6GVU | pdb_00006gvu

NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase

• PDB DOI: https://doi.org/10.2210/pdb6GVU/pdb
• BMRB: 34291
• NAKB: 6GVU

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharolobus islandicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-21 Released: 2018-12-26 
• Deposition Author(s): Boudet, J., Lipps, G., Allain, F.H.-T.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template.

Boudet, J., Devillier, J.C., Wiegand, T., Salmon, L., Meier, B.H., Lipps, G., Allain, F.H.

(2019) Cell 176: 154-166.e13

• PubMed: 30595448 
• DOI: https://doi.org/10.1016/j.cell.2018.11.031
• Primary Citation Related Structures: 
  6GT7, 6GVQ, 6GVT, 6GVU


• PubMed Abstract: 
  

  Primases have a fundamental role in DNA replication. They synthesize a primer that is then extended by DNA polymerases. Archaeoeukaryotic primases require for synthesis a catalytic and an accessory domain, the exact contribution of the latter being unresolved. For the pRN1 archaeal primase, this domain is a 115-amino acid helix bundle domain (HBD). Our structural investigations of this small HBD by liquid- and solid-state nuclear magnetic resonance (NMR) revealed that only the HBD binds the DNA template. DNA binding becomes sequence-specific after a major allosteric change in the HBD, triggered by the binding of two nucleotide triphosphates. The spatial proximity of the two nucleotides and the DNA template in the quaternary structure of the HBD strongly suggests that this small domain brings together the substrates to prepare the first catalytic step of primer synthesis. This efficient mechanism is likely general for all archaeoeukaryotic primases.

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Organizational Affiliation: 
• Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: [e-mail].
Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland.
Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland. Electronic address: [e-mail].
Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 16.24 kDa 
• Atom Count: 1,130 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
functional pRN1 primase	B	115	Saccharolobus islandicus	Mutation(s): 0
UniProt
Find proteins for Q54324 (Saccharolobus islandicus) Explore Q54324  Go to UniProtKB:  Q54324

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	A	9	Saccharolobus islandicus

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Boudet, J., Lipps, G., Allain, F.H.-T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030 141160

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-01-09
  Changes: Data collection, Database references
• Version 1.2: 2019-01-23
  Changes: Data collection, Database references
• Version 1.3: 2019-05-08
  Changes: Data collection
• Version 1.4: 2024-07-03
  Changes: Data collection, Database references, Other
• Version 1.5: 2024-11-06
  Changes: Structure summary