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| | <StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution|resolution]] 1.61Å' scene=''> | | <StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution|resolution]] 1.61Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C2F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C2F 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c2u|2c2u]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2c2u|2c2u]]</div></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=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [http://pdbe.org/2c2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [http://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f 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=2c2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c2f OCA], [https://pdbe.org/2c2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c2f RCSB], [https://www.ebi.ac.uk/pdbsum/2c2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c2f ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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 (By similarity). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref> | + | [[https://www.uniprot.org/uniprot/DPS1_DEIRA DPS1_DEIRA]] 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 (By similarity). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.<ref>PMID:15755446</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 2c2f" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 2c2f" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ferritin 3D structures|Ferritin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Structural highlights
Function
[DPS1_DEIRA] 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 (By similarity). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.[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
The crystal structure of a DNA-binding protein from starved cells (Dps) (DR2263) from Deinococcus radiodurans was determined in two states: a native form, to 1.1-A resolution, and one soaked in an iron solution, to 1.6-A resolution. In comparison with other Dps proteins, DR2263 has an extended N-terminal extension, in both structures presented here, a novel metal binding site was identified in this N-terminal extension and was assigned to bound zinc. The zinc is tetrahedrally coordinated and the ligands, that belong to the N-terminal extension, are two histidines, one glutamate and one aspartate residue, which are unique to this protein within the Dps family. In the iron-soaked crystal structure, a total of three iron sites per monomer were found: one site corresponds to the ferroxidase centre with structural similarities to those found in other Dps family members; the two other sites are located on the two different threefold axes corresponding to small pores in the Dps sphere, which may possibly form the entrance and exit channels for iron storage.
The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.,Romao CV, Mitchell EP, McSweeney S J Biol Inorg Chem. 2006 Oct;11(7):891-902. Epub 2006 Jul 20. PMID:16855817[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Grove A, Wilkinson SP. Differential DNA binding and protection by dimeric and dodecameric forms of the ferritin homolog Dps from Deinococcus radiodurans. J Mol Biol. 2005 Apr 1;347(3):495-508. PMID:15755446 doi:http://dx.doi.org/10.1016/j.jmb.2005.01.055
- ↑ Romao CV, Mitchell EP, McSweeney S. The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus. J Biol Inorg Chem. 2006 Oct;11(7):891-902. Epub 2006 Jul 20. PMID:16855817 doi:10.1007/s00775-006-0142-5
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