7e38: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='7e38' size='340' side='right'caption='[[7e38]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
<StructureSection load='7e38' size='340' side='right'caption='[[7e38]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7e38]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinopodophyllum_hexandrum Sinopodophyllum hexandrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E38 FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E38 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]] 2.05&#8491;</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]] 2.05&#8491;</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=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=YTC:(3~{S},4~{S})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one'>YTC</scene>, <scene name='pdbligand=YTN:(3~{R},4~{R})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one'>YTN</scene></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=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=YTC:(3~{S},4~{S})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one'>YTC</scene>, <scene name='pdbligand=YTN:(3~{R},4~{R})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one'>YTN</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=7e38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e38 OCA], [https://pdbe.org/7e38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e38 RCSB], [https://www.ebi.ac.uk/pdbsum/7e38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e38 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=7e38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e38 OCA], [https://pdbe.org/7e38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e38 RCSB], [https://www.ebi.ac.uk/pdbsum/7e38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e38 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/2ODD_SINHE 2ODD_SINHE]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (+/-)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS's catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel-Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs.
Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase.,Tang H, Wu MH, Lin HY, Han MR, Tu YH, Yang ZJ, Chien TC, Chan NL, Chang WC Proc Natl Acad Sci U S A. 2022 Jan 4;119(1). pii: 2113770119. doi:, 10.1073/pnas.2113770119. PMID:34969844<ref>PMID:34969844</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7e38" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sinopodophyllum hexandrum]]
[[Category: Chan N-L]]
[[Category: Chan N-L]]
[[Category: Chang W-c]]
[[Category: Chang W-c]]
[[Category: Chien T-C]]
[[Category: Chien T-C]]
[[Category: Wu M-H]]
[[Category: Wu M-H]]
Retrieved from "https://proteopedia.org/7e38"