7ypp: Difference between revisions
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The | ==Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.== | ||
<StructureSection load='7ypp' size='340' side='right'caption='[[7ypp]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7ypp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ramazzottius_varieornatus Ramazzottius varieornatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YPP FirstGlance]. <br> | |||
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7ypp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ypp OCA], [https://pdbe.org/7ypp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ypp RCSB], [https://www.ebi.ac.uk/pdbsum/7ypp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ypp ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/SODC_RAMVA SODC_RAMVA] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.[RuleBase:RU000393] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or beta3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades. | |||
Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.,Sim KS, Inoue T Acta Crystallogr F Struct Biol Commun. 2023 Jul 1;79(Pt 7):169-179. doi: , 10.1107/S2053230X2300523X. Epub 2023 Jun 26. PMID:37358501<ref>PMID:37358501</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7ypp" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ramazzottius varieornatus]] | |||
[[Category: Fukuda Y]] | |||
[[Category: Inoue T]] | |||
[[Category: Sim K-S]] | |||
Latest revision as of 12:23, 17 October 2024
Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.
Structural highlights
FunctionSODC_RAMVA Destroys radicals which are normally produced within the cells and which are toxic to biological systems.[RuleBase:RU000393] Publication Abstract from PubMedSuperoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or beta3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades. Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.,Sim KS, Inoue T Acta Crystallogr F Struct Biol Commun. 2023 Jul 1;79(Pt 7):169-179. doi: , 10.1107/S2053230X2300523X. Epub 2023 Jun 26. PMID:37358501[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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