5DOL image
Entry Detail
PDB ID:
5DOL
Keywords:
Title:
Crystal structure of YabA amino-terminal domain from Bacillus subtilis
Biological Source:
PDB Version:
Deposition Date:
2015-09-11
Release Date:
2016-01-20
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Initiation-control protein YabA
Chain IDs:A, B
Chain Length:62
Number of Molecules:2
Biological Source:Bacillus subtilis (strain 168)
Primary Citation
Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners.
Nucleic Acids Res. 44 449 463 (2016)
PMID: 26615189 DOI: 10.1093/nar/gkv1318

Abstact

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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