5DOL

Crystal structure of YabA amino-terminal domain from Bacillus subtilis

Summary for 5DOL

• Entry DOI: 10.2210/pdb5dol/pdb
• Descriptor: Initiation-control protein YabA (2 entities in total)
• Functional Keywords: yaba, dnaa, dnan, zinc finger, initiation control, replication
• Biological source: Bacillus subtilis (strain 168)
• Total number of polymer chains: 2
• Total formula weight: 15002.98

Authors

Cherrier, M.V.,Bazin, A.,Jameson, K.H.,Wilkinson, A.J.,Noirot-Gros, M.F.,Terradot, L. (deposition date: 2015-09-11, release date: 2016-01-20, Last modification date: 2024-05-08)

Primary citation

Felicori, L.,Jameson, K.H.,Roblin, P.,Fogg, M.J.,Garcia-Garcia, T.,Ventroux, M.,Cherrier, M.V.,Bazin, A.,Noirot, P.,Wilkinson, A.J.,Molina, F.,Terradot, L.,Noirot-Gros, M.F.
Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners.
Nucleic Acids Res., 44:449-463, 2016

PubMed 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.

PubMed: 26615189
DOI: 10.1093/nar/gkv1318

Experimental method

X-RAY DIFFRACTION (2.7 Å)