Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication

Landeck, Jacob T.; Pajak, Joshua; Norman, Emily K.; Sedivy, Emma L.; Kelch, Brian A.

doi:10.1016/j.jbc.2024.107166

Cited by 2 publications

(1 citation statement)

References 83 publications

(175 reference statements)

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“…β-clamp is a homo-dimeric, toroidal protein that encircles DNA [3] tethering polymerases to the primer/template junction during DNA synthesis, ensuring processive DNA replication [1,2]. β-clamp is loaded onto DNA in an ATP-dependent crab-claw like motion by the clamp loader complex [4,5] constituting a central hub that interacts with numerous proteins important in translesion synthesis (TLS) [6–8], DNA mismatch repair [9,10] or otherwise involved in DNA homeostasis [10–12].…”

Section: Introductionmentioning

confidence: 99%

Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects

Simonsen,

Prestel,

Østerlund

et al. 2024

Preprint

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The homo-dimeric, ring-shaped bacterial DNA sliding clamp, β-clamp, is a central hub in DNA replication and repair. It interacts with a plethora of proteins via short linear motifs, which bind to the same hydrophobic binding pocket on β-clamp. Although the structure, functions and interactions of β-clamp have been amply studied, less focus has been on understanding its dynamics and how this is influenced by ligand binding. In this work, we have made a backbone nuclear magnetic resonance (NMR) assignment of the 83 kDa dimeric β-clamp and used NMR in combination with hydrogen-deuterium exchange mass spectrometry to scrutinize the dynamics of β-clamp and how different ligands affect this. We found that binding of a small peptide from the polymerase III α subunit affects the dynamics and stability of β-clamp. This effect not only appears locally around the binding pocket, but also globally through dynamic allosteric connections to distant regions of the protein, including the dimer interface. This dissipated dynamic effect is likely a consequence of the binding pocket architecture and may reflect a common mechanism of structural plasticity, where different ligands impose differential responses in the structure and dynamics of β-clamp.HighlightsNMR spectroscopy of β-clamp revealed its inherent dynamicsA peptide ligand from polymerase III stabilizes β-clamp from global unfoldingPeptide binding causes allosteric effects that manifest in changes in dynamicsDynamic changes occur distant to the binding pocket in the dimer interfaceAllostery may be a mechanism for differential responses to interaction partnersGraphical abstract

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Section: Introductionmentioning

confidence: 99%

Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects

Simonsen,

Prestel,

Østerlund

et al. 2024

Preprint

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The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery

Simonsen,

Søgaard,

Olsen

et al. 2024

Cell. Mol. Life Sci.

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DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.

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Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication

Cited by 2 publications

References 83 publications

Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects

Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects

The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery

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