1tkp: Difference between revisions

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-[[Image:1tkp.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1tkp", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1tkp|  PDB=1tkp  |  SCENE=  }}
-'''Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states'''
+==Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states==
+<StructureSection load='1tkp' size='340' side='right'caption='[[1tkp]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1tkp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKP FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1tkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkp OCA], [https://pdbe.org/1tkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkp RCSB], [https://www.ebi.ac.uk/pdbsum/1tkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS_HALSA DPS_HALSA] 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).
+== 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/tk/1tkp_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=1tkp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.
-==Overview==
+Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.,Zeth K, Offermann S, Essen LO, Oesterhelt D Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13780-5. Epub 2004 Sep 13. PMID:15365182<ref>PMID:15365182</ref>
-The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-TKP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKP OCA].
+</div>
+<div class="pdbe-citations 1tkp" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states., Zeth K, Offermann S, Essen LO, Oesterhelt D, Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13780-5. Epub 2004 Sep 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15365182 15365182]
+*[[Ferritin 3D structures|Ferritin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Halobacterium salinarum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Essen, L O.]]
+[[Category: Essen LO]]
-[[Category: Oesterhelt, D.]]
+[[Category: Oesterhelt D]]
-[[Category: Offermann, S.]]
+[[Category: Offermann S]]
-[[Category: Zeth, K.]]
+[[Category: Zeth K]]
-[[Category: Dpsa]]
-[[Category: Ferritin]]
-[[Category: High iron]]
-[[Category: Iron cluster]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 10:04:08 2008''