8yhm
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | The | + | ==The structure of SdnG covalently binding with the cope rearrangement product== |
| + | <StructureSection load='8yhm' size='340' side='right'caption='[[8yhm]], [[Resolution|resolution]] 1.72Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[8yhm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sordaria_araneosa Sordaria araneosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8YHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YHM 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]] 1.72Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1LZG:(3~{a}~{R},5~{R},5~{a}~{R},8~{R},8~{a}~{R},9~{a}~{R})-5-methanoyl-8,9~{a}-dimethyl-2-propan-2-yl-3,3~{a},4,5,5~{a},6,7,8,8~{a},9-decahydrocyclopenta[g]azulene-1-carboxylic+acid'>A1LZG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=8yhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8yhm OCA], [https://pdbe.org/8yhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8yhm RCSB], [https://www.ebi.ac.uk/pdbsum/8yhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8yhm ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/SDNG_SORAA SDNG_SORAA] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Iminium-catalyzed cycloaddition is one of the most prominent examples of organocatalysis, yet a biological counterpart has not been reported despite the wide-spread occurrence of iminium adducts in enzymes. Here, we present biochemical, structural, and computational evidence for iminium catalysis by the natural Diels-Alderase SdnG that catalyzes norbornene formation in sordarin biosynthesis. A Schiff base adduct between the epsilon-nitrogen of active site K127 and the aldehyde group of the enal dienophile was revealed by structural analysis and captured under catalytic conditions via borohydride reduction. This Schiff base adduct positions the substrate into near-attack conformation and decreases the transition state barrier of Diels-Alder cyclization by 8.3 kcal/mol via dienophile activation. A hydrogen bond network consisting of a catalytic triad is proposed to facilitate proton transfer required for iminium formation. This work establishes a new mode of catalysis for Diels-Alderases and points the way to the design of novel iminium based (bio)catalysts. | ||
| - | + | Iminium Catalysis in Natural Diels-Alderase.,Sun Z, Zang X, Zhou Q, Ohashi M, Houk KN, Zhou J, Tang Y Nat Catal. 2025 Mar;8(3):218-228. doi: 10.1038/s41929-025-01294-w. Epub 2025 Feb , 6. PMID:40881614<ref>PMID:40881614</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 8yhm" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Sordaria araneosa]] | ||
| + | [[Category: Yi T]] | ||
| + | [[Category: Zang X]] | ||
| + | [[Category: Zhou J]] | ||
Current revision
The structure of SdnG covalently binding with the cope rearrangement product
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