2v15

From Proteopedia

(Difference between revisions)

Current revision

Terbium binding in Streptococcus suis Dpr protein

Structural highlights

2v15 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 2.1Å
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

Streptococcus suis Dpr is an iron-binding protein involved in oxidative stress resistance. It belongs to the bacterial Dps protein family whose members form dodecameric assemblies. Previous studies have shown that zinc and terbium inhibit iron incorporation in Listeria innocua Dps protein. In order to gain structural insights into the inhibitory effect of zinc and terbium, the crystal structures of Streptococcus suis Dpr complexes with these ions were determined at 1.8 A and 2.1 A, respectively. Both ions were found to bind at the ferroxidase center and in the same location as iron. In addition, a novel zinc-binding site formed by His40 and His44 was identified. Both His residues were found to be present within all known Streptococcus suis Dpr variants and in Streptococcus pneumoniae, Streptococcus gordonii, and Streptococcus sanguinis Dpr proteins. Amino acid sequence alignment of Dpr with other Dps family members revealed that His44 is highly conserved, in contrast to His40. The inhibitory effect of zinc and terbium on iron oxidation in Dpr was studied in vitro, and it was found that both ions at concentrations >0.2 mM almost completely abolish iron binding. These results provide a structural basis for the inhibitory effect of zinc and terbium in the Dps family of proteins, and suggest a potential role of the Dps proteins in zinc detoxification mechanisms involving the second zinc-binding site.

Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.,Havukainen H, Haataja S, Kauko A, Pulliainen AT, Salminen A, Haikarainen T, Finne J, Papageorgiou AC Protein Sci. 2008 Sep;17(9):1513-21. Epub 2008 Jun 13. PMID:18552126^[1]

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

References

↑ Havukainen H, Haataja S, Kauko A, Pulliainen AT, Salminen A, Haikarainen T, Finne J, Papageorgiou AC. Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins. Protein Sci. 2008 Sep;17(9):1513-21. Epub 2008 Jun 13. PMID:18552126 doi:10.1110/ps.036236.108

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/2v15"

Categories: Large Structures | Streptococcus suis | Havukainen H | Kauko A | Papageorgiou AC

@@ Line 3: / Line 3: @@
 <StructureSection load='2v15' size='340' side='right'caption='[[2v15]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v15]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43765 Atcc 43765]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V15 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v15]] 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=2V15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V15 FirstGlance]. <br>
-</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>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1umn|1umn]], [[2bw1|2bw1]], [[2cf7|2cf7]], [[2ux1|2ux1]]</div></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>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</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=2v15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v15 OCA], [https://pdbe.org/2v15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v15 RCSB], [https://www.ebi.ac.uk/pdbsum/2v15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v15 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43765]]
 [[Category: Large Structures]]
-[[Category: Havukainen, H]]
+[[Category: Streptococcus suis]]
-[[Category: Kauko, A]]
+[[Category: Havukainen H]]
-[[Category: Papageorgiou, A C]]
+[[Category: Kauko A]]
-[[Category: Dps-family]]
+[[Category: Papageorgiou AC]]
-[[Category: Ferritin-like]]
-[[Category: Ferroxidase]]
-[[Category: Iron]]
-[[Category: Iron storage]]
-[[Category: Iron-binding]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxide resistance]]

2v15

From Proteopedia

Current revision

Terbium binding in Streptococcus suis Dpr protein

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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