4rzm: Difference between revisions

Latest revision as of 17:59, 20 September 2023

Crystal structure of the Lsd19-lasalocid A complex

Structural highlights

4rzm is a 2 chain structure with sequence from Streptomyces lasalocidi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.33Å
Ligands:	CL, FMT, GOL, LSD, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LSD19_STRLS Epoxide hydrolase responsible for the double epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A, a polyether antibiotic. In vitro, accepts various substrate analogs differing in the left segment of lasalocid and epoxide stereochemistry to afford products with excellent regioselectivity.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product. We report the crystal structure of Lsd19 in complex with lasalocid A. The structure unambiguously shows that the C-terminal domain of Lsd19 catalyzes the intriguing anti-Baldwin cyclization. We propose a general mechanism for epoxide selection by ionophore polyether epoxide hydrolases.

Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.,Wong FT, Hotta K, Chen X, Fang M, Watanabe K, Kim CY J Am Chem Soc. 2015 Jan 14;137(1):86-9. doi: 10.1021/ja511374k. Epub 2014 Dec 31. PMID:25535803^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shichijo Y, Migita A, Oguri H, Watanabe M, Tokiwano T, Watanabe K, Oikawa H. Epoxide hydrolase Lsd19 for polyether formation in the biosynthesis of lasalocid A: direct experimental evidence on polyene-polyepoxide hypothesis in polyether biosynthesis. J Am Chem Soc. 2008 Sep 17;130(37):12230-1. doi: 10.1021/ja8040543. Epub 2008 Aug, 19. PMID:18710235 doi:https://dx.doi.org/10.1021/ja8040543
↑ Smith L, Hong H, Spencer JB, Leadlay PF. Analysis of specific mutants in the lasalocid gene cluster: evidence for enzymatic catalysis of a disfavoured polyether ring closure. Chembiochem. 2008 Dec 15;9(18):2967-75. doi: 10.1002/cbic.200800585. PMID:19025863 doi:https://dx.doi.org/10.1002/cbic.200800585
↑ Matsuura Y, Shichijo Y, Minami A, Migita A, Oguri H, Watanabe M, Tokiwano T, Watanabe K, Oikawa H. Intriguing substrate tolerance of epoxide hydrolase Lsd19 involved in biosynthesis of the ionophore antibiotic lasalocid A. Org Lett. 2010 May 21;12(10):2226-9. doi: 10.1021/ol100541e. PMID:20394359 doi:https://dx.doi.org/10.1021/ol100541e
↑ Minami A, Migita A, Inada D, Hotta K, Watanabe K, Oguri H, Oikawa H. Enzymatic epoxide-opening cascades catalyzed by a pair of epoxide hydrolases in the ionophore polyether biosynthesis. Org Lett. 2011 Apr 1;13(7):1638-41. doi: 10.1021/ol200100e. Epub 2011 Mar 4. PMID:21375229 doi:https://dx.doi.org/10.1021/ol200100e
↑ Wong FT, Hotta K, Chen X, Fang M, Watanabe K, Kim CY. Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis. J Am Chem Soc. 2015 Jan 14;137(1):86-9. doi: 10.1021/ja511374k. Epub 2014 Dec 31. PMID:25535803 doi:https://dx.doi.org/10.1021/ja511374k

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Shichijo Y, Migita A, Oguri H, Watanabe M, Tokiwano T, Watanabe K, Oikawa H. Epoxide hydrolase Lsd19 for polyether formation in the biosynthesis of lasalocid A: direct experimental evidence on polyene-polyepoxide hypothesis in polyether biosynthesis. J Am Chem Soc. 2008 Sep 17;130(37):12230-1. doi: 10.1021/ja8040543. Epub 2008 Aug, 19. PMID:18710235 doi:https://dx.doi.org/10.1021/ja8040543

[2] Smith L, Hong H, Spencer JB, Leadlay PF. Analysis of specific mutants in the lasalocid gene cluster: evidence for enzymatic catalysis of a disfavoured polyether ring closure. Chembiochem. 2008 Dec 15;9(18):2967-75. doi: 10.1002/cbic.200800585. PMID:19025863 doi:https://dx.doi.org/10.1002/cbic.200800585

[3] Matsuura Y, Shichijo Y, Minami A, Migita A, Oguri H, Watanabe M, Tokiwano T, Watanabe K, Oikawa H. Intriguing substrate tolerance of epoxide hydrolase Lsd19 involved in biosynthesis of the ionophore antibiotic lasalocid A. Org Lett. 2010 May 21;12(10):2226-9. doi: 10.1021/ol100541e. PMID:20394359 doi:https://dx.doi.org/10.1021/ol100541e

[4] Minami A, Migita A, Inada D, Hotta K, Watanabe K, Oguri H, Oikawa H. Enzymatic epoxide-opening cascades catalyzed by a pair of epoxide hydrolases in the ionophore polyether biosynthesis. Org Lett. 2011 Apr 1;13(7):1638-41. doi: 10.1021/ol200100e. Epub 2011 Mar 4. PMID:21375229 doi:https://dx.doi.org/10.1021/ol200100e

[5] Wong FT, Hotta K, Chen X, Fang M, Watanabe K, Kim CY. Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis. J Am Chem Soc. 2015 Jan 14;137(1):86-9. doi: 10.1021/ja511374k. Epub 2014 Dec 31. PMID:25535803 doi:https://dx.doi.org/10.1021/ja511374k

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4rzm is ON HOLD
+==Crystal structure of the Lsd19-lasalocid A complex==
+<StructureSection load='4rzm' size='340' side='right'caption='[[4rzm]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4rzm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lasalocidi Streptomyces lasalocidi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.33&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSD:LASALOCID+A'>LSD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=4rzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzm OCA], [https://pdbe.org/4rzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzm RCSB], [https://www.ebi.ac.uk/pdbsum/4rzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LSD19_STRLS LSD19_STRLS] Epoxide hydrolase responsible for the double epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A, a polyether antibiotic. In vitro, accepts various substrate analogs differing in the left segment of lasalocid and epoxide stereochemistry to afford products with excellent regioselectivity.<ref>PMID:18710235</ref> <ref>PMID:19025863</ref> <ref>PMID:20394359</ref> <ref>PMID:21375229</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product. We report the crystal structure of Lsd19 in complex with lasalocid A. The structure unambiguously shows that the C-terminal domain of Lsd19 catalyzes the intriguing anti-Baldwin cyclization. We propose a general mechanism for epoxide selection by ionophore polyether epoxide hydrolases.
-Authors: Mathews, I.I., Hotta, K., Chen, X., Kim, C.-Y.
+Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.,Wong FT, Hotta K, Chen X, Fang M, Watanabe K, Kim CY J Am Chem Soc. 2015 Jan 14;137(1):86-9. doi: 10.1021/ja511374k. Epub 2014 Dec 31. PMID:25535803<ref>PMID:25535803</ref>
-Description: Crystal structure of the Lsd19-lasalocid A complex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Hotta, K]]
+<div class="pdbe-citations 4rzm" style="background-color:#fffaf0;"></div>
-[[Category: Mathews, I.I]]
-[[Category: Chen, X]]
+==See Also==
-[[Category: Kim, C.-Y]]
+*[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Streptomyces lasalocidi]]
+[[Category: Chen X]]
+[[Category: Hotta K]]
+[[Category: Kim C-Y]]
+[[Category: Mathews II]]

4rzm: Difference between revisions

Latest revision as of 17:59, 20 September 2023

Crystal structure of the Lsd19-lasalocid A complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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