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3cwh
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3cwh is ON HOLD Authors: Kovalevsky, A.Y., Langan, P., Glusker, J.P. Description: D-xylose Isomerase in complex with linear product, per-deuterated...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==D-xylose Isomerase in complex with linear product, per-deuterated xylulose== | |
| + | <StructureSection load='3cwh' size='340' side='right'caption='[[3cwh]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3cwh]] 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=3CWH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CWH FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
| + | <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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=XUL:D-XYLULOSE'>XUL</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=3cwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cwh OCA], [https://pdbe.org/3cwh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cwh RCSB], [https://www.ebi.ac.uk/pdbsum/3cwh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cwh 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/cw/3cwh_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=3cwh ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme d-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, d-xylulose, shows, unexpectedly, that O5 of d-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism. | ||
| - | + | Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose.,Kovalevsky AY, Katz AK, Carrell HL, Hanson L, Mustyakimov M, Fisher SZ, Coates L, Schoenborn BP, Bunick GJ, Glusker JP, Langan P Biochemistry. 2008 Jul 22;47(29):7595-7. Epub 2008 Jun 26. PMID:18578508<ref>PMID:18578508</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3cwh" 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: Glusker JP]] | ||
| + | [[Category: Kovalevsky AY]] | ||
| + | [[Category: Langan P]] | ||
Current revision
D-xylose Isomerase in complex with linear product, per-deuterated xylulose
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