9xia: Difference between revisions

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-[[Image:9xia.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_9xia", creates the "Structure Box" on the page.
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-{{STRUCTURE_9xia|  PDB=9xia  |  SCENE=  }}
-'''X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR'''
+==X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR==
+<StructureSection load='9xia' size='340' side='right'caption='[[9xia]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9xia]] 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=9XIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9XIA 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFR:3-DEOXY-3-METHYL-D-FRUCTOSE'>DFR</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=9xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9xia OCA], [https://pdbe.org/9xia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9xia RCSB], [https://www.ebi.ac.uk/pdbsum/9xia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9xia 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/xi/9xia_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=9xia ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==Overview==
+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:2734296<ref>PMID:2734296</ref>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-XIA is a [[Single protein]] structure of 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=9XIA OCA].
+</div>
+<div class="pdbe-citations 9xia" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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://www.ncbi.nlm.nih.gov/pubmed/2734296 2734296]
+*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces rubiginosus]]
-[[Category: Xylose isomerase]]
+[[Category: Carrell HL]]
-[[Category: Carrell, H L.]]
+[[Category: Glusker JP]]
-[[Category: Glusker, J P.]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:55:22 2008''