4okm: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4okm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pristinaespiralis_ATCC_25486 Streptomyces pristinaespiralis ATCC 25486]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OKM FirstGlance]. <br>
<table><tr><td colspan='2'>[[4okm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_pristinaespiralis_ATCC_25486 Streptomyces pristinaespiralis ATCC 25486]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OKM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=4okm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4okm OCA], [https://pdbe.org/4okm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4okm RCSB], [https://www.ebi.ac.uk/pdbsum/4okm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4okm 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=4okm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4okm OCA], [https://pdbe.org/4okm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4okm RCSB], [https://www.ebi.ac.uk/pdbsum/4okm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4okm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/SEDS_STRE2 SEDS_STRE2] Catalyzes the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpene selina-4(15),7(11)-diene via a 1,10-cyclization, which requires the abstraction of the pyrophosphate from FPP leading to a (E,E)-germacradienyl cation (PubMed:23307484, PubMed:24890698). The only accepted substrate is (2E,6E)-farnesyl diphosphate (FPP) (PubMed:23307484, PubMed:24890698).<ref>PMID:23307484</ref> <ref>PMID:24890698</ref>  
[https://www.uniprot.org/uniprot/SEDS_STRE2 SEDS_STRE2] Catalyzes the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpene selina-4(15),7(11)-diene via a 1,10-cyclization, which requires the abstraction of the pyrophosphate from FPP leading to a (E,E)-germacradienyl cation (PubMed:23307484, PubMed:24890698). The only accepted substrate is (2E,6E)-farnesyl diphosphate (FPP) (PubMed:23307484, PubMed:24890698).<ref>PMID:23307484</ref> <ref>PMID:24890698</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We present crystallographic and functional data of selina-4(15),7(11)-diene synthase (SdS) from Streptomyces pristinaespiralis in its open and closed (ligand-bound) conformation. We could identify an induced-fit mechanism by elucidating a rearrangement of the G1/2 helix-break motif upon substrate binding. This rearrangement highlights a novel effector triad comprising the pyrophosphate sensor Arg178, the linker Asp181, and the effector Gly182-O. This structural motif is strictly conserved in class I terpene cyclases from bacteria, fungi, and plants, including epi-isozizaene synthase (3KB9), aristolochene synthase (4KUX), bornyl diphosphate synthase (1N20), limonene synthase (2ONG), 5-epi-aristolochene synthase (5EAT), and taxa-4(5),11(12)-diene synthase (3P5R). An elaborate structure-based mutagenesis in combination with analysis of the distinct product spectra confirmed the mechanistic models of carbocation formation and stabilization in SdS.
Induced-Fit Mechanism in Class I Terpene Cyclases.,Baer P, Rabe P, Fischer K, Citron CA, Klapschinski TA, Groll M, Dickschat JS Angew Chem Int Ed Engl. 2014 May 30. doi: 10.1002/anie.201403648. PMID:24890698<ref>PMID:24890698</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4okm" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 12:40, 1 March 2024

Selinadiene Synthase apo and in complex with diphosphate

4okm, resolution 2.10Å

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