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2bk6

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The X-ray crystal structure of the Listeria innocua H31G Dps mutant.

Structural highlights

2bk6 is a 6 chain structure with sequence from Listeria innocua. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.19Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPS_LISIN 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. Does not bind DNA.^[1] ^[2] ^[3]

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 role of the ferroxidase center in iron uptake and hydrogen peroxide detoxification was investigated in Listeria innocua Dps by substituting the iron ligands His31, His43, and Asp58 with glycine or alanine residues either individually or in combination. The X-ray crystal structures of the variants reveal only small alterations in the ferroxidase center region compared to the native protein. Quenching of the protein fluorescence was exploited to assess stoichiometry and affinity of metal binding. Substitution of either His31 or His43 decreases Fe(II) affinity significantly with respect to wt L. innocua Dps (K approximately 10(5) vs approximately 10(7) M(-)(1)) but does not alter the binding stoichiometry [12 Fe(II)/dodecamer]. In the H31G-H43G and H31G-H43G-D58A variants, binding of Fe(II) does not take place with measurable affinity. Oxidation of protein-bound Fe(II) increases the binding stoichiometry to 24 Fe(III)/dodecamer. However, the extent of fluorescence quenching upon Fe(III) binding decreases, and the end point near 24 Fe(III)/dodecamer becomes less distinct with increase in the number of mutated residues. In the presence of dioxygen, the mutations have little or no effect on the kinetics of iron uptake and in the formation of micelles inside the protein shell. In contrast, in the presence of hydrogen peroxide, with increase in the number of substitutions the rate of iron oxidation and the capacity to inhibit Fenton chemistry, thereby protecting DNA from oxidative damage, appear increasingly compromised, a further indication of the role of ferroxidation in conferring peroxide tolerance to the bacterium.

The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants.,Ilari A, Latella MC, Ceci P, Ribacchi F, Su M, Giangiacomo L, Stefanini S, Chasteen ND, Chiancone E Biochemistry. 2005 Apr 19;44(15):5579-87. PMID:15823016^[4]

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

References

↑ Polidoro M, De Biase D, Montagnini B, Guarrera L, Cavallo S, Valenti P, Stefanini S, Chiancone E. The expression of the dodecameric ferritin in Listeria spp. is induced by iron limitation and stationary growth phase. Gene. 2002 Aug 21;296(1-2):121-8. PMID:12383509
↑ Su M, Cavallo S, Stefanini S, Chiancone E, Chasteen ND. The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties. Biochemistry. 2005 Apr 19;44(15):5572-8. PMID:15823015 doi:http://dx.doi.org/10.1021/bi0472705
↑ Bozzi M, Mignogna G, Stefanini S, Barra D, Longhi C, Valenti P, Chiancone E. A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua. J Biol Chem. 1997 Feb 7;272(6):3259-65. PMID:9013563
↑ Ilari A, Latella MC, Ceci P, Ribacchi F, Su M, Giangiacomo L, Stefanini S, Chasteen ND, Chiancone E. The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants. Biochemistry. 2005 Apr 19;44(15):5579-87. PMID:15823016 doi:10.1021/bi050005e

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/2bk6"

@@ Line 1: / Line 1: @@
-==THE X-RAY CRYSTAL STRUCTURE OF THE LISTERIA INNOCUA H31G DPS MUTANT.==
-<StructureSection load='2bk6' size='340' side='right' caption='[[2bk6]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
+==The X-ray crystal structure of the Listeria innocua H31G Dps mutant.==
+<StructureSection load='2bk6' size='340' side='right'caption='[[2bk6]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bk6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_innocua Listeria innocua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BK6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BK6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bk6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_innocua Listeria innocua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BK6 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qgh|1qgh]], [[2bjy|2bjy]]</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]] 2.19&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bk6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bk6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bk6 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=2bk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bk6 OCA], [https://pdbe.org/2bk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bk6 RCSB], [https://www.ebi.ac.uk/pdbsum/2bk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bk6 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS_LISIN DPS_LISIN] 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. Does not bind DNA.<ref>PMID:12383509</ref> <ref>PMID:15823015</ref> <ref>PMID:9013563</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/bk/2bk6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bk/2bk6_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=2bk6 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2bk6" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ferritin|Ferritin]]
+*[[Ferritin 3D structures|Ferritin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Listeria innocua]]
-[[Category: Chasteen, N D.]]
+[[Category: Chasteen ND]]
-[[Category: Chiancone, E.]]
+[[Category: Chiancone E]]
-[[Category: Giangiacomo, L.]]
+[[Category: Giangiacomo L]]
-[[Category: Ilari, A.]]
+[[Category: Ilari A]]
-[[Category: Latella, M C.]]
+[[Category: Latella MC]]
-[[Category: Ribacchi, F.]]
+[[Category: Ribacchi F]]
-[[Category: Stefanini, S.]]
+[[Category: Stefanini S]]
-[[Category: Su, M.]]
+[[Category: Su M]]
-[[Category: Ferroxidase center]]
-[[Category: Iron oxidation and storage]]
-[[Category: Metal transport]]
-[[Category: Mutagenesis study]]

2bk6

From Proteopedia

Current revision

The X-ray crystal structure of the Listeria innocua H31G Dps mutant.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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