4EDG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.003 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.str.2012.05.017
  • Primary Citation of Related Structures:  

  • 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 ass ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase
A
329Staphylococcus aureusMutation(s): 0 
Gene Names: dnaG
EC: 2.7.7.-
Find proteins for O05338 (Staphylococcus aureus)
Go to UniProtKB:  O05338
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.003 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 151.261α = 90.00
b = 151.261β = 90.00
c = 38.665γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
SCALAdata scaling
Blu-Icedata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references