1e9y

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid

Structural highlights

1e9y is a 2 chain structure with sequence from Helicobacter pylori. The February 2013 RCSB PDB Molecule of the Month feature on Proton-Gated Urea Channel by David Goodsell is 10.2210/rcsb_pdb/mom_2013_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

URE23_HELPY Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach.^[1]

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

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tsuda M, Karita M, Morshed MG, Okita K, Nakazawa T. A urease-negative mutant of Helicobacter pylori constructed by allelic exchange mutagenesis lacks the ability to colonize the nude mouse stomach. Infect Immun. 1994 Aug;62(8):3586-9. PMID:8039935
↑ Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH. Supramolecular assembly and acid resistance of Helicobacter pylori urease. Nat Struct Biol. 2001 Jun;8(6):505-9. PMID:11373617 doi:10.1038/88563

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1e9y"

@@ Line 3: / Line 3: @@
 <StructureSection load='1e9y' size='340' side='right'caption='[[1e9y]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1e9y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. 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>
+<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>
-</td></tr><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=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
+<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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e9z|1e9z]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Urease Urease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></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=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>
 </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>  [[https://www.uniprot.org/uniprot/URE1_HELPY URE1_HELPY]] Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach.<ref>PMID:8039935</ref>
+[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]]
@@ Line 17: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e9/1e9y_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43504]]
+[[Category: Helicobacter pylori]]
 [[Category: Large Structures]]
 [[Category: Proton-Gated Urea Channel]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Urease]]
+[[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: Dodecamer]]
-[[Category: Hydrolase]]

1e9y

From Proteopedia

Current revision

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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