6S6H

Crystal structure of the DNA binding domain of the chromosome-partitioning protein ParB complexed to the centromeric parS site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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:  
    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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome-partitioning protein ParBA, B143Caulobacter vibrioides NA1000Mutation(s): 0 
Gene Names: parBCCNA_03868
UniProt
Find proteins for B8GW30 (Caulobacter vibrioides (strain NA1000 / CB15N))
Explore B8GW30 
Go to UniProtKB:  B8GW30
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*C)-3')C, D20Caulobacter vibrioides
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.099α = 90
b = 40.717β = 121.4
c = 94.004γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited KingdomUF140053
Royal SocietyUnited KingdomRG150448
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P018165/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBBS/E/J/000C0683
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012523/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references