1f30: Difference between revisions

Revision as of 10:24, 18 November 2020

THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN

Structural highlights

1f30 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:	TRS, ZN
Related:	1dps, 1f33
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.

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:https://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:https://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:https://dx.doi.org/32/19/5935

Proteopedia Page Contributors and Editors (what is this?)

OCA

[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:https://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:https://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:https://dx.doi.org/32/19/5935

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN==
-<StructureSection load='1f30' size='340' side='right' caption='[[1f30]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='1f30' size='340' side='right'caption='[[1f30]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1f30]] is a 12 chain structure with sequence from [http://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=1F30 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F30 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1f30]] is a 12 chain structure with sequence from [http://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=1F30 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1F30 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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">[[1dps|1dps]], [[1f33|1f33]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPS ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f30 OCA], [http://pdbe.org/1f30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f30 RCSB], [http://www.ebi.ac.uk/pdbsum/1f30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f30 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1f30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f30 OCA], [http://pdbe.org/1f30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f30 RCSB], [http://www.ebi.ac.uk/pdbsum/1f30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f30 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 21: @@
 </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=1f30 ConSurf].
 <div style="clear:both"></div>
+==See Also==
+*[[Ferritin 3D structures|Ferritin 3D structures]]
 == References ==
 <references/>
@@ Line 26: / Line 29: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Fox, R O]]
 [[Category: Liu, D]]

1f30: Difference between revisions

Revision as of 10:24, 18 November 2020

THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN

Structural highlights

Function

Evolutionary Conservation

See Also

References

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