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2cf7

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Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis.

Structural highlights

2cf7 is a 12 chain structure with sequence from Streptococcus suis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPS_STRSU 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). It binds and incorporates Fe(2+) iron. Is responsible for hydrogen peroxide resistance. Does not bind DNA.

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 Dps-like peroxide resistance protein (Dpr) is a dodecameric protein that protects the human and swine pathogen Streptococcus suis from hydrogen peroxide by removing free Fe2+ from the cytosol. Subsequent oxidation of iron by Dpr results in the deposition of Fe3+ inside the protein's central cavity. Structural changes that occur in the ferroxidase center were studied by X-ray crystallography after soaking Dpr crystals with Fe2+ in the presence of sodium dithionite. Twelve iron-binding sites were identified with each site formed by residues Asp74 and Glu78 from one subunit, and Asp63, His47 and His59 from a 2-fold symmetry-related subunit. Compared to the iron-free Dpr, Asp74 and Glu78 were found to be the most flexible amino acid residues and able to adopt a variety of conformations in different subunits. The crystal structure of an Asp74Ala Dpr mutant soaked with a Fe2+ -solution revealed variations in the Asp63 position and no iron bound to the ferroxidase center. These results indicate an intrinsic flexibility in the active site that may be important for the catalytic reaction and subsequent nucleation events. Two iron cores with remarkably different features were identified in Dpr using X-ray absorption spectroscopy. Purified Dpr was found to have a small-size iron core with only approximately 16 iron atoms/dodecamer forming a ferritin-like ferrihydrite structure. Because of its size, this core represents the smallest iron core identified so far in ferritins and other Dps-like proteins. A large-size core (approximately 180 iron atoms/dodecamer) formed after incubating the protein with a ferrous solution shows differences in iron coordination compared to the small size core. Characterization of the two iron cores in Dpr could provide insights into nucleation events and the mechanism of iron core growth in the Dps family of proteins.

Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core.,Kauko A, Pulliainen AT, Haataja S, Meyer-Klaucke W, Finne J, Papageorgiou AC J Mol Biol. 2006 Nov 17;364(1):97-109. Epub 2006 Aug 26. PMID:16997323^[1]

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

References

↑ Kauko A, Pulliainen AT, Haataja S, Meyer-Klaucke W, Finne J, Papageorgiou AC. Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core. J Mol Biol. 2006 Nov 17;364(1):97-109. Epub 2006 Aug 26. PMID:16997323 doi:10.1016/j.jmb.2006.08.061

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2cf7"

@@ Line 1: / Line 1: @@
-==ASP74ALA MUTANT CRYSTAL STRUCTURE FOR DPS-LIKE PEROXIDE RESISTANCE PROTEIN DPR FROM STREPTOCOCCUS SUIS.==
-<StructureSection load='2cf7' size='340' side='right' caption='[[2cf7]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+==Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis.==
+<StructureSection load='2cf7' size='340' side='right'caption='[[2cf7]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2cf7]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43765 Atcc 43765]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CF7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2cf7]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CF7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1umn|1umn]], [[2bw1|2bw1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></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=2cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cf7 OCA], [http://pdbe.org/2cf7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/2cf7 PDBsum]</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=2cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cf7 OCA], [https://pdbe.org/2cf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cf7 RCSB], [https://www.ebi.ac.uk/pdbsum/2cf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cf7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPS_STRSU DPS_STRSU]] 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). It binds and incorporates Fe(2+) iron. Is responsible for hydrogen peroxide resistance. Does not bind DNA.
+[https://www.uniprot.org/uniprot/DPS_STRSU DPS_STRSU] 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). It binds and incorporates Fe(2+) iron. Is responsible for hydrogen peroxide resistance. Does not bind DNA.
 == 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/cf/2cf7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cf/2cf7_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2cf7 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43765]]
+[[Category: Large Structures]]
-[[Category: Finne, J]]
+[[Category: Streptococcus suis]]
-[[Category: Haataja, S]]
+[[Category: Finne J]]
-[[Category: Kauko, A]]
+[[Category: Haataja S]]
-[[Category: Papageorgiou, A C]]
+[[Category: Kauko A]]
-[[Category: Pulliainen, A T]]
+[[Category: Papageorgiou AC]]
-[[Category: Dps-family]]
+[[Category: Pulliainen AT]]
-[[Category: Ferritin-like]]
-[[Category: Ferroxidase]]
-[[Category: Iron-binding]]
-[[Category: Peroxide resistance]]

2cf7

From Proteopedia

Current revision

Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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