8A3V

Crystal structure of the Vibrio cholerae replicative helicase (VcDnaB) in complex with its loader protein (VcDciA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders.

Cargemel, C.Marsin, S.Noiray, M.Legrand, P.Bounoua, H.Li de la Sierra-Gallay, I.Walbott, H.Quevillon-Cheruel, S.

(2023) Acta Crystallogr D Struct Biol 79: 177-187

  • DOI: https://doi.org/10.1107/S2059798323000281
  • Primary Citation of Related Structures:  
    8A3V

  • PubMed Abstract: 

    During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data showed that the VcDciA binding site on VcDnaB is the conserved module formed by the linker helix LH of one monomer and the determinant helix DH of the second monomer. Interestingly, DnaC from Escherichia coli also targets this module onto EcDnaB. Thanks to their common target site, it was shown that VcDciA and EcDnaC could be functionally interchanged in vitro despite sharing no structural similarity. This represents a milestone in understanding the mechanism employed by phage helicase loaders to hijack bacterial replicative helicases during evolution.


  • Organizational Affiliation

    Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicative DNA helicase
A, B
474Vibrio choleraeMutation(s): 0 
Gene Names: dnaBBC353_11625C9J66_17780ERS013165_03687ERS013200_03939ERS013206_03692F0315_03560FLM02_14585HPY05_12185
EC: 3.6.4.12
UniProt
Find proteins for A0A085R2T8 (Vibrio cholerae)
Explore A0A085R2T8 
Go to UniProtKB:  A0A085R2T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A085R2T8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF721 domain-containing protein
C, D
163Vibrio choleraeMutation(s): 0 
Gene Names: D6U24_04005ERS013186_02533ERS013198_03405ERS013202_01773ERS013207_01848F0M16_07320
UniProt
Find proteins for A0A0H5ZA06 (Vibrio cholerae)
Explore A0A0H5ZA06 
Go to UniProtKB:  A0A0H5ZA06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H5ZA06
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.515α = 90
b = 186.515β = 90
c = 252.839γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
STARANISOdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection