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5mal

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Revision as of 07:13, 19 August 2020

Crystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution

Structural highlights

5mal is a 2 chain structure with sequence from Streptomyces rimosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] [REFERENCE:5]

Publication Abstract from PubMed

SrLip 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.

References

↑ Lescic Asler I, Ivic N, Kovacic F, Schell S, Knorr J, Krauss U, Wilhelm S, Kojic-Prodic B, Jaeger KE. Probing enzyme promiscuity of SGNH hydrolases. Chembiochem. 2010 Oct 18;11(15):2158-67. doi: 10.1002/cbic.201000398. PMID:20931591 doi:10.1002/cbic.201000398
↑ Lescic Asler I, Ivic N, Kovacic F, Schell S, Knorr J, Krauss U, Wilhelm S, Kojic-Prodic B, Jaeger KE. Probing enzyme promiscuity of SGNH hydrolases. Chembiochem. 2010 Oct 18;11(15):2158-67. doi: 10.1002/cbic.201000398. PMID:20931591 doi:10.1002/cbic.201000398
↑ Lescic Asler I, Stefanic Z, Marsavelski A, Vianello R, Kojic-Prodic B. Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus. ACS Chem Biol. 2017 Jul 21;12(7):1928-1936. doi: 10.1021/acschembio.6b01140. Epub, 2017 Jun 14. PMID:28558229 doi:http://dx.doi.org/10.1021/acschembio.6b01140

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5mal"

@@ Line 1: / Line 1: @@
 ==Crystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution==
-<StructureSection load='5mal' size='340' side='right' caption='[[5mal]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
+<StructureSection load='5mal' size='340' side='right'caption='[[5mal]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mal]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MAL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mal]] is a 2 chain structure with sequence from [http://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 [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5mal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mal OCA], [http://pdbe.org/5mal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mal RCSB], [http://www.ebi.ac.uk/pdbsum/5mal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mal ProSAT]</span></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mal OCA], [http://pdbe.org/5mal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mal RCSB], [http://www.ebi.ac.uk/pdbsum/5mal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mal ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
 </div>
 <div class="pdbe-citations 5mal" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Lipase 3D Structures|Lipase 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces rimosus]]
 [[Category: Stefanic, Z]]

5mal

From Proteopedia

Revision as of 07:13, 19 August 2020

Crystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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