT]</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=3f7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f7k OCA], [http://pdbe.org/3f7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f7k RCSB], [http://www.ebi.ac.uk/pdbsum/3f7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f7k ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B6CHW7_9ANNE B6CHW7_9ANNE] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.[RuleBase:RU000393]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/3f7k_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Superoxide Dismutase|Superoxide Dismutase]]
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Alvinella pompejana]]
-[[Category: Superoxide dismutase]]
+[[Category: Large Structures]]
-[[Category: Barondeau, D P]]
+[[Category: Barondeau DP]]
-[[Category: DiDonato, M]]
+[[Category: DiDonato M]]
-[[Category: Getzoff, E D]]
+[[Category: Getzoff ED]]
-[[Category: Shin, D S]]
+[[Category: Shin DS]]
-[[Category: Tainer, J A]]
+[[Category: Tainer JA]]
-[[Category: Al]]
-[[Category: Amyloid filament]]
-[[Category: Amyotrophic lateral sclerosis]]
-[[Category: Eukaryotic thermophile]]
-[[Category: Fal]]
-[[Category: Greek key beta-barrel]]
-[[Category: Hydrogen peroxide product complex]]
-[[Category: Lou gehrig's disease]]
-[[Category: Oxidoreductase]]
-[[Category: Pompeii worm]]
-[[Category: Thermostable protein]]

3f7k

From Proteopedia

Current revision

X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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