Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46756.92 
• Atom Count: 3261 
• Residue Count: 407 
• Unique protein chains: 1

2AU3

Crystal Structure of the Aquifex aeolicus primase (Zinc Binding and RNA Polymerase Domains)

• DOI: 10.2210/pdb2AU3/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus (strain VF5)
• Expression System: Escherichia coli


• Deposited: 2005-08-26 Released: 2005-11-15 
• Deposition Author(s): Corn, J.E., Pease, P.J., Hura, G.L., Berger, J.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.238 
• R-Value Work: 0.203 

Literature

Crosstalk between primase subunits can act to regulate primer synthesis in trans.

Corn, J.E., Pease, P.J., Hura, G.L., Berger, J.M.

(2005) Mol.Cell 20: 391-401

• PubMed: 16285921 
• DOI: 10.1016/j.molcel.2005.09.004


• PubMed Abstract: 
  

The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer in trans. This intersubunit interaction allows primase to select initiation sites on template DNA and implicates the regulatory domain as a "molecular brake" that restricts primer length. Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis.

---

Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA primase	A	407	Aquifex aeolicus (strain VF5)	Mutation(s): 0  Gene Names: dnaG EC: 2.7.7.-
Find proteins for O67465 (Aquifex aeolicus (strain VF5)) Go to UniProtKB:  O67465

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.238 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 43.222	α = 90.00
b = 66.403	β = 90.00
c = 138.157	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
SCALEPACK	data scaling
REFMAC	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-26 
• Released Date: 2005-11-15 
• Deposition Author(s): Corn, J.E., Pease, P.J., Hura, G.L., Berger, J.M.

Revision History 

• Version 1.0: 2005-11-15
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance