1ed9: Difference between revisions

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-{{Seed}}
-[[Image:1ed9.png|left|200px]]
-<!--
+==STRUCTURE OF E. COLI ALKALINE PHOSPHATASE WITHOUT THE INORGANIC PHOSPHATE AT 1.75A RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_1ed9", creates the "Structure Box" on the page.
+<StructureSection load='1ed9' size='340' side='right'caption='[[1ed9]], [[Resolution|resolution]] 1.75&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'>[[1ed9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ED9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ED9 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1ed9|  PDB=1ed9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ed9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ed9 OCA], [https://pdbe.org/1ed9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ed9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ed9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ed9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPB_ECOLI PPB_ECOLI]
+== 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/ed/1ed9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ed9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Here, X-ray crystallography has been used to investigate the proposed double in-line displacement mechanism of Escherichia coli alkaline phosphatase in which two of the three active-site metal ions have a direct role in catalysis. Two new X-ray crystal structures of the wild-type enzyme in the absence and presence of inorganic phosphate have been refined at 1.75 A to final working R-factors of 15.4% and 16.4%, respectively. In the refinement of both structures, residues in the active sites were treated anisotropically. The ellipsoids resulting from the partial anisotropic refinement show a clear route for the binding and release of substrate/product. In addition, a direct comparison of the refined structures with and without phosphate reveal a strong correlation between the occupancy of the third metal-binding site and the conformation of the Ser102 nucleophile. These findings clarify two important and unresolved aspects of the previously proposed catalytic mechanism, how Ser102 is activated for nucleophilic attack and why a magnesium ion in the third metal site is required for catalysis. Analysis of these results suggest that three metal-ion assisted catalysis is a more accurate description of the mechanism of the alkaline phosphatase reaction. A revised mechanism for the catalytic reaction of alkaline phosphatase is proposed on the basis of the two new X-ray crystal structures reported.
-===STRUCTURE OF E. COLI ALKALINE PHOSPHATASE WITHOUT THE INORGANIC PHOSPHATE AT 1.75A RESOLUTION===
+A revised mechanism for the alkaline phosphatase reaction involving three metal ions.,Stec B, Holtz KM, Kantrowitz ER J Mol Biol. 2000 Jun 23;299(5):1303-11. PMID:10873454<ref>PMID:10873454</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ed9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10873454}}, adds the Publication Abstract to the page
+*[[Alkaline phosphatase 3D structures|Alkaline phosphatase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10873454 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10873454}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ED9 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ED9 OCA].
-==Reference==
-<ref group="xtra">PMID:10873454</ref><references group="xtra"/>
-[[Category: Alkaline phosphatase]]
 [[Category: Escherichia coli]]
-[[Category: Holtz, K M.]]
+[[Category: Large Structures]]
-[[Category: Kantrowitz, E R.]]
+[[Category: Holtz KM]]
-[[Category: Stec, B.]]
+[[Category: Kantrowitz ER]]
-[[Category: Free of phosphate]]
+[[Category: Stec B]]
-[[Category: Wild type]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:22:56 2009''