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Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

Abstract : YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.
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Liza Felicori, Katie Jameson, Pierre Roblin, Mark Fogg, Transito Garcia-Garcia, et al.. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners. Nucleic Acids Research, Oxford University Press, 2016, 44 (1), pp.449-463. ⟨10.1093/nar/gkv1318⟩. ⟨hal-01991824⟩

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