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5nhd

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==Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose==
==Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose==
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<StructureSection load='5nhd' size='340' side='right' caption='[[5nhd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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<StructureSection load='5nhd' size='340' side='right'caption='[[5nhd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5nhd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pirse Pirse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NHD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5nhd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Piromyces_sp._E2 Piromyces sp. E2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NHD 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XLS:D-XYLOSE+(LINEAR+FORM)'>XLS</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 1.8&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[d_1200004044|d_1200004044]]</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XLS:D-XYLOSE+(LINEAR+FORM)'>XLS</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=73868 PIRSE])</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=5nhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nhd OCA], [https://pdbe.org/5nhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nhd RCSB], [https://www.ebi.ac.uk/pdbsum/5nhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nhd ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nhd OCA], [http://pdbe.org/5nhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nhd RCSB], [http://www.ebi.ac.uk/pdbsum/5nhd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nhd ProSAT]</span></td></tr>
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</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/Q9P8C9_PIRSE Q9P8C9_PIRSE]
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Xylose isomerase from Piromyces sp. E2 (PirXI) can be used for equipping Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in E. coli, analyzed the metal-dependence of its catalytic properties and solved twelve crystal structures in the presence of different metals, substrates, and substrate analogs. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn2+ which was established by measuring the activation constants (Kact) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals which is determined by metal availability as well as the affinity, indicating that native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a D-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal-dependence of the isomerase activity.
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Metal-dependence of xylose isomerase from Piromyces sp. E2 explored by activity profiling and protein crystallography.,Lee M, Rozeboom HJ, de Waal P, de Jong R, Dudek HM, Janssen DB Biochemistry. 2017 Oct 18. doi: 10.1021/acs.biochem.7b00777. PMID:29045784<ref>PMID:29045784</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 5nhd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Pirse]]
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[[Category: Large Structures]]
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[[Category: Xylose isomerase]]
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[[Category: Piromyces sp. E2]]
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[[Category: Janssen, D B]]
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[[Category: Janssen DB]]
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[[Category: Rozeboom, H J]]
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[[Category: Rozeboom HJ]]
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[[Category: Isomerase]]
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[[Category: Tim-barrel]]
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Current revision

Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose

PDB ID 5nhd

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