1e9y

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[[Image:1e9y.gif|left|200px]]
 
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==Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid==
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The line below this paragraph, containing "STRUCTURE_1e9y", creates the "Structure Box" on the page.
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<StructureSection load='1e9y' size='340' side='right'caption='[[1e9y]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1e9y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. The February 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Proton-Gated Urea Channel'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_2 10.2210/rcsb_pdb/mom_2013_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E9Y FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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{{STRUCTURE_1e9y| PDB=1e9y | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e9y OCA], [https://pdbe.org/1e9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e9y RCSB], [https://www.ebi.ac.uk/pdbsum/1e9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e9y ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e9/1e9y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1e9y ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE IN COMPLEX WITH ACETOHYDROXAMIC ACID'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1E9Y is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E9Y OCA].
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</div>
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<div class="pdbe-citations 1e9y" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/11373617 11373617]
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*[[Urease 3D structures|Urease 3D structures]]
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[[Category: Protein complex]]
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== References ==
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[[Category: Ha, N C.]]
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<references/>
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[[Category: Oh, B H.]]
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__TOC__
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[[Category: Oh, S T.]]
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</StructureSection>
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[[Category: Acetohydroxamic acid]]
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[[Category: Helicobacter pylori]]
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[[Category: Dodecamer]]
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[[Category: Large Structures]]
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[[Category: Helicobacter]]
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[[Category: Proton-Gated Urea Channel]]
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[[Category: Hydrolase]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Urease]]
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[[Category: Ha N-C]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:51:02 2008''
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[[Category: Oh B-H]]
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[[Category: Oh S-T]]

Current revision

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid

PDB ID 1e9y

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