8avl: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8avl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis_YCH46 Bacteroides fragilis YCH46]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AVL FirstGlance]. <br>
<table><tr><td colspan='2'>[[8avl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis_YCH46 Bacteroides fragilis YCH46]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AVL FirstGlance]. <br>
</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.6&#8491;</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=8avl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8avl OCA], [https://pdbe.org/8avl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8avl RCSB], [https://www.ebi.ac.uk/pdbsum/8avl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8avl 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=8avl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8avl OCA], [https://pdbe.org/8avl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8avl RCSB], [https://www.ebi.ac.uk/pdbsum/8avl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8avl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/SODF_BACFR SODF_BACFR] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
[https://www.uniprot.org/uniprot/SODF_BACFR SODF_BACFR] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens' exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein's evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes.


An ancient metalloenzyme evolves through metal preference modulation.,Sendra KM, Barwinska-Sendra A, Mackenzie ES, Basle A, Kehl-Fie TE, Waldron KJ Nat Ecol Evol. 2023 Apr 10. doi: 10.1038/s41559-023-02012-0. PMID:37037909<ref>PMID:37037909</ref>
==See Also==
 
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8avl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 11:14, 7 February 2024

Superoxide dismutase SodFM2 from Bacteroides fragilisSuperoxide dismutase SodFM2 from Bacteroides fragilis

Structural highlights

8avl is a 8 chain structure with sequence from Bacteroides fragilis YCH46. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SODF_BACFR Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.

See Also

8avl, resolution 1.60Å

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