6wn6

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Current revision (14:45, 6 March 2024) (edit) (undo)
 
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<StructureSection load='6wn6' size='340' side='right'caption='[[6wn6]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
<StructureSection load='6wn6' size='340' side='right'caption='[[6wn6]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<table><tr><td colspan='2'>[[6wn6]] 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=6WN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WN6 FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.86&#8491;</td></tr>
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<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>
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<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>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6wn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wn6 OCA], [https://pdbe.org/6wn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wn6 RCSB], [https://www.ebi.ac.uk/pdbsum/6wn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wn6 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/YCJR_ECOLI YCJR_ECOLI] Catalyzes the epimerization at C4 of 3-dehydro-D-gulosides leading to 3-dehydro-D-glucosides. Probably functions in a metabolic pathway that transforms D-gulosides to D-glucosides. Can use methyl alpha-3-dehydro-D-glucoside and methyl beta-3-dehydro-D-glucoside as substrates in vitro. However, the actual specific physiological substrates for this metabolic pathway are unknown. Cannot act on D-psicose, D-fructose, D-tagatose, D-sorbose, L-xylulose, or L-ribulose.<ref>PMID:30742415</ref>
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6wn6" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Mabanglo, M F]]
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[[Category: Mabanglo MF]]
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[[Category: Mukherjee, K]]
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[[Category: Mukherjee K]]
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[[Category: Raushel, F M]]
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[[Category: Raushel FM]]
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[[Category: Epimerase]]
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[[Category: Isomerase]]
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[[Category: Microbiome]]
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[[Category: Prebiotic]]
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Current revision

Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form

PDB ID 6wn6

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