1jz2: Difference between revisions

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-{{Seed}}
-[[Image:1jz2.png|left|200px]]
-<!--
+==E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC)==
-The line below this paragraph, containing "STRUCTURE_1jz2", creates the "Structure Box" on the page.
+<StructureSection load='1jz2' size='340' side='right'caption='[[1jz2]], [[Resolution|resolution]] 2.10&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'>[[1jz2]] 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=1JZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JZ2 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2FG:2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE'>2FG</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <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_1jz2|  PDB=1jz2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jz2 OCA], [https://pdbe.org/1jz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jz2 RCSB], [https://www.ebi.ac.uk/pdbsum/1jz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jz2 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/jz/1jz2_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=1jz2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.
-===E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC)===
+A structural view of the action of Escherichia coli (lacZ) beta-galactosidase.,Juers DH, Heightman TD, Vasella A, McCarter JD, Mackenzie L, Withers SG, Matthews BW Biochemistry. 2001 Dec 11;40(49):14781-94. PMID:11732897<ref>PMID:11732897</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1jz2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11732897}}, adds the Publication Abstract to the page
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11732897 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11732897}}
+__TOC__
+</StructureSection>
-==About this Structure==
-JZ2 is a [[Single protein]] structure of sequence 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=1JZ2 OCA].
-==Reference==
-A structural view of the action of Escherichia coli (lacZ) beta-galactosidase., Juers DH, Heightman TD, Vasella A, McCarter JD, Mackenzie L, Withers SG, Matthews BW, Biochemistry. 2001 Dec 11;40(49):14781-94. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11732897 11732897]
-[[Category: Beta-galactosidase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Juers, D H.]]
+[[Category: Juers DH]]
-[[Category: Mackenzie, L.]]
+[[Category: Mackenzie L]]
-[[Category: Matthews, B W.]]
+[[Category: Matthews BW]]
-[[Category: McCarter, J D.]]
+[[Category: McCarter JD]]
-[[Category: Withers, S G.]]
+[[Category: Withers SG]]
-[[Category: Beta supersandwich]]
-[[Category: Immunoglobulin]]
-[[Category: Jelly-roll barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:37:37 2008''