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8xia

From Proteopedia

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(New page: 200px<br /><applet load="8xia" size="450" color="white" frame="true" align="right" spinBox="true" caption="8xia, resolution 1.9&Aring;" /> '''X-RAY ANALYSIS OF D-X...)
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[[Image:8xia.jpg|left|200px]]<br /><applet load="8xia" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="8xia, resolution 1.9&Aring;" />
 
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'''X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR'''<br />
 
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==Overview==
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==X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR==
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The structures of crystalline D-xylose isomerase (D-xylose, ketol-isomerase; EC 5.3.1.5) from Streptomyces rubiginosus and of its, complexes with substrate and with an active-site-directed inhibitor have, been determined by x-ray diffraction techniques and refined to 1.9-A, resolution. This study identifies the active site, as well as two, metal-binding sites. The metal ions are important in maintaining the, structure of the active-site region and one of them binds C3-O and C5-O of, the substrate forming a six-membered ring. This study has revealed a very, close contact between histidine and C1 of a substrate, suggesting that, this is the active-site base that abstracts a proton from substrate. The, mechanism-based inhibitor is a substrate analog and is turned over by the, enzyme to give a product that alkylates this same histidine, reinforcing, our interpretation. The changes in structure of the native enzyme, the, enzyme with bound substrate, and the alkylated enzyme indicate that the, mechanism involves an "open-chain" conformation of substrate and that the, intermediate in the isomerization reaction is probably a cis-ene diol, because the active-site histidine is correctly placed to abstract a proton, from C1 or C2 of the substrate. A water molecule binds to C1O and C2O of, the substrate and so may act as a proton donor or acceptor in the, enolization of a ring-opened substrate.
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<StructureSection load='8xia' size='340' side='right'caption='[[8xia]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[8xia]] 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=8XIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XIA FirstGlance]. <br>
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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]] 1.9&#8491;</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XLS:D-XYLOSE+(LINEAR+FORM)'>XLS</scene></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=8xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xia OCA], [https://pdbe.org/8xia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xia RCSB], [https://www.ebi.ac.uk/pdbsum/8xia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xia ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
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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/xi/8xia_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/main_output.php?pdb_ID=8xia ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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8XIA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus] with XLS and MN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=8XIA OCA].
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator., Carrell HL, Glusker JP, Burger V, Manfre F, Tritsch D, Biellmann JF, Proc Natl Acad Sci U S A. 1989 Jun;86(12):4440-4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2734296 2734296]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Streptomyces rubiginosus]]
[[Category: Streptomyces rubiginosus]]
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[[Category: Xylose isomerase]]
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[[Category: Carrell HL]]
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[[Category: Carrell, H.L.]]
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[[Category: Glusker JP]]
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[[Category: Glusker, J.P.]]
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[[Category: MN]]
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[[Category: XLS]]
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[[Category: isomerase(intramolecular oxidoreductse)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:01:40 2007''
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Current revision

X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR

PDB ID 8xia

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