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

Experimental Data Snapshot

  • 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

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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: https://doi.org/10.1016/j.celrep.2020.107928
  • Primary Citation of Related Structures:  
    6S6H, 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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoid occlusion protein
A, B
146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: nocyyaABSU40990
Find proteins for P37524 (Bacillus subtilis (strain 168))
Explore P37524 
Go to UniProtKB:  P37524
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37524
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Noc Binding Site (NBS)
C, D
22synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
DIALSdata reduction

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  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description