2ga3: Difference between revisions

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-{{Seed}}
-[[Image:2ga3.png|left|200px]]
-<!--
+==Structure of S102T E. coli Alkaline Phosphatase-phosphate intermediate at 2.20A resolution==
-The line below this paragraph, containing "STRUCTURE_2ga3", creates the "Structure Box" on the page.
+<StructureSection load='2ga3' size='340' side='right'caption='[[2ga3]], [[Resolution|resolution]] 2.20&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'>[[2ga3]] 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=2GA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GA3 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]] 2.2&#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=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2ga3|  PDB=2ga3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ga3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ga3 OCA], [https://pdbe.org/2ga3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ga3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ga3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ga3 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/ga/2ga3_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=2ga3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report here the construction of a mutant version of Escherichia coli alkaline phosphatase (AP) in which the active site Ser was replaced by Thr (S102T), in order to investigate whether the enzyme can utilize Thr as the nucleophile and whether the rates of the critical steps in the mechanism are altered by the substitution. The mutant AP with Thr at position 102 exhibited an approximately 4000-fold decrease in k(cat) along with a small decrease in Km. The decrease in catalytic efficiency of approximately 2000-fold was a much smaller drop than that observed when Ala or Gly were substituted at position 102. The mechanism by which Thr can substitute for Ser in AP was further investigated by determining the X-ray structure of the S102T enzyme in the presence of the Pi (S102T_Pi), and after soaking the crystals with substrate (S102T_sub). In the S102T_Pi structure, the Pi was coordinated differently with its position shifted by 1.3 A compared to the structure of the wild-type enzyme in the presence of Pi. In the S102T_sub structure, a covalent Thr-Pi intermediate was observed, instead of the expected bound substrate. The stereochemistry of the phosphorus in the S102T_sub structure was inverted compared to the stereochemistry in the wild-type structure, as would be expected after the first step of a double in-line displacement mechanism. We conclude that the S102T mutation resulted in a shift in the rate-determining step in the mechanism allowing us to trap the covalent intermediate of the reaction in the crystal.
-===Structure of S102T E. coli Alkaline Phosphatase-phosphate intermediate at 2.20A resolution===
+Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine.,Wang J, Kantrowitz ER Protein Sci. 2006 Oct;15(10):2395-401. PMID:17008720<ref>PMID:17008720</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ga3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17008720}}, 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 17008720 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17008720}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GA3 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=2GA3 OCA].
-==Reference==
-<ref group="xtra">PMID:17008720</ref><references group="xtra"/>
-[[Category: Alkaline phosphatase]]
 [[Category: Escherichia coli]]
-[[Category: Kantrowitz, E R.]]
+[[Category: Large Structures]]
-[[Category: Wang, J.]]
+[[Category: Kantrowitz ER]]
-[[Category: Covalent intermediate]]
+[[Category: Wang J]]
-[[Category: Mutagenesis]]
-[[Category: Rate-determining step]]
-[[Category: Side chain conformation]]
-[[Category: X-ray crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:45:13 2009''