1NUI

Crystal Structure of the primase fragment of Bacteriophage T7 primase-helicase protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Modular Architecture of the Bacteriophage T7 Primase Couples RNA primer Synthesis to DNA Synthesis

Kato, M.Ito, T.Wagner, G.Richardson, C.C.Ellenberger, T.

(2003) Mol.Cell 11: 1349-1360


  • PubMed Abstract: 
  • DNA primases are template-dependent RNA polymerases that synthesize oligoribonucleotide primers that can be extended by DNA polymerase. The bacterial primases consist of zinc binding and RNA polymerase domains that polymerize ribonucleotides at templ ...

    DNA primases are template-dependent RNA polymerases that synthesize oligoribonucleotide primers that can be extended by DNA polymerase. The bacterial primases consist of zinc binding and RNA polymerase domains that polymerize ribonucleotides at templating sequences of single-stranded DNA. We report a crystal structure of bacteriophage T7 primase that reveals its two domains and the presence of two Mg(2+) ions bound to the active site. NMR and biochemical data show that the two domains remain separated until the primase binds to DNA and nucleotide. The zinc binding domain alone can stimulate primer extension by T7 DNA polymerase. These findings suggest that the zinc binding domain couples primer synthesis with primer utilization by securing the DNA template in the primase active site and then delivering the primed DNA template to DNA polymerase. The modular architecture of the primase and a similar mechanism of priming DNA synthesis are likely to apply broadly to prokaryotic primases.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase/helicase
A, B
255Enterobacteria phage T7EC: 3.6.4.12, 2.7.7.-
Find proteins for P03692 (Enterobacteria phage T7)
Go to UniProtKB:  P03692
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.459α = 90.00
b = 136.460β = 90.00
c = 85.445γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MLPHAREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance