7e5v

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Current revision (07:11, 3 April 2024) (edit) (undo)
 
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<StructureSection load='7e5v' size='340' side='right'caption='[[7e5v]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
<StructureSection load='7e5v' size='340' side='right'caption='[[7e5v]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7e5v]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrsx Pyrsx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E5V FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7e5v]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrenochaetopsis_sp. Pyrenochaetopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E5V FirstGlance]. <br>
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</td></tr><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=HZC:[(1S,2S,5R)-5-methyl-2-propan-2-yl-cyclohexyl]methanamine'>HZC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.61&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phm7 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1756125 PYRSX])</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=HZC:[(1S,2S,5R)-5-methyl-2-propan-2-yl-cyclohexyl]methanamine'>HZC</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=7e5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e5v OCA], [https://pdbe.org/7e5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e5v RCSB], [https://www.ebi.ac.uk/pdbsum/7e5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e5v 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=7e5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e5v OCA], [https://pdbe.org/7e5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e5v RCSB], [https://www.ebi.ac.uk/pdbsum/7e5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e5v 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/PHM7_PYRSX PHM7_PYRSX] Diels-Alderase; part of the gene cluster that mediates the biosynthesis of the trans-fused decalin-containing tetramic acid phomasetin, the stereochemical opposite of the HIV-1 integrase inhibitor equisetin (PubMed:29972614). The PKS module of phm1 together with the enoylreductase phm4 catalyze the formation of the polyketide unit which is then conjugated to L-serine by the condensation domain of the phm1 NRPS module (PubMed:29972614). Activity of the Dieckmann cyclase domain (RED) of phm1 results in release of the Dieckmann product intermediate (PubMed:29972614). The Diels-Alderase phm7 then uses the Dieckmann product of phm1 as substrate and catalyzes the Diels-Alder cycloaddition to form the decalin ring of N-desmethylphomasetin (PubMed:29972614, PubMed:34121297). N-desmethylphomasetin is further methylated to phomasetin by the methyltransferase phm5 (PubMed:29972614).<ref>PMID:29972614</ref> <ref>PMID:34121297</ref>
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Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.
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Molecular basis for two stereoselective Diels-Alderases that produce decalin skeletons.,Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S Angew Chem Int Ed Engl. 2021 Jun 13. doi: 10.1002/anie.202106186. PMID:34121297<ref>PMID:34121297</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 7e5v" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Pyrsx]]
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[[Category: Pyrenochaetopsis sp]]
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[[Category: Fujiyama, K]]
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[[Category: Fujiyama K]]
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[[Category: Hino, T]]
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[[Category: Hino T]]
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[[Category: Kato, N]]
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[[Category: Kato N]]
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[[Category: Kinugasa, K]]
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[[Category: Kinugasa K]]
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[[Category: Nagano, S]]
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[[Category: Nagano S]]
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[[Category: Takahashi, S]]
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[[Category: Takahashi S]]
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[[Category: Biosynthetic protein]]
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[[Category: Cyclase]]
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[[Category: Diels alder]]
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[[Category: Diels-alderase]]
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Current revision

Crystal structure of Phm7 in complex with inhibitor

PDB ID 7e5v

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