Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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Crystal structure of the C-terminal domain of human DNA primase large subunit: Implications for the mechanism of the primase - polymerase alpha switch.

Agarkar, V.B.Babayeva, N.D.Pavlov, Y.I.Tahirov, T.H.

(2011) Cell Cycle 10: 926-931

  • DOI: https://doi.org/10.4161/cc.10.6.15010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DNA polymerases cannot synthesize DNA without a primer, and DNA primase is the only specialized enzyme capable of de novo synthesis of short RNA primers. In eukaryotes, primase functions within a heterotetrameric complex in concert with a tightly bound DNA polymerase α (Pol α). In humans, the Pol α part is comprised of a catalytic subunit (p180) and an accessory subunit B (p70), and the primase part consists of a small catalytic subunit (p49) and a large essential subunit (p58). The latter subunit participates in primer synthesis, counts the number of nucleotides in a primer, assists the release of the primer-template from primase and transfers it to the Pol α active site. Recently reported crystal structures of the C-terminal domains of the yeast and human enzymes' large subunits provided critical information related to their structure, possible sites for binding of nucleotides and template DNA, as well as the overall organization of eukaryotic primases. However, the structures also revealed a difference in the folding of their proposed DNA-binding fragments, raising the possibility that yeast and human proteins are functionally different. Here we report new structure of the C-terminal domain of the human primase p58 subunit. This structure exhibits a fold similar to a fold reported for the yeast protein but different than a fold reported for the human protein. Based on a comparative analysis of all three C-terminal domain structures, we propose a mechanism of RNA primer length counting and dissociation of the primer-template from primase by a switch in conformation of the ssDNA-binding region of p58.

  • Organizational Affiliation

    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit
A, B
192Homo 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: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.476α = 90
b = 83.724β = 97.65
c = 47.561γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description