1px3: Difference between revisions

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-{{Seed}}
-[[Image:1px3.png|left|200px]]
-<!--
+==E. COLI (LACZ) BETA-GALACTOSIDASE (G794A)==
-The line below this paragraph, containing "STRUCTURE_1px3", creates the "Structure Box" on the page.
+<StructureSection load='1px3' size='340' side='right'caption='[[1px3]], [[Resolution|resolution]] 1.60&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'>[[1px3]] is a 4 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=1PX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PX3 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1px3|  PDB=1px3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1px3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1px3 OCA], [https://pdbe.org/1px3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1px3 RCSB], [https://www.ebi.ac.uk/pdbsum/1px3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1px3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BGAL_ECOLI BGAL_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/px/1px3_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=1px3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The open-closed conformational switch in the active site of Escherichia coli beta-galactosidase was studied by X-ray crystallography and enzyme kinetics. Replacement of Gly794 by alanine causes the apoenzyme to adopt the closed rather than the open conformation. Binding of the competitive inhibitor isopropyl thio-beta-D-galactoside (IPTG) requires the mutant enzyme to adopt its less favored open conformation, weakening affinity relative to wild type. In contrast, transition-state inhibitors bind to the enzyme in the closed conformation, which is favored for the mutant, and display increased affinity relative to wild type. Changes in affinity suggest that the free energy difference between the closed and open forms is 1-2 kcal/mol. By favoring the closed conformation, the substitution moves the resting state of the enzyme along the reaction coordinate relative to the native enzyme and destabilizes the ground state relative to the first transition state. The result is that the rate constant for galactosylation is increased but degalactosylation is slower. The covalent intermediate may be better stabilized than the second transition state. The substitution also results in better binding of glucose to both the free and the galactosylated enzyme. However, transgalactosylation with glucose to produce allolactose (the inducer of the lac operon) is slower with the mutant than with the native enzyme. This suggests either that the glucose is misaligned for the reaction or that the galactosylated enzyme with glucose bound is stabilized relative to the transition state for transgalactosylation.
-===E. COLI (LACZ) BETA-GALACTOSIDASE (G794A)===
+Structural basis for the altered activity of Gly794 variants of Escherichia coli beta-galactosidase.,Juers DH, Hakda S, Matthews BW, Huber RE Biochemistry. 2003 Nov 25;42(46):13505-11. PMID:14621996<ref>PMID:14621996</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1px3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14621996}}, adds the Publication Abstract to the page
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14621996 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14621996}}
+__TOC__
+</StructureSection>
-==About this Structure==
-PX3 is a 4 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=1PX3 OCA].
-==Reference==
-<ref group="xtra">PMID:14621996</ref><references group="xtra"/>
-[[Category: Beta-galactosidase]]
 [[Category: Escherichia coli]]
-[[Category: Hakda, S.]]
+[[Category: Large Structures]]
-[[Category: Huber, R E.]]
+[[Category: Hakda S]]
-[[Category: Juers, D H.]]
+[[Category: Huber RE]]
-[[Category: Matthews, B W.]]
+[[Category: Juers DH]]
-[[Category: Loop conformation]]
+[[Category: Matthews BW]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:38:37 2009''