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| - | [[Image:1qgh.gif|left|200px]] | |
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| - | {{Structure
| + | ==THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.== |
| - | |PDB= 1qgh |SIZE=350|CAPTION= <scene name='initialview01'>1qgh</scene>, resolution 2.35Å
| + | <StructureSection load='1qgh' size='340' side='right'caption='[[1qgh]], [[Resolution|resolution]] 2.35Å' scene=''> |
| - | |SITE= <scene name='pdbsite=ASA:Fe-Binding+Site'>ASA</scene>, <scene name='pdbsite=ASB:Fe-Binding+Site'>ASB</scene>, <scene name='pdbsite=ASC:Fe-Binding+Site'>ASC</scene>, <scene name='pdbsite=ASD:Fe-Binding+Site'>ASD</scene>, <scene name='pdbsite=ASE:Fe-Binding+Site'>ASE</scene>, <scene name='pdbsite=ASF:Fe-Binding+Site'>ASF</scene>, <scene name='pdbsite=ASG:Fe-Binding+Site'>ASG</scene>, <scene name='pdbsite=ASH:Fe-Binding+Site'>ASH</scene>, <scene name='pdbsite=ASI:Fe-Binding+Site'>ASI</scene>, <scene name='pdbsite=ASJ:Fe-Binding+Site'>ASJ</scene>, <scene name='pdbsite=ASK:Fe-Binding+Site'>ASK</scene> and <scene name='pdbsite=ASL:Fe-Binding+Site'>ASL</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>
| + | <table><tr><td colspan='2'>[[1qgh]] is a 12 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=1QGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QGH FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qgh OCA], [https://pdbe.org/1qgh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qgh RCSB], [https://www.ebi.ac.uk/pdbsum/1qgh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qgh ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qgh OCA], [http://www.ebi.ac.uk/pdbsum/1qgh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qgh RCSB]</span>
| + | == 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/qg/1qgh_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/main_output.php?pdb_ID=1qgh ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ferritin is characterized by a highly conserved architecture that comprises 24 subunits assembled into a spherical cage with 432 symmetry. The only known exception is the dodecameric ferritin from Listeria innocua. The structure of Listeria ferritin has been determined to a resolution of 2.35 A by molecular replacement, using as a search model the structure of Dps from Escherichia coli. The Listeria 12-mer is endowed with 23 symmetry and displays the functionally relevant structural features of the ferritin 24-mer, namely the negatively charged channels along the three-fold symmetry axes that serve for iron entry into the cavity and a negatively charged internal cavity for iron deposition. The electron density map shows 12 iron ions on the inner surface of the hollow core, at the interface between monomers related by two-fold axes. Analysis of the nature and stereochemistry of the iron-binding ligands reveals strong similarities with known ferroxidase sites. The L. innocua ferritin site, however, is the first described so far that has ligands belonging to two different subunits and is not contained within a four-helix bundle. |
| | | | |
| - | '''THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.'''
| + | The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.,Ilari A, Stefanini S, Chiancone E, Tsernoglou D Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425<ref>PMID:10625425</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 1qgh" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | Ferritin is characterized by a highly conserved architecture that comprises 24 subunits assembled into a spherical cage with 432 symmetry. The only known exception is the dodecameric ferritin from Listeria innocua. The structure of Listeria ferritin has been determined to a resolution of 2.35 A by molecular replacement, using as a search model the structure of Dps from Escherichia coli. The Listeria 12-mer is endowed with 23 symmetry and displays the functionally relevant structural features of the ferritin 24-mer, namely the negatively charged channels along the three-fold symmetry axes that serve for iron entry into the cavity and a negatively charged internal cavity for iron deposition. The electron density map shows 12 iron ions on the inner surface of the hollow core, at the interface between monomers related by two-fold axes. Analysis of the nature and stereochemistry of the iron-binding ligands reveals strong similarities with known ferroxidase sites. The L. innocua ferritin site, however, is the first described so far that has ligands belonging to two different subunits and is not contained within a four-helix bundle. | + | *[[Ferritin 3D structures|Ferritin 3D structures]] |
| - | | + | == References == |
| - | ==About this Structure== | + | <references/> |
| - | 1QGH is a [[Single protein]] structure of 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=1QGH OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference==
| + | [[Category: Large Structures]] |
| - | The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site., Ilari A, Stefanini S, Chiancone E, Tsernoglou D, Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10625425 10625425]
| + | |
| | [[Category: Listeria innocua]] | | [[Category: Listeria innocua]] |
| - | [[Category: Single protein]]
| + | [[Category: Chiancone E]] |
| - | [[Category: Chiancone, E.]] | + | [[Category: Ilari A]] |
| - | [[Category: Ilari, A.]] | + | [[Category: Stefanini S]] |
| - | [[Category: Stefanini, S.]] | + | [[Category: Tsernoglou D]] |
| - | [[Category: Tsernoglou, D.]] | + | |
| - | [[Category: ferritin]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:13:09 2008''
| + | |
| Structural highlights
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
Ferritin is characterized by a highly conserved architecture that comprises 24 subunits assembled into a spherical cage with 432 symmetry. The only known exception is the dodecameric ferritin from Listeria innocua. The structure of Listeria ferritin has been determined to a resolution of 2.35 A by molecular replacement, using as a search model the structure of Dps from Escherichia coli. The Listeria 12-mer is endowed with 23 symmetry and displays the functionally relevant structural features of the ferritin 24-mer, namely the negatively charged channels along the three-fold symmetry axes that serve for iron entry into the cavity and a negatively charged internal cavity for iron deposition. The electron density map shows 12 iron ions on the inner surface of the hollow core, at the interface between monomers related by two-fold axes. Analysis of the nature and stereochemistry of the iron-binding ligands reveals strong similarities with known ferroxidase sites. The L. innocua ferritin site, however, is the first described so far that has ligands belonging to two different subunits and is not contained within a four-helix bundle.
The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.,Ilari A, Stefanini S, Chiancone E, Tsernoglou D Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
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, Stefanini S, Chiancone E, Tsernoglou D. The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site. Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425 doi:10.1038/71236
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