3dym: Difference between revisions

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-{{Seed}}
-[[Image:3dym.png|left|200px]]
-<!--
+==E. coli (lacZ) beta-galactosidase (H418E)==
-The line below this paragraph, containing "STRUCTURE_3dym", creates the "Structure Box" on the page.
+<StructureSection load='3dym' size='340' side='right'caption='[[3dym]], [[Resolution|resolution]] 2.05&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'>[[3dym]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DYM 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]] 2.05&#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_3dym|  PDB=3dym  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dym OCA], [https://pdbe.org/3dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dym RCSB], [https://www.ebi.ac.uk/pdbsum/3dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dym 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/dy/3dym_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=3dym ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The active site of ss-galactosidase (E. coli) contains a Mg(2+) ion ligated by Glu-416, His-418 and Glu-461 plus three water molecules. A Na(+) ion binds nearby. To better understand the role of the active site Mg(2+) and its ligands, His-418 was substituted with Asn, Glu and Phe. The Asn-418 and Glu-418 variants could be crystallized and the structures were shown to be very similar to native enzyme. The Glu-418 variant showed increased mobility of some residues in the active site, which explains why the substitutions at the Mg(2+) site also reduce Na(+) binding affinity. The Phe variant had reduced stability, bound Mg(2+) weakly and could not be crystallized. All three variants have low catalytic activity due to large decreases in the degalactosylation rate. Large decreases in substrate binding affinity were also observed but transition state analogs bound as well or better than to native. The results indicate that His-418, together with the Mg(2+), modulate the central role of Glu-461 in binding and as a general acid/base catalyst in the overall catalytic mechanism. Glucose binding as an acceptor was also dramatically decreased, indicating that His-418 is very important for the formation of allolactose (the natural inducer of the lac operon).
-===E. coli (lacZ) beta-galactosidase (H418E)===
+Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).,Juers DH, Rob B, Dugdale ML, Rahimzadeh N, Giang C, Lee M, Matthews BW, Huber RE Protein Sci. 2009 Jun;18(6):1281-92. PMID:19472413<ref>PMID:19472413</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dym" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-DYM is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DYM OCA].
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
-[[Category: Beta-galactosidase]]
+== References ==
-[[Category: Escherichia coli k12]]
+<references/>
-[[Category: Huber, R E.]]
+__TOC__
-[[Category: Juers, D H.]]
+</StructureSection>
-[[Category: Matthews, B W.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Beta-galactosidase]]
+[[Category: Large Structures]]
-[[Category: Glycosidase]]
+[[Category: Huber RE]]
-[[Category: Hydrolase]]
+[[Category: Juers DH]]
+[[Category: Matthews BW]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:49:27 2009''