3kbn

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[[Image:3kbn.png|left|200px]]
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==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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<StructureSection load='3kbn' size='340' side='right' caption='[[3kbn]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3kbn]] 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=3KBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KBN FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kbj|3kbj]], [[3kbm|3kbm]], [[3kbs|3kbs]], [[3kbv|3kbv]], [[3kbw|3kbw]], [[3kcj|3kcj]], [[3kcl|3kcl]], [[3kco|3kco]]</td></tr>
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<tr><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=1929 Streptomyces rubiginosus])</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kbn RCSB], [http://www.ebi.ac.uk/pdbsum/3kbn PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/3kbn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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The line below this paragraph, containing "STRUCTURE_3kbn", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_3kbn| PDB=3kbn | SCENE= }}
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===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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From MEDLINE®/PubMed®, 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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<!--
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_20541506}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 20541506 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_20541506}}
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==About this Structure==
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[[3kbn]] 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=3KBN OCA].
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==Reference==
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<ref group="xtra">PMID:020541506</ref><references group="xtra"/>
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[[Category: Streptomyces rubiginosus]]
[[Category: Streptomyces rubiginosus]]
[[Category: Xylose isomerase]]
[[Category: Xylose isomerase]]

Revision as of 09:44, 21 May 2014

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form

3kbn, resolution 1.53Å

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