9buo: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 9buo is ~~ON HOLD until Paper~~ Publication

==CryoEM structure of DPOR in the presence of ADP-AlF3==

== Structural highlights ==

<table><tr><td colspan='2'>[[9buo]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9BUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9BUO FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.68Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=9buo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9buo OCA], [https://pdbe.org/9buo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9buo RCSB], [https://www.ebi.ac.uk/pdbsum/9buo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9buo ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/BCHL_CERS4 BCHL_CERS4] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP.[HAMAP-Rule:MF_00355]<ref>PMID:19006326</ref>

== Publication Abstract from PubMed ==

Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an alpha(2)beta(2) heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.

~~Authors~~:

Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR.,Kashyap R, Walsh N, Deveryshetty J, Tokmina-Lukaszewska M, Zhao K, Gan YJ, Hoffman BM, Sarangi R, Bothner B, Bennett B, Antony E Nat Commun. 2025 Apr 24;16(1):3866. doi: 10.1038/s41467-025-59158-7. PMID:40274796<ref>PMID:40274796</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Cereibacter sphaeroides]]

[[Category: Large Structures]]

[[Category: Antony E]]

[[Category: Kashyap R]]

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-'''Unreleased structure'''
-The entry 9buo is ON HOLD  until Paper Publication
+==CryoEM structure of DPOR in the presence of ADP-AlF3==
+<StructureSection load='9buo' size='340' side='right'caption='[[9buo]], [[Resolution|resolution]] 3.68&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9buo]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9BUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9BUO FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.68&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=9buo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9buo OCA], [https://pdbe.org/9buo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9buo RCSB], [https://www.ebi.ac.uk/pdbsum/9buo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9buo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BCHL_CERS4 BCHL_CERS4] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP.[HAMAP-Rule:MF_00355]<ref>PMID:19006326</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an alpha(2)beta(2) heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.
-Authors:
+Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR.,Kashyap R, Walsh N, Deveryshetty J, Tokmina-Lukaszewska M, Zhao K, Gan YJ, Hoffman BM, Sarangi R, Bothner B, Bennett B, Antony E Nat Commun. 2025 Apr 24;16(1):3866. doi: 10.1038/s41467-025-59158-7. PMID:40274796<ref>PMID:40274796</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9buo" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Cereibacter sphaeroides]]
+[[Category: Large Structures]]
+[[Category: Antony E]]
+[[Category: Kashyap R]]