1ec7: Difference between revisions

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 ==E. COLI GLUCARATE DEHYDRATASE NATIVE ENZYME==
-<StructureSection load='1ec7' size='340' side='right' caption='[[1ec7]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1ec7' size='340' side='right'caption='[[1ec7]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ec7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EC7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ec7]] 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=1EC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EC7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bqg|1bqg]], [[1ec8|1ec8]], [[1ec9|1ec9]], [[1ecq|1ecq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ec7 OCA], [https://pdbe.org/1ec7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ec7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ec7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ec7 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ec7 OCA], [http://pdbe.org/1ec7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/1ec7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ec7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GUDD_ECOLI GUDD_ECOLI]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.
+[https://www.uniprot.org/uniprot/GUDD_ECOLI GUDD_ECOLI] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1ec7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-D-Glucarate dehydratase (GlucD) from Escherichia coli catalyzes the dehydration of both D-glucarate and L-idarate as well as their interconversion via epimerization. GlucD is a member of the mandelate racemase (MR) subgroup of the enolase superfamily, the members of which catalyze reactions that are initiated by abstraction of the alpha-proton of a carboxylate anion substrate. Alignment of the sequence of GlucD with that of MR reveals a conserved Lys-X-Lys motif and a His-Asp dyad homologous to the S- and R-specific bases in the active site of MR. Crystals of GlucD have been obtained into which the substrate D-glucarate and two competitive inhibitors, 4-deoxy-D-glucarate and xylarohydroxamate, could be diffused; D-glucarate is converted to the dehydration product, 5-keto-4-deoxy-D-glucarate (KDG). The structures of these complexes have been determined and reveal the identities of the ligands for the required Mg(2+) (Asp(235), Glu(266), and Asn(289)) as well as confirm the expected presence of Lys(207) and His(339), the catalytic bases that are properly positioned to abstract the proton from C5 of L-idarate and D-glucarate, respectively. Surprisingly, the C6 carboxylate group of KDG is a bidentate ligand to the Mg(2+), with the resulting geometry of the bound KDG suggesting that stereochemical roles of Lys(207) and His(339) are reversed from the predictions made on the basis of the established structure-function relationships for the MR-catalyzed reaction. The catalytic roles of these residues have been examined by characterization of mutant enzymes, although we were unable to use these to demonstrate the catalytic independence of Lys(207) and His(339) as was possible for the homologous Lys(166) and His(297) in the MR-catalyzed reaction.
-Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.,Gulick AM, Hubbard BK, Gerlt JA, Rayment I Biochemistry. 2000 Apr 25;39(16):4590-602. PMID:10769114<ref>PMID:10769114</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ec7" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Glucarate dehydratase]]
+[[Category: Large Structures]]
-[[Category: Gerlt, J A]]
+[[Category: Gerlt JA]]
-[[Category: Gulick, A M]]
+[[Category: Gulick AM]]
-[[Category: Hubbard, B K]]
+[[Category: Hubbard BK]]
-[[Category: Rayment, I]]
+[[Category: Rayment I]]
-[[Category: Lyase]]