3kbn
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3kbn is ON HOLD Authors: Kovalevsky, A.Y., Hanson, L., Langan, P. Description: Room temperature structure of D-Xylose Isomerase in complex with 2Ni...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form== | |
| + | <StructureSection load='3kbn' size='340' side='right'caption='[[3kbn]], [[Resolution|resolution]] 1.53Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3kbn]] 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=3KBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KBN FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kbn OCA], [https://pdbe.org/3kbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kbn RCSB], [https://www.ebi.ac.uk/pdbsum/3kbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kbn ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism. | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/3kbn_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kbn ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction. | ||
| - | + | Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.,Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P Structure. 2010 Jun 9;18(6):688-99. PMID:20541506<ref>PMID:20541506</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3kbn" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Streptomyces rubiginosus]] | ||
| + | [[Category: Hanson L]] | ||
| + | [[Category: Kovalevsky AY]] | ||
| + | [[Category: Langan P]] | ||
Current revision
Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form
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