3o0d: Difference between revisions
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==Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution== | ==Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution== | ||
<StructureSection load='3o0d' size='340' side='right' caption='[[3o0d]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='3o0d' size='340' side='right'caption='[[3o0d]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3o0d]] is a 7 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3o0d]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18942 Atcc 18942]. 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> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | </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> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lip2, YALI0A20350g ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lip2, YALI0A20350g ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4952 ATCC 18942])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[Lipase|Lipase]] | *[[Lipase 3D Structures|Lipase 3D Structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Atcc 18942]] | [[Category: Atcc 18942]] | ||
[[Category: Large Structures]] | |||
[[Category: Triacylglycerol lipase]] | [[Category: Triacylglycerol lipase]] | ||
[[Category: Bordes, F]] | [[Category: Bordes, F]] | ||
Revision as of 10:12, 12 May 2022
Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolutionCrystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution
Structural highlights
Publication Abstract from PubMedWe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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