7BM8

Crystal structure of the C-terminally truncated chromosome-partitioning protein ParB from Caulobacter crescentus complexed with CTP-gamma-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A CTP-dependent gating mechanism enables ParB spreading on DNA.

Jalal, A.S.Tran, N.T.Stevenson, C.E.Chimthanawala, A.Badrinarayanan, A.Lawson, D.M.Le, T.B.

(2021) Elife 10

  • DOI: 10.7554/eLife.69676
  • Primary Citation of Related Structures:  
    6T1F, 7BM8

  • PubMed Abstract: 
  • Proper chromosome segregation is essential in all living organisms. The ParA-ParB- parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al ...

    Proper chromosome segregation is essential in all living organisms. The ParA-ParB- parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al., 2020). Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with reopening of the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.


    Organizational Affiliation

    Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome-partitioning protein ParBA, B257Caulobacter 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTP (Subject of Investigation/LOI)
Query on CTP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.461α = 90
b = 56.076β = 98.4
c = 71.36γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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/000PR9791

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references