7de2: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='7de2' size='340' side='right'caption='[[7de2]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='7de2' size='340' side='right'caption='[[7de2]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7de2]] 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=7DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DE2 FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DE2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <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></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <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></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=7de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7de2 OCA], [https://pdbe.org/7de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7de2 RCSB], [https://www.ebi.ac.uk/pdbsum/7de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7de2 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=7de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7de2 OCA], [https://pdbe.org/7de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7de2 RCSB], [https://www.ebi.ac.uk/pdbsum/7de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7de2 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7de2" 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: Zhai, R]]
[[Category: Zhai R]]
[[Category: Endoperoxidase]]
[[Category: Iron and alpha-ketoglutarate-dependent enzyme]]
[[Category: Novofumigatonin]]
[[Category: Oxidoreductase]]
Retrieved from "https://proteopedia.org/7de2"