View source for 9oyd


==Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 3 with disordered DNA at the shoulder==
<StructureSection load='9oyd' size='340' side='right'caption='[[9oyd]], [[Resolution|resolution]] 2.73&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9oyd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9OYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9OYD 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]] 2.73&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=9oyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9oyd OCA], [https://pdbe.org/9oyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9oyd RCSB], [https://www.ebi.ac.uk/pdbsum/9oyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9oyd ProSAT]</span></td></tr>
</table>
<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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9oyd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: DNA molecule]]
[[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]]