The structure of the S. aureus DnaG RNA Polymerase Domain bound to ATP and Manganese

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.

Rymer, R.U.Solorio, F.A.Tehranchi, A.K.Chu, C.Corn, J.E.Keck, J.L.Wang, J.D.Berger, J.M.

(2012) Structure 20: 1478-1489

  • DOI: https://doi.org/10.1016/j.str.2012.05.017
  • Primary Citation of Related Structures:  
    4E2K, 4EDG, 4EDK, 4EDR, 4EDT, 4EDV, 4EE1

  • PubMed Abstract: 

    Primases are DNA-dependent RNA polymerases found in all cellular organisms. In bacteria, primer synthesis is carried out by DnaG, an essential enzyme that serves as a key component of DNA replication initiation, progression, and restart. How DnaG associates with nucleotide substrates and how certain naturally prevalent nucleotide analogs impair DnaG function are unknown. We have examined one of the earliest stages in primer synthesis and its control by solving crystal structures of the S. aureus DnaG catalytic core bound to metal ion cofactors and either individual nucleoside triphosphates or the nucleotidyl alarmones, pppGpp and ppGpp. These structures, together with both biochemical analyses and comparative studies of enzymes that use the same catalytic fold as DnaG, pinpoint the predominant nucleotide-binding site of DnaG and explain how the induction of the stringent response in bacteria interferes with primer synthesis.

  • Organizational Affiliation

    California Institute for Quantitative Biosciences, 374D Stanley Hall #3220, University of California, Berkeley, Berkeley, CA 94720-3220, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase329Staphylococcus aureusMutation(s): 0 
Gene Names: dnaG
EC: 2.7.7
Find proteins for O05338 (Staphylococcus aureus)
Explore O05338 
Go to UniProtKB:  O05338
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05338
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.261α = 90
b = 151.261β = 90
c = 38.665γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description