Crystal Structure Analysis of primosome protein DnaB (resiues 1-300) from Geobacillus stearothermophilus

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein

Li, Y.C.Naveen, V.Lin, M.G.Hsiao, C.D.

(2017) J Biol Chem 292: 15744-15757

  • DOI: https://doi.org/10.1074/jbc.M117.792002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The DnaB primosomal protein from Gram-positive bacteria plays a key role in DNA replication and restart as a loader protein for the recruitment of replisome cascade proteins. Previous investigations have established that DnaB is composed of an N-terminal domain, a middle domain, and a C-terminal domain. However, structural evidence for how DnaB functions at the atomic level is lacking. Here, we report the crystal structure of DnaB, encompassing the N-terminal and middle domains (residues 1-300), from Geobacillus stearothermophilus ( Gst DnaB 1-300 ) at 2.8 Å resolution. Our structure revealed that Gst DnaB 1-300 forms a tetramer with two basket-like architectures, a finding consistent with those from solution studies using analytical ultracentrifugation. Furthermore, our results from both GST pulldown assays and analytical ultracentrifugation show that Gst DnaB 1-300 is sufficient to form a complex with PriA, the primosomal reinitiation protein. Moreover, with the aid of small angle X-ray scattering experiments, we also determined the structural envelope of full-length DnaB ( Gst DnaB FL ) in solution. These small angle X-ray scattering studies indicated that Gst DnaB FL has an elongated conformation and that the protruding density envelopes originating from Gst DnaB 1-300 could completely accommodate the Gst DnaB C-terminal domain (residues 301-461). Taken together with biochemical assays, our results suggest that Gst DnaB uses different domains to distinguish the PriA interaction and single-stranded DNA binding. These findings can further extend our understanding of primosomal assembly in replication restart.

  • Organizational Affiliation

    From the Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan and hsiao@gate.sinica.edu.tw.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication initiation and membrane attachment protein
A, B, C, D
300Geobacillus stearothermophilus 10Mutation(s): 0 
Gene Names: GT50_05100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.356α = 90
b = 118.98β = 90
c = 157.917γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references