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7enb
From Proteopedia
(Difference between revisions)
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==iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation== | ==iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation== | ||
| - | <StructureSection load='7enb' size='340' side='right'caption='[[7enb]]' scene=''> | + | <StructureSection load='7enb' size='340' side='right'caption='[[7enb]], [[Resolution|resolution]] 2.30Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ENB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ENB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7enb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspn1 Aspn1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ENB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ENB FirstGlance]. <br> |
| - | </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=7enb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7enb OCA], [https://pdbe.org/7enb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7enb RCSB], [https://www.ebi.ac.uk/pdbsum/7enb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7enb ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=H3X:methyl+(3~{a}~{R},4~{S},5~{S},5~{a}~{S},6~{S},7~{S},9~{a}~{R})-1,1,3~{a},4,5~{a},7,7-heptamethyl-3,6-bis(oxidanylidene)spiro[4,5,7,8,9,9~{a}-hexahydrobenzo[c]oxepine-6,2-4,5-dihydro-3~{H}-1-benzofuran]-5-carboxylate'>H3X</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=7enb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7enb OCA], [https://pdbe.org/7enb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7enb RCSB], [https://www.ebi.ac.uk/pdbsum/7enb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7enb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Endoperoxide-containing natural products are a group of compounds with structurally unique cyclized peroxide moieties. Although numerous endoperoxide-containing compounds have been isolated, the biosynthesis of the endoperoxides remains unclear. NvfI from Aspergillus novofumigatus IBT 16806 is an endoperoxidase that catalyzes the formation of fumigatonoid A in the biosynthesis of novofumigatonin. Here, we describe our structural and functional analyses of NvfI. The structural elucidation and mutagenesis studies indicate that NvfI does not utilize a tyrosyl radical in the reaction, in contrast to other characterized endoperoxidases. Further, the crystallographic analysis reveals significant conformational changes of two loops upon substrate binding, which suggests a dynamic movement of active site during the catalytic cycle. As a result, NvfI installs three oxygen atoms onto a substrate in a single enzyme turnover. Based on these results, we propose a mechanism for the NvfI-catalyzed, unique endoperoxide formation reaction to produce fumigatonoid A. | ||
| + | |||
| + | Molecular insights into the endoperoxide formation by Fe(II)/alpha-KG-dependent oxygenase NvfI.,Mori T, Zhai R, Ushimaru R, Matsuda Y, Abe I Nat Commun. 2021 Jul 20;12(1):4417. doi: 10.1038/s41467-021-24685-6. PMID:34285212<ref>PMID:34285212</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7enb" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Aspn1]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Abe I]] | + | [[Category: Abe, I]] |
| - | [[Category: Mori T]] | + | [[Category: Mori, T]] |
| + | [[Category: Endoperoxidase]] | ||
| + | [[Category: Novofumigatonin]] | ||
| + | [[Category: Oxidoreductase]] | ||
Revision as of 07:08, 27 January 2022
iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation
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