5mal: Difference between revisions
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<StructureSection load='5mal' size='340' side='right'caption='[[5mal]], [[Resolution|resolution]] 1.71Å' scene=''> | <StructureSection load='5mal' size='340' side='right'caption='[[5mal]], [[Resolution|resolution]] 1.71Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5mal]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5mal]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rimosus Streptomyces rimosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MAL FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.708Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5mal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mal OCA], [https://pdbe.org/5mal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mal RCSB], [https://www.ebi.ac.uk/pdbsum/5mal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mal ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/LIP_STRRM LIP_STRRM] Catalyzes the hydrolysis of p-nitrophenyl esters, alpha- and beta-naphthyl esters, and triacylglycerols, with a preference for medium acyl chain length (C8-C12). Shows a much higher hydrolysis rate of glycerol esters of unsaturated C16 and C18 fatty acids than that of their saturated counterparts, and a preference for cis double bond. Is also able to hydrolyze several natural oils and Tween detergents. Also displays thioesterase and phospholipase activities, towards palmitoyl-coenzyme A and diheptanoyl glycerophosphocholine, respectively. Shows transesterification activity of racemic 1-phenyl ethanol with vinyl acetate in hexane, proceeding with partial (R)-enantioselectivity.<ref>PMID:20931591</ref> <ref>PMID:20931591</ref> [REFERENCE:5] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Streptomyces rimosus]] | [[Category: Streptomyces rimosus]] | ||
[[Category: Stefanic | [[Category: Stefanic Z]] | ||
Latest revision as of 21:35, 1 November 2023
Crystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolutionCrystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution
Structural highlights
FunctionLIP_STRRM Catalyzes the hydrolysis of p-nitrophenyl esters, alpha- and beta-naphthyl esters, and triacylglycerols, with a preference for medium acyl chain length (C8-C12). Shows a much higher hydrolysis rate of glycerol esters of unsaturated C16 and C18 fatty acids than that of their saturated counterparts, and a preference for cis double bond. Is also able to hydrolyze several natural oils and Tween detergents. Also displays thioesterase and phospholipase activities, towards palmitoyl-coenzyme A and diheptanoyl glycerophosphocholine, respectively. Shows transesterification activity of racemic 1-phenyl ethanol with vinyl acetate in hexane, proceeding with partial (R)-enantioselectivity.[1] [2] [REFERENCE:5] Publication Abstract from PubMedSrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 A resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A1 from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer alphabetaalpha sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OgammaH...NepsilonHis216, His216-NdeltaH...O horizontal lineC-Ser214, and Gly54-NH...Ogamma-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of DeltaGENZ = 17.9 kcal mol-1, being in reasonable agreement with the experimental value of 14.5 kcal mol-1, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad. Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus.,Lescic Asler I, Stefanic Z, Marsavelski A, Vianello R, Kojic-Prodic B ACS Chem Biol. 2017 Jul 21;12(7):1928-1936. doi: 10.1021/acschembio.6b01140. Epub, 2017 Jun 14. PMID:28558229[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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