9oyg: Difference between revisions

Line 1:

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

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

==Structure of the E. coli clamp loader DnaX-complex alone==

== Structural highlights ==

<table><tr><td colspan='2'>[[9oyg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9OYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9OYG 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]] 2.95Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9oyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9oyg OCA], [https://pdbe.org/9oyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9oyg RCSB], [https://www.ebi.ac.uk/pdbsum/9oyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9oyg ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/HOLA_ECOLI HOLA_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA.

== Publication Abstract from PubMed ==

DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small ssDNA gaps-common intermediates during DNA repair-remains incompletely understood. Here, we show that the bacterial Escherichia coli DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the beta-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by ~150 degrees , promoting insertion of the 3'-dsDNA into the clamp. This DNA-bending mechanism allows efficient beta-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair.

~~Authors~~:

The E. coli DnaX clamp loader sharply bends DNA to load beta-clamp at nicks and small gaps.,Zheng F, Yao NY, Georgescu RE, Lyu M, O'Donnell ME, Li H bioRxiv [Preprint]. 2026 Jan 20:2026.01.17.700081. doi: , 10.64898/2026.01.17.700081. PMID:41648351<ref>PMID:41648351</ref>

~~Description~~:

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

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

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Escherichia coli]]

[[Category: Large Structures]]

[[Category: Georgescu R]]

[[Category: Li H]]

[[Category: Lyu M]]

[[Category: O'Donnell ME]]

[[Category: Yao YN]]

[[Category: Zheng F]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9oyg is ON HOLD  until Paper Publication
+==Structure of the E. coli clamp loader DnaX-complex alone==
+<StructureSection load='9oyg' size='340' side='right'caption='[[9oyg]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9oyg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9OYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9OYG 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]] 2.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9oyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9oyg OCA], [https://pdbe.org/9oyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9oyg RCSB], [https://www.ebi.ac.uk/pdbsum/9oyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9oyg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HOLA_ECOLI HOLA_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small ssDNA gaps-common intermediates during DNA repair-remains incompletely understood. Here, we show that the bacterial Escherichia coli DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the beta-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by ~150 degrees , promoting insertion of the 3'-dsDNA into the clamp. This DNA-bending mechanism allows efficient beta-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair.
-Authors:
+The E. coli DnaX clamp loader sharply bends DNA to load beta-clamp at nicks and small gaps.,Zheng F, Yao NY, Georgescu RE, Lyu M, O'Donnell ME, Li H bioRxiv [Preprint]. 2026 Jan 20:2026.01.17.700081. doi: , 10.64898/2026.01.17.700081. PMID:41648351<ref>PMID:41648351</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 9oyg" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Georgescu R]]
+[[Category: Li H]]
+[[Category: Lyu M]]
+[[Category: O'Donnell ME]]
+[[Category: Yao YN]]
+[[Category: Zheng F]]