6Y93

Crystal structure of the DNA-binding domain of the Nucleoid Occlusion Factor (Noc) complexed to the Noc-binding site (NBS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report



Literature

Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family.

Jalal, A.S.B.Tran, N.T.Stevenson, C.E.Chan, E.W.Lo, R.Tan, X.Noy, A.Lawson, D.M.Le, T.B.K.

(2020) Cell Rep 32: 107928-107928

  • DOI: 10.1016/j.celrep.2020.107928
  • Primary Citation of Related Structures:  
    6Y93

  • PubMed Abstract: 
  • Specific interactions between proteins and DNA are essential to many biological processes. Yet, it remains unclear how the diversification in DNA-binding specificity was brought about, and the mutational paths that led to changes in specificity are u ...

    Specific interactions between proteins and DNA are essential to many biological processes. Yet, it remains unclear how the diversification in DNA-binding specificity was brought about, and the mutational paths that led to changes in specificity are unknown. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB [Partitioning Protein B] and Noc [Nucleoid Occlusion Factor], which both play roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity and that mutational paths to new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc and, in a broader context, might be useful for understanding the evolution of other classes of DNA-binding proteins.


    Organizational Affiliation

    Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK. Electronic address: tung.le@jic.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoid occlusion proteinAB146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: nocyyaABSU40990
Find proteins for P37524 (Bacillus subtilis (strain 168))
Explore P37524 
Go to UniProtKB:  P37524
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Noc Binding Site (NBS)C, D22synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.139α = 90
b = 60.567β = 116.88
c = 81.053γ = 90
Software Package:
Software NamePurpose
STARANISOdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited KingdomUF140053
Royal SocietyUnited KingdomRG150448
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P018165/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBBS/E/J/000C0683
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBBS/E/J/000PR9791

Revision History 

  • Version 1.0: 2020-08-05
    Type: Initial release