1dps: Difference between revisions

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New page: left|200px<br /><applet load="1dps" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dps, resolution 1.60Å" /> '''THE CRYSTAL STRUCTUR...
 
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[[Image:1dps.jpg|left|200px]]<br /><applet load="1dps" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dps, resolution 1.60&Aring;" />
'''THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA'''<br />


==Overview==
==THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA==
The crystal structure of Dps, a DNA-binding protein from starved E. coli, that protects DNA from oxidative damage, has been solved at 1.6 A, resolution. The Dps monomer has essentially the same fold as ferritin, which forms a 24-mer with 432 symmetry, a hollow core and pores at the, three-fold axes. Dps forms a dodecamer with 23 (tetrahedral) point group, symmetry which also has a hollow core and pores at the three-folds. The, structure suggests a novel DNA-binding motif and a mechanism for DNA, protection based on the sequestration of Fe ions.
<StructureSection load='1dps' size='340' side='right'caption='[[1dps]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dps]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DPS 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1dps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dps OCA], [https://pdbe.org/1dps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dps RCSB], [https://www.ebi.ac.uk/pdbsum/1dps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dps ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPS_ECOLI DPS_ECOLI] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.<ref>PMID:1340475</ref> <ref>PMID:10403254</ref> <ref>PMID:15205421</ref> <ref>PMID:15534364</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/1dps_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dps ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DPS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DPS OCA].
*[[Ferritin 3D structures|Ferritin 3D structures]]
 
== References ==
==Reference==
<references/>
The crystal structure of Dps, a ferritin homolog that binds and protects DNA., Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM, Nat Struct Biol. 1998 Apr;5(4):294-303. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9546221 9546221]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Filman, D.J.]]
[[Category: Filman DJ]]
[[Category: Finkel, S.E.]]
[[Category: Finkel SE]]
[[Category: Grant, R.A.]]
[[Category: Grant RA]]
[[Category: Hogle, J.M.]]
[[Category: Hogle JM]]
[[Category: Kolter, R.]]
[[Category: Kolter R]]
[[Category: NA]]
[[Category: dna-binding protein]]
[[Category: ferritin]]
[[Category: iron sequestration]]
[[Category: oxidative damage]]
[[Category: stationary phase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:28:53 2007''

Latest revision as of 09:57, 7 February 2024

THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNATHE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA

Structural highlights

1dps is a 12 chain structure with sequence from Escherichia coli. 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

DPS_ECOLI During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.[1] [2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Almiron M, Link AJ, Furlong D, Kolter R. A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 1992 Dec;6(12B):2646-54. PMID:1340475
  2. ↑ Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A. DNA protection by stress-induced biocrystallization. Nature. 1999 Jul 1;400(6739):83-5. PMID:10403254 doi:http://dx.doi.org/10.1038/21918
  3. ↑ Nair S, Finkel SE. Dps protects cells against multiple stresses during stationary phase. J Bacteriol. 2004 Jul;186(13):4192-8. PMID:15205421 doi:http://dx.doi.org/10.1128/JB.186.13.4192-4198.2004
  4. ↑ Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E. DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res. 2004 Nov 8;32(19):5935-44. Print 2004. PMID:15534364 doi:http://dx.doi.org/32/19/5935

1dps, resolution 1.60Å

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