9qu8: Difference between revisions

Line 1:

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

~~The entry~~ 9qu8 is ~~ON HOLD until Paper~~ Publication

==apPol-DNA-nucleotide complex (ternary2)==

== Structural highlights ==

<table><tr><td colspan='2'>[[9qu8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule] and [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QU8 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]] 4.2Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=9qu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qu8 OCA], [https://pdbe.org/9qu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qu8 RCSB], [https://www.ebi.ac.uk/pdbsum/9qu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qu8 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A024WKD7_PLAFA A0A024WKD7_PLAFA]

== Publication Abstract from PubMed ==

Plasmodium falciparum is a eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and, like most members of this phylum, contains a non-photosynthetic plastid called the apicoplast. The apicoplast has its own genome, replicated by a dedicated replisome. Unlike other cellular replisomes, the apicoplast replisome uses a single DNA polymerase (apPol). This suggests that apPol can multitask and catalyse both replicative and lesion bypass synthesis. Replicative synthesis relies on a restrictive active site for high accuracy while lesion bypass typically requires an open active site. This raises the question: how does apPol combine the structural features of multiple DNA polymerases in a single protein? Using single-particle electron cryomicroscopy (cryoEM), we have solved the structures of apPol bound to its undamaged DNA and nucleotide substrates in five pre-chemistry conformational states. We found that apPol can accommodate a nascent base pair with the fingers in an open configuration, which might facilitate the lesion bypass activity. In the fingers-open state, we identified a nascent base pair checkpoint that preferentially selects Watson-Crick base pairs, an essential requirement for replicative synthesis. Taken together, these structural features might explain how apPol balances replicative and lesion bypass synthesis.

~~Authors: Lahiri, I~~., Kumari, A.

Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.,Kumari A, Enache T, Craggs TD, Pata JD, Lahiri I Nucleic Acids Res. 2025 Oct 14;53(19):gkaf1005. doi: 10.1093/nar/gkaf1005. PMID:41099714<ref>PMID:41099714</ref>

~~Description~~: ~~apPol-~~DNA~~-nucleotide complex (ternary2)~~

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

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

</div>

[[Category: ~~Lahiri, I~~]]

[[Category: Kumari, A]]

== References ==

__TOC__

</StructureSection>

[[Category: DNA molecule]]

[[Category: Large Structures]]

[[Category: Plasmodium falciparum]]

[[Category: Kumari A]]

[[Category: Lahiri I]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9qu8 is ON HOLD  until Paper Publication
+==apPol-DNA-nucleotide complex (ternary2)==
+<StructureSection load='9qu8' size='340' side='right'caption='[[9qu8]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9qu8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule] and [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QU8 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]] 4.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=9qu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qu8 OCA], [https://pdbe.org/9qu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qu8 RCSB], [https://www.ebi.ac.uk/pdbsum/9qu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qu8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A024WKD7_PLAFA A0A024WKD7_PLAFA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Plasmodium falciparum is a eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and, like most members of this phylum, contains a non-photosynthetic plastid called the apicoplast. The apicoplast has its own genome, replicated by a dedicated replisome. Unlike other cellular replisomes, the apicoplast replisome uses a single DNA polymerase (apPol). This suggests that apPol can multitask and catalyse both replicative and lesion bypass synthesis. Replicative synthesis relies on a restrictive active site for high accuracy while lesion bypass typically requires an open active site. This raises the question: how does apPol combine the structural features of multiple DNA polymerases in a single protein? Using single-particle electron cryomicroscopy (cryoEM), we have solved the structures of apPol bound to its undamaged DNA and nucleotide substrates in five pre-chemistry conformational states. We found that apPol can accommodate a nascent base pair with the fingers in an open configuration, which might facilitate the lesion bypass activity. In the fingers-open state, we identified a nascent base pair checkpoint that preferentially selects Watson-Crick base pairs, an essential requirement for replicative synthesis. Taken together, these structural features might explain how apPol balances replicative and lesion bypass synthesis.
-Authors: Lahiri, I., Kumari, A.
+Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.,Kumari A, Enache T, Craggs TD, Pata JD, Lahiri I Nucleic Acids Res. 2025 Oct 14;53(19):gkaf1005. doi: 10.1093/nar/gkaf1005. PMID:41099714<ref>PMID:41099714</ref>
-Description: apPol-DNA-nucleotide complex (ternary2)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Lahiri, I]]
+<div class="pdbe-citations 9qu8" style="background-color:#fffaf0;"></div>
-[[Category: Kumari, A]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: DNA molecule]]
+[[Category: Large Structures]]
+[[Category: Plasmodium falciparum]]
+[[Category: Kumari A]]
+[[Category: Lahiri I]]