1e9z: Difference between revisions

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-{{Seed}}
-[[Image:1e9z.png|left|200px]]
-<!--
+==Crystal structure of Helicobacter pylori urease==
-The line below this paragraph, containing "STRUCTURE_1e9z", creates the "Structure Box" on the page.
+<StructureSection load='1e9z' size='340' side='right'caption='[[1e9z]], [[Resolution|resolution]] 3.00&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'>[[1e9z]] is a 2 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=1E9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E9Z 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-{{STRUCTURE_1e9z|  PDB=1e9z  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e9z OCA], [https://pdbe.org/1e9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e9z RCSB], [https://www.ebi.ac.uk/pdbsum/1e9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e9z ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/URE23_HELPY URE23_HELPY] Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach.<ref>PMID:8039935</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/e9/1e9z_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=1e9z ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Helicobacter pylori, an etiologic agent in a variety of gastroduodenal diseases, produces a large amount of urease, which is believed to neutralize gastric acid by producing ammonia for the survival of the bacteria. Up to 30% of the enzyme associates with the surface of intact cells upon lysis of neighboring bacteria. The role of the enzyme at the extracellular location has been a subject of controversy because the purified enzyme is irreversibly inactivated below pH 5. We have determined the crystal structure of H. pylori urease, which has a 1.1 MDa spherical assembly of 12 catalytic units with an outer diameter of approximately 160 A. Under physiologically relevant conditions, the activity of the enzyme remains unaffected down to pH 3. Activity assays under different conditions indicated that the cluster of the 12 active sites on the supramolecular assembly may be critical for the survival of the enzyme at low pH. The structure provides a novel example of a molecular assembly adapted for acid resistance that, together with the low Km value of the enzyme, is likely to enable the organism to inhabit the hostile niche.
-===CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE===
+Supramolecular assembly and acid resistance of Helicobacter pylori urease.,Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH Nat Struct Biol. 2001 Jun;8(6):505-9. PMID:11373617<ref>PMID:11373617</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e9z" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11373617}}, adds the Publication Abstract to the page
+*[[Urease|Urease]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11373617 is the PubMed ID number.
+*[[Urease 3D structures|Urease 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_11373617}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-E9Z is a 2 chains structure with sequences 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=1E9Z OCA].
-==Reference==
-<ref group="xtra">PMID:11373617</ref><references group="xtra"/>
 [[Category: Helicobacter pylori]]
-[[Category: Urease]]
+[[Category: Large Structures]]
-[[Category: Ha, N C.]]
+[[Category: Ha N-C]]
-[[Category: Oh, B H.]]
+[[Category: Oh B-H]]
-[[Category: Oh, S T.]]
+[[Category: Oh S-T]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:26:03 2010''