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| | <StructureSection load='6oh8' size='340' side='right'caption='[[6oh8]], [[Resolution|resolution]] 2.17Å' scene=''> | | <StructureSection load='6oh8' size='340' side='right'caption='[[6oh8]], [[Resolution|resolution]] 2.17Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6oh8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chainia_sp. Chainia sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5a0i 5a0i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OH8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6oh8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5a0i 5a0i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OH8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.17Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(12E)-labda-8(17),12,14-triene_synthase (12E)-labda-8(17),12,14-triene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.193 4.2.3.193] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=6oh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oh8 OCA], [http://pdbe.org/6oh8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oh8 RCSB], [http://www.ebi.ac.uk/pdbsum/6oh8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oh8 ProSAT]</span></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=6oh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oh8 OCA], [https://pdbe.org/6oh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oh8 RCSB], [https://www.ebi.ac.uk/pdbsum/6oh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oh8 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A0A158RFK9_STRSQ A0A158RFK9_STRSQ] |
| - | The labdane-related diterpenoids (LRDs) are a large group of natural products with a broad range of biological activities. They are synthesized through two consecutive reactions catalyzed by class II and I diterpene synthases (DTSs). The structural complexity of LRDs mainly depends on the catalytic activity of class I DTSs, which catalyze the formation of bicyclic to pentacyclic LRDs, using as a substrate the catalytic product of class II DTSs. To date, the structural and mechanistic details for the biosynthesis of bicyclic LRDs skeletons catalyzed by class I DTSs remain unclear. This work presents the first X-ray crystal structure of an (E)-biformene synthase, LrdC, from the soil bacterium Streptomyces sp. strain K155. LrdC was identified as a part of an LRD cluster of five genes and was found to be a class I DTS that catalyzes the Mg(2+)-dependent synthesis of bicyclic LRD (E)-biformene by the dephosphorylation and rearrangement of normal copalyl pyrophosphate (CPP). Structural analysis of LrdC coupled with docking studies suggests that Phe189 prevents cyclization beyond the bicyclic LRD product through a strong stabilization of the allylic carbocation intermediate, while Tyr317 functions as a general base catalyst to deprotonate the CPP substrate. Structural comparisons of LrdC with homology models of bacterial bicyclic LRD-forming enzymes (CldD, RmnD and SclSS), as well as with the crystallographic structure of bacterial tetracyclic LRD ent-kaurene synthase (BjKS), provide further structural insights into the biosynthesis of bacterial LRD natural products.
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| - | | + | |
| - | The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids.,Centeno-Leija S, Tapia-Cabrera S, Guzman-Trampe S, Esquivel B, Esturau-Escofet N, Tierrafria VH, Rodriguez-Sanoja R, Zarate-Romero A, Stojanoff V, Rudino-Pinera E, Sanchez S, Serrano-Posada H J Struct Biol. 2019 Apr 11. pii: S1047-8477(19)30076-0. doi:, 10.1016/j.jsb.2019.04.010. PMID:30981884<ref>PMID:30981884</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6oh8" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chainia sp]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Centeno-Leija, S]] | + | [[Category: Streptomyces sp]] |
| - | [[Category: Serrano-Posada, H]] | + | [[Category: Centeno-Leija S]] |
| - | [[Category: Biformene]]
| + | [[Category: Serrano-Posada H]] |
| - | [[Category: Bioactive natural product]]
| + | |
| - | [[Category: Diterpene synthase]]
| + | |
| - | [[Category: Labdatriene]]
| + | |
| - | [[Category: Lyase]]
| + | |
