1ie7: Difference between revisions

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OCA

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-[[Image:1ie7.gif|left|200px]]<br /><applet load="1ie7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ie7, resolution 1.85&Aring;" />
-'''PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE'''<br />
-==Overview==
+==PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE==
-The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate, was solved and refined using synchrotron X-ray diffraction data from a, vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy, 4.6, R-factor 17.3%, PDB code 6UBP). A distance of 3.5 A separates the two, Ni ions in the active site. The binding mode of the inhibitor involves the, formation of four coordination bonds with the two Ni ions: one phosphate, oxygen atom symmetrically bridges the two metal ions (1.9-2.0 A), while, two of the remaining phosphate oxygen atoms bind to the Ni atoms at 2.4 A., The fourth phosphate oxygen is directed into the active site channel., Analysis of the H-bonding network around the bound inhibitor indicates, that phosphate is bound as the H2PO4- anion, and that an additional proton, is present on the Odelta2 atom of Asp(alpha363), an active site residue, involved in Ni coordination through Odelta1. The flexible flap flanking, the active site cavity is in the open conformation. Analysis of the, complex reveals why phosphate is a relatively weak inhibitor and why, sulfate does not bind to the nickels in the active site. The implications, of the results for the understanding of the urease catalytic mechanism are, reviewed. A novel alternative for the proton donor is presented.
+<StructureSection load='1ie7' size='340' side='right'caption='[[1ie7]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ie7]] 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=1IE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IE7 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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1ie7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ie7 OCA], [https://pdbe.org/1ie7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ie7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ie7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ie7 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/ie/1ie7_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=1ie7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate was solved and refined using synchrotron X-ray diffraction data from a vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy 4.6, R-factor 17.3%, PDB code 6UBP). A distance of 3.5 A separates the two Ni ions in the active site. The binding mode of the inhibitor involves the formation of four coordination bonds with the two Ni ions: one phosphate oxygen atom symmetrically bridges the two metal ions (1.9-2.0 A), while two of the remaining phosphate oxygen atoms bind to the Ni atoms at 2.4 A. The fourth phosphate oxygen is directed into the active site channel. Analysis of the H-bonding network around the bound inhibitor indicates that phosphate is bound as the H2PO4- anion, and that an additional proton is present on the Odelta2 atom of Asp(alpha363), an active site residue involved in Ni coordination through Odelta1. The flexible flap flanking the active site cavity is in the open conformation. Analysis of the complex reveals why phosphate is a relatively weak inhibitor and why sulfate does not bind to the nickels in the active site. The implications of the results for the understanding of the urease catalytic mechanism are reviewed. A novel alternative for the proton donor is presented.
-==About this Structure==
+Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism.,Benini S, Rypniewski WR, Wilson KS, Ciurli S, Mangani S J Biol Inorg Chem. 2001 Oct;6(8):778-90. PMID:11713685<ref>PMID:11713685</ref>
-IE7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii] with NI and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IE7 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism., Benini S, Rypniewski WR, Wilson KS, Ciurli S, Mangani S, J Biol Inorg Chem. 2001 Oct;6(8):778-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11713685 11713685]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 1ie7" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Urease 3D structures|Urease 3D structures]]
+== References ==
+<references/>
+__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: NI]]
-[[Category: PO4]]
-[[Category: bacillus pasteurii]]
-[[Category: metalloenzyme]]
-[[Category: nickel]]
-[[Category: urease]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:20:10 2007''