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6oh7

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Current revision (14:51, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6oh7' size='340' side='right'caption='[[6oh7]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
<StructureSection load='6oh7' size='340' side='right'caption='[[6oh7]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6oh7]] is a 1 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=5a0k 5a0k]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OH7 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6oh7]] is a 1 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=5a0k 5a0k]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OH7 FirstGlance]. <br>
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</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</td></tr>
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<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>
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<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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<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=6oh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oh7 OCA], [http://pdbe.org/6oh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oh7 RCSB], [http://www.ebi.ac.uk/pdbsum/6oh7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oh7 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6oh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oh7 OCA], [https://pdbe.org/6oh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oh7 RCSB], [https://www.ebi.ac.uk/pdbsum/6oh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oh7 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A158RFK9_STRSQ A0A158RFK9_STRSQ]
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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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6oh7" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Chainia sp]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Centeno-Leija, S]]
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[[Category: Streptomyces sp]]
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[[Category: Serrano-Posada, H]]
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[[Category: Centeno-Leija S]]
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[[Category: Biformene]]
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[[Category: Serrano-Posada H]]
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[[Category: Bioactive natural product]]
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[[Category: Diterpene synthase]]
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[[Category: Labdatriene]]
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[[Category: Lyase]]
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Current revision

Crystal structure of (E)-biformene synthase LrdC from Streptomyces sp. strain K155 in complex with Mg

PDB ID 6oh7

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