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==Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphate== | ==Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphate== | ||
<StructureSection load='5hc8' size='340' side='right' caption='[[5hc8]], [[Resolution|resolution]] 1.87Å' scene=''> | <StructureSection load='5hc8' size='340' side='right'caption='[[5hc8]], [[Resolution|resolution]] 1.87Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5hc8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HC8 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5hc8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lavandula_lanata Lavandula lanata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HC8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=61G:2-METHYLBUTA-1,3-DIENE'>61G</scene>, <scene name='pdbligand=ISY:3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC+ACID'>ISY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIS:TRIHYDROGEN+THIODIPHOSPHATE'>PIS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=61G:2-METHYLBUTA-1,3-DIENE'>61G</scene>, <scene name='pdbligand=ISY:3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC+ACID'>ISY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIS:TRIHYDROGEN+THIODIPHOSPHATE'>PIS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5hc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hc8 OCA], [https://pdbe.org/5hc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hc8 RCSB], [https://www.ebi.ac.uk/pdbsum/5hc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hc8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A140UHQ1_LAVLA A0A140UHQ1_LAVLA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a precursor to the fragrance lavandulol. The structure is similar to that of the bacterial cis-prenyl synthase, undecaprenyl diphosphate synthase (UPPS), and contains an allylic site (S1) in which DMAPP ionizes and a second site (S2) which houses the DMAPP nucleophile. Both S-thiolo-dimethylallyl diphosphate and S-thiolo-isopentenyl diphosphate bind intact to S2, but are cleaved to (thio)diphosphate, in S1. His78 (Asn in UPPS) is essential for catalysis and is proposed to facilitate diphosphate release in S1, while the P1 phosphate in S2 abstracts a proton from the lavandulyl carbocation to form the LPP product. The results are of interest since they provide the first structure and structure-based mechanism of this unusual prenyl synthase. | |||
Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase.,Liu M, Chen CC, Chen L, Xiao X, Zheng Y, Huang JW, Liu W, Ko TP, Cheng YS, Feng X, Oldfield E, Guo RT, Ma Y Angew Chem Int Ed Engl. 2016 Apr 4;55(15):4721-4. doi: 10.1002/anie.201600656., Epub 2016 Feb 29. PMID:26922900<ref>PMID:26922900</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5hc8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Lavandula lanata]] | ||
[[Category: | [[Category: Chen CC]] | ||
[[Category: | [[Category: Gao J]] | ||
[[Category: | [[Category: Guo RT]] | ||
[[Category: | [[Category: Liu MX]] | ||
[[Category: | [[Category: Liu WD]] | ||
[[Category: | [[Category: Zheng YY]] | ||
Latest revision as of 10:30, 9 August 2023
Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphateCrystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphate
Structural highlights
FunctionPublication Abstract from PubMedWe report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a precursor to the fragrance lavandulol. The structure is similar to that of the bacterial cis-prenyl synthase, undecaprenyl diphosphate synthase (UPPS), and contains an allylic site (S1) in which DMAPP ionizes and a second site (S2) which houses the DMAPP nucleophile. Both S-thiolo-dimethylallyl diphosphate and S-thiolo-isopentenyl diphosphate bind intact to S2, but are cleaved to (thio)diphosphate, in S1. His78 (Asn in UPPS) is essential for catalysis and is proposed to facilitate diphosphate release in S1, while the P1 phosphate in S2 abstracts a proton from the lavandulyl carbocation to form the LPP product. The results are of interest since they provide the first structure and structure-based mechanism of this unusual prenyl synthase. Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase.,Liu M, Chen CC, Chen L, Xiao X, Zheng Y, Huang JW, Liu W, Ko TP, Cheng YS, Feng X, Oldfield E, Guo RT, Ma Y Angew Chem Int Ed Engl. 2016 Apr 4;55(15):4721-4. doi: 10.1002/anie.201600656., Epub 2016 Feb 29. PMID:26922900[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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