1dyo: Difference between revisions

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-{{Seed}}
-[[Image:1dyo.png|left|200px]]
-<!--
+==Xylan-Binding Domain from CBM 22, formally x6b domain==
-The line below this paragraph, containing "STRUCTURE_1dyo", creates the "Structure Box" on the page.
+<StructureSection load='1dyo' size='340' side='right'caption='[[1dyo]], [[Resolution|resolution]] 2.10&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'>[[1dyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus Acetivibrio thermocellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DYO 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]] 2.1&#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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1dyo|  PDB=1dyo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyo OCA], [https://pdbe.org/1dyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dyo RCSB], [https://www.ebi.ac.uk/pdbsum/1dyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dyo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYNY_ACETH XYNY_ACETH]
+== 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/dy/1dyo_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=1dyo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many polysaccharide-degrading enzymes display a modular structure in which a catalytic module is attached to one or more noncatalytic modules. Several xylanases contain a module of previously unknown function (termed "X6" modules) that had been implicated in thermostability. We have investigated the properties of two such "thermostabilizing" modules, X6a and X6b from the Clostridium thermocellumxylanase Xyn10B. These modules, expressed either as discrete entities or as their natural fusions with the catalytic module, were assayed, and their capacity to bind various carbohydrates and potentiate hydrolytic activity was determined. The data showed that X6b, but not X6a, increased the activity of the enzyme against insoluble xylan and bound specifically to xylooligosaccharides and various xylans. In contrast, X6a exhibited no affinity for soluble or insoluble forms of xylan. Isothermal titration calorimetry revealed that the ligand-binding site of X6b accommodates approximately four xylose residues. The protein exhibited K(d) values in the low micromolar range for xylotetraose, xylopentaose, and xylohexaose; 24 microM for xylotriose; and 50 microM for xylobiose. Negative DeltaH and DeltaS values indicate that the interaction of X6b with xylooligosaccharides and xylan is driven by enthalpic forces. The three-dimensional structure of X6b has been solved by X-ray crystallography to a resolution of 2.1 A. The protein is a beta-sandwich that presents a tryptophan and two tyrosine residues on the walls of a shallow cleft that is likely to be the xylan-binding site. In view of the structural and carbohydrate-binding properties of X6b, it is proposed that this and related modules be re-assigned as family 22 carbohydrate-binding modules.
-===XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN===
+The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain.,Charnock SJ, Bolam DN, Turkenburg JP, Gilbert HJ, Ferreira LM, Davies GJ, Fontes CM Biochemistry. 2000 May 2;39(17):5013-21. PMID:10819965<ref>PMID:10819965</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10353814}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1dyo" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10353814 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10353814}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Acetivibrio thermocellus]]
-DYO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYO OCA].
+[[Category: Large Structures]]
+[[Category: Charnock SJ]]
-==Reference==
+[[Category: Davies GJ]]
-Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level., Millard CB, Kryger G, Ordentlich A, Greenblatt HM, Harel M, Raves ML, Segall Y, Barak D, Shafferman A, Silman I, Sussman JL, Biochemistry. 1999 Jun 1;38(22):7032-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10353814 10353814]
+[[Category: Fontes CMGA]]
-[[Category: Clostridium thermocellum]]
+[[Category: Gilbert HJ]]
-[[Category: Single protein]]
-[[Category: Charnock, S J.]]
-[[Category: Davies, G J.]]
-[[Category: Fontes, C M.G A.]]
-[[Category: Gilbert, H J.]]
-[[Category: Carbohydrate-binding module]]
-[[Category: Xylan-binding]]
-[[Category: Xylanase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:49:03 2008''