2c2f

From Proteopedia

(Difference between revisions)

Revision as of 11:25, 22 May 2024

Dps from Deinococcus radiodurans

Structural highlights

2c2f is a 1 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.61Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

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/2c2f"

Categories: Deinococcus radiodurans R1 | Large Structures | McSweeney S | Mitchell E | Romao CV

@@ Line 3: / Line 3: @@
 <StructureSection load='2c2f' size='340' side='right'caption='[[2c2f]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<table><tr><td colspan='2'>[[2c2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. 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" 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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.61&#8491;</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='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='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>
 == Function ==
-[[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>
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Deira]]
+[[Category: Deinococcus radiodurans R1]]
 [[Category: Large Structures]]
-[[Category: McSweeney, S]]
+[[Category: McSweeney S]]
-[[Category: Mitchell, E]]
+[[Category: Mitchell E]]
-[[Category: Romao, C V]]
+[[Category: Romao CV]]
-[[Category: Deinococcus radioduran]]
-[[Category: Dna binding protein]]
-[[Category: Dna-binding protein]]
-[[Category: Dp]]
-[[Category: Iron]]

2c2f

From Proteopedia

Revision as of 11:25, 22 May 2024

Dps from Deinococcus radiodurans

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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