9m7d: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9m7d is ~~ON HOLD until Paper~~ Publication

==Crystal structure of AsDMS D333N mutant==

== Structural highlights ==

<table><tr><td colspan='2'>[[9m7d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquimarina_spongiae Aquimarina spongiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9M7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9M7D 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]] 2.3000002Å</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=SO4:SULFATE+ION'>SO4</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=9m7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9m7d OCA], [https://pdbe.org/9m7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9m7d RCSB], [https://www.ebi.ac.uk/pdbsum/9m7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9m7d ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A1M6CXF0_9FLAO A0A1M6CXF0_9FLAO]

== Publication Abstract from PubMed ==

Terpene cyclases (TCs), consisting of various combinations of alpha, beta, and gamma domains, have been extensively studied. Recently, non-canonical enzymes comprising a TCbeta domain and a haloacid dehalogenase (HAD)-like domain (referred to as HAD-TCbeta) have been discovered. However, their overall structure remains unclear. In this study, we determined the co-crystal structures of drimenol synthase from Aquimarina spongiae (AsDMS), which catalyzes the conversion of farnesyl pyrophosphate (1) into drimenol (2). Crystallographic analyses of the enzyme bound to substrates 1 and drimenyl monophosphate (3) demonstrated that the TCbeta domain catalyzes a class II cyclization reaction initiated by protonation, whereas the HAD domain catalyzes a phosphatase-like dephosphorylation reaction dependent on a divalent metal. Crystallographic and gel filtration analyses revealed that AsDMS adopts a dimeric assembly. This dimerization positioned the TCbeta and HAD domains to facilitate efficient substrate transfer via electrostatic substrate channeling. Furthermore, to investigate the structure-function relationship of the AsDMS TCbeta domain, we used AlphaFold2 to model the structure of the fungal albicanol (4) synthase. Comparative analysis of active-site residues between AsDMS and fungal 4-synthase enabled rational protein engineering, converting AsDMS activity from 2-synthase to 4-synthase. This study provides insights into the biosynthesis of valuable drimane-type sesquiterpenes via targeted mutagenesis.

~~Authors~~:

Structural insights into a bacterial terpene cyclase fused with haloacid Dehalogenase-like phosphatase.,Fujiyama K, Takagi H, Vo NNQ, Morita N, Nogawa T, Takahashi S Chem Sci. 2025 Jul 28;16(34):15310-15319. doi: 10.1039/d5sc04719f. eCollection , 2025 Aug 27. PMID:40852458<ref>PMID:40852458</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Aquimarina spongiae]]

[[Category: Large Structures]]

[[Category: Fujiyama K]]

[[Category: Takahashi S]]

[[Category: Vo NNQ]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9m7d is ON HOLD  until Paper Publication
+==Crystal structure of AsDMS D333N mutant==
+<StructureSection load='9m7d' size='340' side='right'caption='[[9m7d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9m7d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquimarina_spongiae Aquimarina spongiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9M7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9M7D 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]] 2.3000002&#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=SO4:SULFATE+ION'>SO4</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=9m7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9m7d OCA], [https://pdbe.org/9m7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9m7d RCSB], [https://www.ebi.ac.uk/pdbsum/9m7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9m7d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A1M6CXF0_9FLAO A0A1M6CXF0_9FLAO]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Terpene cyclases (TCs), consisting of various combinations of alpha, beta, and gamma domains, have been extensively studied. Recently, non-canonical enzymes comprising a TCbeta domain and a haloacid dehalogenase (HAD)-like domain (referred to as HAD-TCbeta) have been discovered. However, their overall structure remains unclear. In this study, we determined the co-crystal structures of drimenol synthase from Aquimarina spongiae (AsDMS), which catalyzes the conversion of farnesyl pyrophosphate (1) into drimenol (2). Crystallographic analyses of the enzyme bound to substrates 1 and drimenyl monophosphate (3) demonstrated that the TCbeta domain catalyzes a class II cyclization reaction initiated by protonation, whereas the HAD domain catalyzes a phosphatase-like dephosphorylation reaction dependent on a divalent metal. Crystallographic and gel filtration analyses revealed that AsDMS adopts a dimeric assembly. This dimerization positioned the TCbeta and HAD domains to facilitate efficient substrate transfer via electrostatic substrate channeling. Furthermore, to investigate the structure-function relationship of the AsDMS TCbeta domain, we used AlphaFold2 to model the structure of the fungal albicanol (4) synthase. Comparative analysis of active-site residues between AsDMS and fungal 4-synthase enabled rational protein engineering, converting AsDMS activity from 2-synthase to 4-synthase. This study provides insights into the biosynthesis of valuable drimane-type sesquiterpenes via targeted mutagenesis.
-Authors:
+Structural insights into a bacterial terpene cyclase fused with haloacid Dehalogenase-like phosphatase.,Fujiyama K, Takagi H, Vo NNQ, Morita N, Nogawa T, Takahashi S Chem Sci. 2025 Jul 28;16(34):15310-15319. doi: 10.1039/d5sc04719f. eCollection , 2025 Aug 27. PMID:40852458<ref>PMID:40852458</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9m7d" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Aquimarina spongiae]]
+[[Category: Large Structures]]
+[[Category: Fujiyama K]]
+[[Category: Takahashi S]]
+[[Category: Vo NNQ]]