1dps

From Proteopedia

(Difference between revisions)

Revision as of 15:01, 3 November 2021

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

Structural highlights

1dps is a 12 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	DPS ("Bacillus coli" Migula 1895)
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.

Publication Abstract from PubMed

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.

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:9546221^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol. 1998 Apr;5(4):294-303. PMID:9546221

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/1dps"

@@ Line 3: / Line 3: @@
 <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. 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>
+<table><tr><td colspan='2'>[[1dps]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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='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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus coli migula 1895]]
 [[Category: Large Structures]]
 [[Category: Filman, D J]]
@@ Line 41: / Line 43: @@
 [[Category: Hogle, J M]]
 [[Category: Kolter, R]]
+[[Category: Dna binding protein]]
 [[Category: Dna-binding protein]]
 [[Category: Ferritin]]

1dps

From Proteopedia

Revision as of 15:01, 3 November 2021

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

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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