4E2K | pdb_00004e2k

The structure of the S. aureus DnaG RNA Polymerase Domain

• PDB DOI: https://doi.org/10.2210/pdb4E2K/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-08 Released: 2012-08-01 
• Deposition Author(s): Rymer, R.U., Solorio, F.A., Clement, C., Corn, J.E., Wang, J.D., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.219 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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

• PubMed: 22795082 
• DOI: https://doi.org/10.1016/j.str.2012.05.017
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.92 kDa 
• Atom Count: 2,905 
• Modeled Residue Count: 319 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A	329	Staphylococcus aureus	Mutation(s): 0  Gene Names: dnaG EC: 2.7.7 (PDB Primary Data), 2.7.7.101 (UniProt)
UniProt
Find proteins for O05338 (Staphylococcus aureus) Explore O05338  Go to UniProtKB:  O05338

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	B [auth A], C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.219 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.334	α = 90
b = 151.334	β = 90
c = 38.571	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Rymer, R.U., Solorio, F.A., Clement, C., Corn, J.E., Wang, J.D., Berger, J.M.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description