2W58

Crystal Structure of the DnaI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular Interplay between the Replicative Helicase Dnac and its Loader Protein Dnai from Geobacillus Kaustophilus.

Tsai, K.L.Lo, Y.H.Sun, Y.J.Hsiao, C.D.

(2009) J Mol Biol 393: 1056

  • DOI: https://doi.org/10.1016/j.jmb.2009.09.002
  • Primary Citation of Related Structures:  
    2W58

  • PubMed Abstract: 

    Helicase loading factors are thought to transfer the hexameric ring-shaped helicases onto the replication fork during DNA replication. However, the mechanism of helicase transfer onto DNA remains unclear. In Bacillus subtilis, the protein DnaI, which belongs to the AAA+ family of ATPases, is responsible for delivering the hexameric helicase DnaC onto DNA. Here we investigated the interaction between DnaC and DnaI from Geobacillus kaustophilus HTA426 (GkDnaC and GkDnaI, respectively) and determined that GkDnaI forms a stable complex with GkDnaC with an apparent stoichiometry of GkDnaC(6)-GkDnaI(6) in the absence of ATP. Surface plasmon resonance analysis indicated that GkDnaI facilitates loading of GkDnaC onto single-stranded DNA (ssDNA) and supports complex formation with ssDNA in the presence of ATP. Additionally, the GkDnaI C-terminal AAA+ domain alone could bind ssDNA, and binding was modulated by nucleotides. We also determined the crystal structure of the C-terminal AAA+ domain of GkDnaI in complex with ADP at 2.5 A resolution. The structure not only delineates the binding of ADP in the expected Walker A and B motifs but also reveals a positively charged region that may be involved in ssDNA binding. These findings provide insight into the mechanism of replicative helicase loading onto ssDNA.


  • Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, ROC.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRIMOSOME COMPONENT (HELICASE LOADER)
A, B
202Geobacillus kaustophilus HTA426Mutation(s): 0 
UniProt
Find proteins for Q5KWD0 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KWD0 
Go to UniProtKB:  Q5KWD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KWD0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.632α = 90
b = 59.53β = 90
c = 115.636γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-10-16
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations