2vme: 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: @@
-[[Image:2vme.png|left|200px]]
-<!--
+==Structure of the wild-type discoidin II from Dictyostelium discoideum==
-The line below this paragraph, containing "STRUCTURE_2vme", creates the "Structure Box" on the page.
+<StructureSection load='2vme' size='340' side='right'caption='[[2vme]], [[Resolution|resolution]] 2.45&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'>[[2vme]] is a 6 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=2VME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VME 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]] 2.45&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HIP:ND1-PHOSPHONOHISTIDINE'>HIP</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2vme|  PDB=2vme  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vme OCA], [https://pdbe.org/2vme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vme RCSB], [https://www.ebi.ac.uk/pdbsum/2vme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vme ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DIS2_DICDI DIS2_DICDI] Galactose-binding lectin. May be necessary for the primary process of spore formation and may be involved in spore coat formation.
+== 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/vm/2vme_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=2vme ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The social amoeba Dictyostelium discoideum adopts a cohesive stage upon starvation and then produces Discoidin I and II, two proteins able to bind galactose and N-acetyl-galactosamine. The N-terminal domain or discoidin domain (DS) is widely distributed in eukaryotes where it plays a role in extracellular matrix binding while the C-terminal domain displays sequence similarities to invertebrate lectins. We present the first X-ray structures of the wild-type and recombinant Discoidin II in unliganded state and in complex with monosaccharides. The protein forms a homotrimer which presents two binding surfaces situated on the opposite boundaries of the structure. The binding sites of the N-terminal domain contain PEG molecules that could mimics binding of natural ligand. The C-terminal lectin domain interactions with N-acetyl-D-galactosamine and methyl-beta-galactoside are described. The carbohydrate binding sites are located at the interface between monomers. Specificity for galacto configuration can be rationalized since the axial O4 hydroxyl group is involved in several hydrogen bonds with protein side chains. Titration microcalorimetry allowed characterization of affinity and demonstrated the enthalpy-driven character of the interaction. Those results highlight the structural differentiation of the DS domain involved in many cell-adhesion processes from the lectin activity of Dictyostelium discoidins.
-===STRUCTURE OF THE WILD-TYPE DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM===
+Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.,Aragao KS, Satre M, Imberty A, Varrot A Proteins. 2008 Oct;73(1):43-52. PMID:18384150<ref>PMID:18384150</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_18384150}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vme" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18384150 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18384150}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Dictyostelium discoideum AX2]]
-[[2vme]] is a 6 chain structure with sequence 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=2VME OCA].
+[[Category: Large Structures]]
+[[Category: Aragao KS]]
-==Reference==
+[[Category: Imberty A]]
-<ref group="xtra">PMID:018384150</ref><references group="xtra"/>
+[[Category: Satre M]]
-[[Category: Dictyostelium discoideum]]
+[[Category: Varrot A]]
-[[Category: Aragao, K S.]]
-[[Category: Imberty, A.]]
-[[Category: Satre, M.]]
-[[Category: Varrot, A.]]