Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase.

Vaithiyalingam, S.Warren, E.M.Eichman, B.F.Chazin, W.J.

(2010) Proc Natl Acad Sci U S A 107: 13684-13689

  • DOI: https://doi.org/10.1073/pnas.1002009107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-A resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.

  • Organizational Affiliation

    Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit
A, B
195Homo sapiensMutation(s): 0 
Gene Names: PRIM2PRIM2A
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P49643 (Homo sapiens)
Explore P49643 
Go to UniProtKB:  P49643
PHAROS:  P49643
GTEx:  ENSG00000146143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49643
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.441α = 90
b = 53.05β = 115.09
c = 88.844γ = 90
Software Package:
Software NamePurpose
MD2data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model