5DOL

Crystal structure of YabA amino-terminal domain from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 

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Literature

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

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.

(2016) Nucleic Acids Res 44: 449-463

  • DOI: 10.1093/nar/gkv1318
  • Primary Citation of Related Structures:  
    5DOL

  • 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 ...

    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.


    Organizational Affiliation

    INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France marie-francoise.gros@jouy.inra.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Initiation-control protein YabAA, B62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yabABSU00330
Find proteins for P37542 (Bacillus subtilis (strain 168))
Explore P37542 
Go to UniProtKB:  P37542
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.48α = 90
b = 83.48β = 90
c = 64.71γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Region Rhone-AlpesFranceCIBLE 2011

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release