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4duo

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==Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7==
==Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7==
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<StructureSection load='4duo' size='340' side='right' caption='[[4duo]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='4duo' size='340' side='right'caption='[[4duo]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4duo]] 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=4DUO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DUO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4duo]] 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=4DUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DUO 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</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]] 2&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene></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=4duo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4duo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4duo RCSB], [http://www.ebi.ac.uk/pdbsum/4duo PDBsum]</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=4duo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4duo OCA], [https://pdbe.org/4duo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4duo RCSB], [https://www.ebi.ac.uk/pdbsum/4duo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4duo ProSAT]</span></td></tr>
</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) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 A resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.
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Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.,Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1201-6. Epub 2012 Aug 18. PMID:22948921<ref>PMID:22948921</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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==See Also==
==See Also==
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*[[D-xylose isomerase|D-xylose isomerase]]
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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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: Hanson L]]
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[[Category: Hanson, L]]
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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: Isomerase-isomerase inhibitor complex]]
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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 2Mg2+ ions and xylitol at pH 7.7

PDB ID 4duo

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