6hx2: Difference between revisions
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The | ==The structure of Dps from Listeria innocua soaked with Cobalt== | ||
<StructureSection load='6hx2' size='340' side='right'caption='[[6hx2]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6hx2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lisin Lisin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HX2 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dps, flp, fri, lin0942 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272626 LISIN])</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=6hx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hx2 OCA], [http://pdbe.org/6hx2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hx2 RCSB], [http://www.ebi.ac.uk/pdbsum/6hx2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hx2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/DPS_LISIN DPS_LISIN]] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Does not bind DNA.<ref>PMID:12383509</ref> <ref>PMID:15823015</ref> <ref>PMID:9013563</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Iron storage in biology is carried out by cage-shaped proteins of the ferritin superfamily, one of which is the dodecameric protein Dps. In Dps, four distinct steps lead to the formation of metal nanoparticles: attraction of ion-aquo complexes to the protein matrix, passage of these complexes through translocation pores, oxidation of these complexes at ferroxidase centers, and, ultimately, nanoparticle formation. In this study, we investigated Dps from Listeria innocua to structurally characterize these steps for Co(2+), Zn(2+), and La(3+) ions. The structures reveal that differences in their ion coordination chemistry determine alternative metal ion-binding sites on the areas of the surface surrounding the translocation pore that captures nine La(3+), three Co(2+), or three Zn(2+) ions as aquo clusters and passes them on for translocation. Inside these pores, ion-selective conformational changes at key residues occur before a gating residue to actively move ions through the constriction zone. Ions upstream of the Asp130 gate residue are typically hydrated, while ions downstream directly interact with the protein matrix. Inside the cavity, ions move along negatively charged residues to the ferroxidase center, where seven main residues adapt to the three different ions by dynamically changing their conformations. In total, we observed more than 20 metal-binding sites per Dps monomer, which clearly highlights the metal-binding capacity of this protein family. Collectively, our results provide a detailed structural description of the preparative steps for amino acid-assisted biomineralization in Dps proteins, demonstrating unexpected protein matrix plasticity. | |||
Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.,Zeth K, Sancho-Vaello E, Okuda M Inorg Chem. 2019 Sep 3;58(17):11351-11363. doi: 10.1021/acs.inorgchem.9b00301., Epub 2019 Aug 21. PMID:31433627<ref>PMID:31433627</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6hx2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Lisin]] | |||
[[Category: Okuda, M]] | [[Category: Okuda, M]] | ||
[[Category: Zeth, K]] | [[Category: Zeth, K]] | ||
[[Category: Dp]] | |||
[[Category: Ferroxidase]] | |||
[[Category: Itron translocation]] | |||
[[Category: Metal binding protein]] | |||
[[Category: Metal binding. cage shaped protein]] | |||
Latest revision as of 20:26, 20 November 2019
The structure of Dps from Listeria innocua soaked with CobaltThe structure of Dps from Listeria innocua soaked with Cobalt
Structural highlights
Function[DPS_LISIN] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Does not bind DNA.[1] [2] [3] Publication Abstract from PubMedIron storage in biology is carried out by cage-shaped proteins of the ferritin superfamily, one of which is the dodecameric protein Dps. In Dps, four distinct steps lead to the formation of metal nanoparticles: attraction of ion-aquo complexes to the protein matrix, passage of these complexes through translocation pores, oxidation of these complexes at ferroxidase centers, and, ultimately, nanoparticle formation. In this study, we investigated Dps from Listeria innocua to structurally characterize these steps for Co(2+), Zn(2+), and La(3+) ions. The structures reveal that differences in their ion coordination chemistry determine alternative metal ion-binding sites on the areas of the surface surrounding the translocation pore that captures nine La(3+), three Co(2+), or three Zn(2+) ions as aquo clusters and passes them on for translocation. Inside these pores, ion-selective conformational changes at key residues occur before a gating residue to actively move ions through the constriction zone. Ions upstream of the Asp130 gate residue are typically hydrated, while ions downstream directly interact with the protein matrix. Inside the cavity, ions move along negatively charged residues to the ferroxidase center, where seven main residues adapt to the three different ions by dynamically changing their conformations. In total, we observed more than 20 metal-binding sites per Dps monomer, which clearly highlights the metal-binding capacity of this protein family. Collectively, our results provide a detailed structural description of the preparative steps for amino acid-assisted biomineralization in Dps proteins, demonstrating unexpected protein matrix plasticity. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.,Zeth K, Sancho-Vaello E, Okuda M Inorg Chem. 2019 Sep 3;58(17):11351-11363. doi: 10.1021/acs.inorgchem.9b00301., Epub 2019 Aug 21. PMID:31433627[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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