2xom: Difference between revisions

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-{{Seed}}
-[[Image:2xom.jpg|left|200px]]
-<!--
+==Atomic resolution structure of TmCBM61 in complex with beta-1,4- galactotriose==
-The line below this paragraph, containing "STRUCTURE_2xom", creates the "Structure Box" on the page.
+<StructureSection load='2xom' size='340' side='right'caption='[[2xom]], [[Resolution|resolution]] 0.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2xom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XOM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PRD_900114:4beta-beta-galactotriose'>PRD_900114</scene></td></tr>
-{{STRUCTURE_2xom|  PDB=2xom  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xom OCA], [https://pdbe.org/2xom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xom RCSB], [https://www.ebi.ac.uk/pdbsum/2xom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xom ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9X0S8_THEMA Q9X0S8_THEMA]
+== 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/xo/2xom_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=2xom ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The microbial enzymes that depolymerize plant cell wall polysaccharides, ultimately promoting energy liberation and carbon recycling, are typically complex in their modularity and often contain carbohydrate-binding modules (CBMs). Here, through analysis of an unknown module from a Thermotoga maritima endo-beta-1,4-galactanase, we identify a new family of CBMs that are most frequently found appended to proteins with beta-1,4-galactanase activity. Polysaccharide microarray screening, immunofluorescence microscopy, and biochemical analysis of the isolated module demonstrate the specificity of the module, here called TmCBM61, for beta-1,4-linked galactose-containing ligands, making it the founding member of family CBM61. The ultra-high resolution X-ray crystal structures of TmCBM61 (0.95 and 1.4 A resolution) in complex with beta-1,4-galactotriose reveal the molecular basis of the specificity of the CBM for beta-1,4-galactan. Analysis of these structures provides insight into the recognition of an unexpected helical galactan conformation through a mode of binding that resembles the recognition of starch.
-===ATOMIC RESOLUTION STRUCTURE OF TMCBM61 IN COMPLEX WITH BETA-1,4-GALACTOTRIOSE===
+Recognition of the helical structure of beta-1,4-galactan by a new family of carbohydrate-binding modules.,Cid M, Pedersen HL, Kaneko S, Coutinho PM, Henrissat B, Willats WG, Boraston AB J Biol Chem. 2010 Nov 12;285(46):35999-6009. Epub 2010 Sep 8. PMID:20826814<ref>PMID:20826814</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xom" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-XOM is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XOM OCA].
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Boraston, A B.]]
+[[Category: Boraston AB]]
-[[Category: Cid, M.]]
+[[Category: Cid M]]
-[[Category: Coutinho, P M.]]
+[[Category: Coutinho PM]]
-[[Category: Henrissat, B.]]
+[[Category: Henrissat B]]
-[[Category: Kaneko, S.]]
+[[Category: Kaneko S]]
-[[Category: Lodberg-Pedersen, H.]]
+[[Category: Lodberg-Pedersen H]]
-[[Category: Willats, W G.T.]]
+[[Category: Willats WGT]]
-[[Category: Beta-sandwich.]]
-[[Category: Carbohydrate-binding module]]
-[[Category: Galactan]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Sep 10 13:54:35 2010''