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4qee

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==Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribose==
==Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribose==
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<StructureSection load='4qee' size='340' side='right' caption='[[4qee]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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<StructureSection load='4qee' size='340' side='right'caption='[[4qee]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qee]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QEE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QEE FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qee]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QEE FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</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]] 1.6&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qdp|4qdp]], [[4qdw|4qdw]], [[4qe1|4qe1]], [[4qe4|4qe4]], [[4qe5|4qe5]], [[4qeh|4qeh]]</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=4qee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qee OCA], [https://pdbe.org/4qee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qee RCSB], [https://www.ebi.ac.uk/pdbsum/4qee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qee ProSAT]</span></td></tr>
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<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=4qee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qee OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qee RCSB], [http://www.ebi.ac.uk/pdbsum/4qee PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.
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[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy 5S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni2+ cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.
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L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.,Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A Structure. 2014 Aug 12. pii: S0969-2126(14)00210-X. doi:, 10.1016/j.str.2014.07.002. PMID:25132082<ref>PMID:25132082</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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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Large Structures]]
[[Category: Streptomyces rubiginosus]]
[[Category: Streptomyces rubiginosus]]
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[[Category: Xylose isomerase]]
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[[Category: Kovalevsky AY]]
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[[Category: Kovalevsky, A Y]]
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[[Category: Langan P]]
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[[Category: Langan, P]]
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[[Category: Isomerase]]
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[[Category: Monosaccharide]]
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[[Category: Sugar isomerase]]
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[[Category: Tim barrel]]
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Current revision

Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribose

PDB ID 4qee

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