3o0d: Difference between revisions

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-[[Image:3o0d.png|left|200px]]
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+==Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution==
-The line below this paragraph, containing "STRUCTURE_3o0d", creates the "Structure Box" on the page.
+<StructureSection load='3o0d' size='340' side='right'caption='[[3o0d]], [[Resolution|resolution]] 1.70&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'>[[3o0d]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O0D 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_3o0d|  PDB=3o0d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o0d OCA], [https://pdbe.org/3o0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o0d RCSB], [https://www.ebi.ac.uk/pdbsum/3o0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o0d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9P8F7_YARLL Q9P8F7_YARLL]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the 1.7 A resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.
-===Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution===
+Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.,Bordes F, Barbe S, Escalier P, Mourey L, Andre I, Marty A, Tranier S Biophys J. 2010 Oct 6;99(7):2225-34. PMID:20923657<ref>PMID:20923657</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_20923657}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3o0d" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20923657 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20923657}}
-==About this Structure==
-[[3o0d]] is a 7 chain structure of [[Lipase]] with sequence from [http://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O0D OCA].
 ==See Also==
-*[[Lipase]]
+*[[Lipase 3D Structures|Lipase 3D Structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:20923657</ref><references group="xtra"/>
+__TOC__
-[[Category: Triacylglycerol lipase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Yarrowia lipolytica]]
-[[Category: Bordes, F.]]
+[[Category: Bordes F]]
-[[Category: Marty, A.]]
+[[Category: Marty A]]
-[[Category: Mourey, L.]]
+[[Category: Mourey L]]
-[[Category: Tranier, S.]]
+[[Category: Tranier S]]
-[[Category: Alpha/beta-hydrolase]]
-[[Category: Extracellular]]
-[[Category: Glycosylation]]
-[[Category: Hydrolase]]
-[[Category: Lipase]]
-[[Category: Lipids binding]]