2cdo: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2cdo.png|left|200px]]
-<!--
+==structure of agarase carbohydrate binding module in complex with neoagarohexaose==
-The line below this paragraph, containing "STRUCTURE_2cdo", creates the "Structure Box" on the page.
+<StructureSection load='2cdo' size='340' side='right'caption='[[2cdo]], [[Resolution|resolution]] 1.64&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'>[[2cdo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharophagus_degradans Saccharophagus degradans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CDO 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]] 1.64&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAL:3,6-ANHYDRO-L-GALACTOSE'>AAL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2cdo|  PDB=2cdo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cdo OCA], [https://pdbe.org/2cdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cdo RCSB], [https://www.ebi.ac.uk/pdbsum/2cdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cdo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6DN99_9GAMM Q6DN99_9GAMM]
+== 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/cd/2cdo_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=2cdo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Carbohydrate recognition is central to the biological and industrial exploitation of plant structural polysaccharides. These insoluble polymers are recalcitrant to microbial degradation, and enzymes that catalyze this process generally contain non-catalytic carbohydrate binding modules (CBMs) that potentiate activity by increasing substrate binding. Agarose, a repeat of the disaccharide 3,6-anhydro-alpha-L-galactose-(1,3)-beta-D-galactopyranose-(1,4), is the dominant matrix polysaccharide in marine algae, yet the role of CBMs in the hydrolysis of this important polymer has not previously been explored. Here we show that family 6 CBMs, present in two different beta-agarases, bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide. The crystal structure of one of these modules Aga16B-CBM6-2, in complex with neoagarohexaose, reveals the mechanism by which the protein displays exquisite specificity, targeting the equatorial O4 and the axial O3 of the anhydro-L-galactose. Targeting of the CBM6 to the non-reducing end of agarose chains may direct the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases where the matrix polysaccharide is likely to be more amenable to further enzymic hydrolysis.
-===STRUCTURE OF AGARASE CARBOHYDRATE BINDING MODULE IN COMPLEX WITH NEOAGAROHEXAOSE===
+Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.,Henshaw J, Horne-Bitschy A, van Bueren AL, Money VA, Bolam DN, Czjzek M, Ekborg NA, Weiner RM, Hutcheson SW, Davies GJ, Boraston AB, Gilbert HJ J Biol Chem. 2006 Jun 23;281(25):17099-107. Epub 2006 Apr 6. PMID:16601125<ref>PMID:16601125</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_16601125}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2cdo" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16601125 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16601125}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CDO is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharophagus_degradans Saccharophagus degradans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CDO OCA].
-==Reference==
-<ref group="xtra">PMID:16601125</ref><references group="xtra"/>
 [[Category: Saccharophagus degradans]]
-[[Category: Bolam, D N.]]
+[[Category: Bolam DN]]
-[[Category: Boraston, A B.]]
+[[Category: Boraston AB]]
-[[Category: Bueren, A L.Van.]]
+[[Category: Czjzek M]]
-[[Category: Czjzek, M.]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J.]]
+[[Category: Gilbert HJ]]
-[[Category: Gilbert, H J.]]
+[[Category: Henshaw J]]
-[[Category: Henshaw, J.]]
+[[Category: Horne A]]
-[[Category: Horne, A.]]
+[[Category: Hutcheson SW]]
-[[Category: Hutcheson, S W.]]
+[[Category: Money VA]]
-[[Category: Money, V A.]]
+[[Category: Van Bueren AL]]
-[[Category: Weiner, R M.]]
+[[Category: Weiner RM]]
-[[Category: Carbohydrate-binding module]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:55:22 2009''