4qdw

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==Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose==
==Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose==
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<StructureSection load='4qdw' size='340' side='right' caption='[[4qdw]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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<StructureSection load='4qdw' size='340' side='right'caption='[[4qdw]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qdw]] 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=4QDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QDW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qdw]] 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=4QDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QDW FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=LAI:L-ARABINOSE'>LAI</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qdp|4qdp]], [[4qe1|4qe1]], [[4qe4|4qe4]], [[4qe5|4qe5]], [[4qee|4qee]], [[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=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=LAI:L-ARABINOSE'>LAI</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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<tr><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=4qdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdw OCA], [https://pdbe.org/4qdw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qdw RCSB], [https://www.ebi.ac.uk/pdbsum/4qdw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qdw ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qdw RCSB], [http://www.ebi.ac.uk/pdbsum/4qdw PDBsum]</span></td></tr>
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</table>
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<table>
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== Function ==
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<div style="background-color:#fffaf0;">
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[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
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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

Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose

PDB ID 4qdw

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