21ii: Difference between revisions
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==Crystal structure of terpeniod cyclase SpSODS in complex with GPP and Mg2+== | |||
<StructureSection load='21ii' size='340' side='right'caption='[[21ii]], [[Resolution|resolution]] 1.74Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[21ii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_plymuthica_4Rx13 Serratia plymuthica 4Rx13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=21II OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=21II 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]] 1.74Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=21ii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=21ii OCA], [https://pdbe.org/21ii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=21ii RCSB], [https://www.ebi.ac.uk/pdbsum/21ii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=21ii ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Terpenoid cyclases (TCs) utilize acyclic linear C(5n) precursors as substrates to synthesize structurally diverse terpenoids that contain mono- or polycyclic carbon skeletons. A C(16) terpenoid cyclase SpSODS from Rhizobacterium Serratia plymuthica 4Rx13 transforms the monocyclic alpha-pre-sodorifen pyrophosphate (alpha-PSPP, C(16)) to homoterpenoid sodorifen with a bicyclo[3.2.1]octadiene skeleton. Here, we report the crystal structure of SpSODS and its complexes with pyrophosphate (PPi) and substrate analogue geranyl pyrophosphate (GPP) in a closed conformation. These structures reveal the conformational transitions between the open and closed states, and demonstrate the residues involved in the substrate-interaction network. Combining the mutagenesis experiments and the docking assays, we inferred key residues that could play an essential role in each step of the previously proposed sodorifen synthesis process. Notably, a water molecule that is stabilized by Y318, N241, and R237, and invariantly seen in all resolved structures might involve in the deprotonation at the final stage of the reaction. These findings provide insight into the structure and catalytic mechanism of SpSODS and lay an important foundation for future investigations of this type of non-canonical TCs. | |||
Structure and catalytic mechanism of C(16) terpenoid cyclase SpSODS from Serratia plymuthica.,Li X, Zhang L, Zheng Y, Pan N, Zhou Z, Huang Y, Liang Q, Huang JW, Chen CC, Guo RT Int J Biol Macromol. 2026 Mar;352:151065. doi: 10.1016/j.ijbiomac.2026.151065. , Epub 2026 Feb 24. PMID:41747984<ref>PMID:41747984</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 21ii" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Chen | <references/> | ||
[[Category: Guo | __TOC__ | ||
[[Category: Huang | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Serratia plymuthica 4Rx13]] | |||
[[Category: Chen C-C]] | |||
[[Category: Guo R-T]] | |||
[[Category: Huang J-W]] | |||
[[Category: Li XQ]] | |||
[[Category: Zhang LL]] | |||
Latest revision as of 07:24, 19 March 2026
Crystal structure of terpeniod cyclase SpSODS in complex with GPP and Mg2+
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