1Z8S | pdb_00001z8s

DnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597)

• PDB DOI: https://doi.org/10.2210/pdb1Z8S/pdb
• BMRB: 6716

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-03-31 Released: 2005-10-04 
• Deposition Author(s): Syson, K., Thirlway, J., Hounslow, A.M., Soultanas, P., Waltho, J.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation

Syson, K., Thirlway, J., Hounslow, A.M., Soultanas, P., Waltho, J.P.

(2005) Structure 13: 609-616

• PubMed: 15837199 
• DOI: https://doi.org/10.1016/j.str.2005.01.022
• Primary Citation Related Structures: 
  1Z8S


• PubMed Abstract: 
  

  The helicase-primase interaction is a critical event in DNA replication and is mediated by a putative helicase-interaction domain within the primase. The solution structure of the helicase-interaction domain of DnaG reveals that it is made up of two independent subdomains: an N-terminal six-helix module and a C-terminal two-helix module that contains the residues of the primase previously identified as important in the interaction with the helicase. We show that the two-helix module alone is sufficient for strong binding between the primase and the helicase but fails to activate the helicase; both subdomains are required for helicase activation. The six-helix module of the primase has only one close structural homolog, the N-terminal domain of the corresponding helicase. This surprising structural relationship, coupled with the differences in surface properties of the two molecules, suggests how the helicase-interaction domain may perturb the structure of the helicase and lead to activation.

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Organizational Affiliation: 
• Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield S10 2TN, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.85 kDa 
• Atom Count: 1,180 
• Modeled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A	146	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: dnaG EC: 2.7.7 (PDB Primary Data), 2.7.7.101 (UniProt)
UniProt
Find proteins for Q9X4D0 (Geobacillus stearothermophilus) Explore Q9X4D0  Go to UniProtKB:  Q9X4D0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Syson, K., Thirlway, J., Hounslow, A.M., Soultanas, P., Waltho, J.P.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection