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6wn6
From Proteopedia
(Difference between revisions)
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==Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form== | ==Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form== | ||
| - | <StructureSection load='6wn6' size='340' side='right'caption='[[6wn6]]' scene=''> | + | <StructureSection load='6wn6' size='340' side='right'caption='[[6wn6]], [[Resolution|resolution]] 1.86Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WN6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WN6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6wn6]] 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=6WN6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WN6 FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wn6 OCA], [http://pdbe.org/6wn6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wn6 RCSB], [http://www.ebi.ac.uk/pdbsum/6wn6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wn6 ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ycjR, PGD_01932 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wn6 OCA], [http://pdbe.org/6wn6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wn6 RCSB], [http://www.ebi.ac.uk/pdbsum/6wn6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wn6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | YcjR from Escherichia coli K-12 MG1655 catalyzes the manganese-dependent reversible epimerization of 3-keto-alpha-d-gulosides to the corresponding 3-keto-alpha-d-glucosides as a part of a proposed catabolic pathway for the transformation of d-gulosides to d-glucosides. The three-dimensional structure of the manganese-bound enzyme was determined by X-ray crystallography. The divalent manganese ion is coordinated to the enzyme by ligation to Glu-146, Asp-179, His-205, and Glu-240. When either of the two active site glutamate residues is mutated to glutamine, the enzyme loses all catalytic activity for the epimerization of alpha-methyl-3-keto-d-glucoside at C4. However, the E240Q mutant can catalyze hydrogen-deuterium exchange of the proton at C4 of alpha-methyl-3-keto-d-glucoside in solvent D2O. The E146Q mutant does not catalyze this exchange reaction. These results indicate that YcjR catalyzes the isomerization of 3-keto-d-glucosides via proton abstraction at C4 by Glu-146 to form a cis-enediolate intermediate that is subsequently protonated on the opposite face by Glu-240 to generate the corresponding 3-keto-d-guloside. This conclusion is supported by docking of the cis-enediolate intermediate into the active site of YcjR based on the known binding orientation of d-fructose and d-psicose in the active site of d-psicose-3-epimerase. | ||
| + | |||
| + | Structure and Reaction Mechanism of YcjR, an Epimerase That Facilitates the Interconversion of d-Gulosides to d-Glucosides in Escherichia coli.,Mabanglo MF, Huddleston JP, Mukherjee K, Taylor ZW, Raushel FM Biochemistry. 2020 Jun 9;59(22):2069-2077. doi: 10.1021/acs.biochem.0c00334. Epub, 2020 May 28. PMID:32437133<ref>PMID:32437133</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6wn6" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Mabanglo | + | [[Category: Mabanglo, M F]] |
| - | [[Category: Mukherjee K]] | + | [[Category: Mukherjee, K]] |
| - | [[Category: Raushel | + | [[Category: Raushel, F M]] |
| + | [[Category: Epimerase]] | ||
| + | [[Category: Isomerase]] | ||
| + | [[Category: Microbiome]] | ||
| + | [[Category: Prebiotic]] | ||
Revision as of 10:49, 17 June 2020
Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form
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