2wn3: Difference between revisions

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-{{Seed}}
-[[Image:2wn3.png|left|200px]]
-<!--
+==Crystal structure of Discoidin I from Dictyostelium discoideum in complex with the disaccharide GalNAc beta 1-3 galactose, at 1.6 A resolution.==
-The line below this paragraph, containing "STRUCTURE_2wn3", creates the "Structure Box" on the page.
+<StructureSection load='2wn3' size='340' side='right'caption='[[2wn3]], [[Resolution|resolution]] 1.59&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'>[[2wn3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum_AX2 Dictyostelium discoideum AX2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WN3 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]] 1.59&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PG:2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>1PG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2wn3|  PDB=2wn3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wn3 OCA], [https://pdbe.org/2wn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wn3 RCSB], [https://www.ebi.ac.uk/pdbsum/2wn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wn3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DIS1A_DICDI DIS1A_DICDI]
+== 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/wn/2wn3_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=2wn3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Discoidin I (DiscI) and discoidin II (DiscII) are N-acetylgalactosamine (GalNAc)-binding proteins from Dictyostelium discoideum. They consist of two domains: an N-terminal discoidin domain and a C-terminal H-type lectin domain. They were cloned and expressed in high yield in recombinant form in Escherichia coli. Although both lectins bind galactose (Gal) and GalNAc, glycan array experiments performed on the recombinant proteins displayed strong differences in their specificity for oligosaccharides. DiscI and DiscII bind preferentially to Gal/GalNAcbeta1-3Gal/GalNAc-containing and Gal/GalNAcbeta1-4GlcNAcbeta1-6Gal/GalNAc-containing glycans, respectively. The affinity of the interaction of DiscI with monosaccharides and disaccharides was evaluated using isothermal titration calorimetry experiments. The three-dimensional structures of native DiscI and its complexes with GalNAc, GalNAcbeta1-3Gal, and Galbeta1-3GalNAc were solved by X-ray crystallography. DiscI forms trimers with involvement of calcium at the monomer interface. The N-terminal discoidin domain presents a structural similarity to F-type lectins such as the eel agglutinin, where an amphiphilic binding pocket suggests possible carbohydrate-binding activity. In the C-terminal H-type lectin domain, the GalNAc residue establishes specific hydrogen bonds that explain the observed affinity (K(d)=3x10(-4) M). The different specificities of DiscI and DiscII for oligosaccharides were rationalized from the different structures obtained by either X-ray crystallography or molecular modeling.
-===CRYSTAL STRUCTURE OF DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH THE DISACCHARIDE GALNAC BETA 1-3 GALACTOSE, AT 1.6 A RESOLUTION.===
+Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II.,Mathieu SV, Aragao KS, Imberty A, Varrot A J Mol Biol. 2010 Jul 16;400(3):540-54. Epub 2010 May 24. PMID:20580724<ref>PMID:20580724</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_20580724}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2wn3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20580724 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20580724}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Dictyostelium discoideum AX2]]
-WN3 is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WN3 OCA].
+[[Category: Large Structures]]
+[[Category: Imberty A]]
-==Reference==
+[[Category: Mathieu S]]
-<ref group="xtra">PMID:20580724</ref><references group="xtra"/>
+[[Category: Varrot A]]
-[[Category: Dictyostelium discoideum]]
-[[Category: Imberty, A.]]
-[[Category: Mathieu, S.]]
-[[Category: Varrot, A.]]
-[[Category: Cell adhesion]]
-[[Category: Discoidin domain]]
-[[Category: Lectin]]
-[[Category: Type-h lectin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  7 08:00:40 2010''