1ji4: Difference between revisions

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-[[Image:1ji4.png|left|200px]]
-<!--
+==NAP protein from helicobacter pylori==
-The line below this paragraph, containing "STRUCTURE_1ji4", creates the "Structure Box" on the page.
+<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.52&#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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-{{STRUCTURE_1ji4|  PDB=1ji4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [https://pdbe.org/1ji4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY] 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). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</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/ji/1ji4_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=1ji4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Helicobacter pylori is a major human pathogen associated with severe gastroduodenal diseases, including ulcers and cancers. An H.pylori protein that is highly immunogenic in humans and mice has been identified recently. This protein has been termed HP-NAP, due to its ability of activating neutrophils. In order to achieve a molecular understanding of its unique immunogenic and pro-inflammatory properties, we have determined its three-dimensional structure. Its quaternary structure is similar to that of the dodecameric bacterial ferritins (Dps-like family), but it has a different surface potential charge distribution. This is due to the presence of a large number of positively charged residues, which could well account for its unique ability in activating human leukocytes.
-===NAP protein from helicobacter pylori===
+Structure of the neutrophil-activating protein from Helicobacter pylori.,Zanotti G, Papinutto E, Dundon W, Battistutta R, Seveso M, Giudice G, Rappuoli R, Montecucco C J Mol Biol. 2002 Oct 11;323(1):125-30. PMID:12368104<ref>PMID:12368104</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12368104}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ji4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12368104 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12368104}}
-==About this Structure==
-[[1ji4]] is a 12 chain structure of [[Ferritin]] with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA].
 ==See Also==
-*[[Ferritin]]
+*[[Ferritin 3D structures|Ferritin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:12368104</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Helicobacter pylori]]
-[[Category: Battistutta, R.]]
+[[Category: Large Structures]]
-[[Category: Dundon, W G.]]
+[[Category: Battistutta R]]
-[[Category: Giudice, G Del.]]
+[[Category: Del Giudice G]]
-[[Category: Montecucco, C.]]
+[[Category: Dundon WG]]
-[[Category: Papinutto, E.]]
+[[Category: Montecucco C]]
-[[Category: Rappuoli, R.]]
+[[Category: Papinutto E]]
-[[Category: Seveso, M.]]
+[[Category: Rappuoli R]]
-[[Category: Zanotti, G.]]
+[[Category: Seveso M]]
-[[Category: Dodecamer]]
+[[Category: Zanotti G]]
-[[Category: Four-helix bundle]]
-[[Category: Metal transport]]