2ubp: Difference between revisions

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-[[Image:2ubp.png|left|200px]]
-{{STRUCTURE_2ubp|  PDB=2ubp  |  SCENE=  }}
+==STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII==
+<StructureSection load='2ubp' size='340' side='right'caption='[[2ubp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ubp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UBP 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=2ubp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ubp OCA], [https://pdbe.org/2ubp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ubp RCSB], [https://www.ebi.ac.uk/pdbsum/2ubp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ubp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/URE3_SPOPA URE3_SPOPA]
+== 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/ub/2ubp_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=2ubp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Urease catalyzes the hydrolysis of urea, the final step of organic nitrogen mineralization, using a bimetallic nickel centre. The role of the active site metal ions and amino acid residues has not been elucidated to date. Many pathologies are associated with the activity of ureolytic bacteria, and the efficiency of soil nitrogen fertilization with urea is severely decreased by urease activity. Therefore, the development of urease inhibitors would lead to a reduction of environmental pollution, to enhanced efficiency of nitrogen uptake by plants, and to improved therapeutic strategies for treatment of infections due to ureolytic bacteria. Structure-based design of urease inhibitors would require knowledge of the enzyme mechanism at the molecular level. RESULTS: The structures of native and inhibited urease from Bacillus pasteurii have been determined at a resolution of 2.0 A by synchrotron X-ray cryogenic crystallography. In the native enzyme, the coordination sphere of each of the two nickel ions is completed by a water molecule and a bridging hydroxide. A fourth water molecule completes a tetrahedral cluster of solvent molecules. The enzyme crystallized in the presence of phenylphosphorodiamidate contains the tetrahedral transition-state analogue diamidophosphoric acid, bound to the two nickel ions in an unprecedented mode. Comparison of the native and inhibited structures reveals two distinct conformations of the flap lining the active-site cavity. CONCLUSIONS: The mode of binding of the inhibitor, and a comparison between the native and inhibited urease structures, indicate a novel mechanism for enzymatic urea hydrolysis which reconciles the available structural and biochemical data.
-===STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII===
+A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.,Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S Structure. 1999 Feb 15;7(2):205-16. PMID:10368287<ref>PMID:10368287</ref>
-{{ABSTRACT_PUBMED_10368287}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2ubp" style="background-color:#fffaf0;"></div>
-[[2ubp]] is a 3 chain structure of [[Urease]] with sequence from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UBP OCA].
 ==See Also==
-*[[Urease|Urease]]
+*[[Urease 3D structures|Urease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010368287</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Sporosarcina pasteurii]]
-[[Category: Urease]]
+[[Category: Benini S]]
-[[Category: Benini, S.]]
+[[Category: Ciurli S]]
-[[Category: Ciurli, S.]]
+[[Category: Mangani S]]
-[[Category: Mangani, S.]]
+[[Category: Rypniewski WR]]
-[[Category: Rypniewski, W R.]]
+[[Category: Wilson KS]]
-[[Category: Wilson, K S.]]
-[[Category: Bacillus pasteurii]]
-[[Category: Hydrolase]]
-[[Category: Nickel]]
-[[Category: Urease]]