Crystal structure of the catalytic subunit of human primase bound to UTP and Mn

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

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Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase.

Vaithiyalingam, S.Arnett, D.R.Aggarwal, A.Eichman, B.F.Fanning, E.Chazin, W.J.

(2014) J Mol Biol 426: 558-569

  • DOI: https://doi.org/10.1016/j.jmb.2013.11.007
  • Primary Citation of Related Structures:  
    4LIK, 4LIL, 4LIM

  • PubMed Abstract: 

    DNA replication in all organisms requires polymerases to synthesize copies of the genome. DNA polymerases are unable to function on a bare template and require a primer. Primases are crucial RNA polymerases that perform the initial de novo synthesis, generating the first 8-10 nucleotides of the primer. Although structures of archaeal and bacterial primases have provided insights into general priming mechanisms, these proteins are not well conserved with heterodimeric (p48/p58) primases in eukaryotes. Here, we present X-ray crystal structures of the catalytic engine of a eukaryotic primase, which is contained in the p48 subunit. The structures of p48 reveal that eukaryotic primases maintain the conserved catalytic prim fold domain, but with a unique subdomain not found in the archaeal and bacterial primases. Calorimetry experiments reveal that Mn(2+) but not Mg(2+) significantly enhances the binding of nucleotide to primase, which correlates with higher catalytic efficiency in vitro. The structure of p48 with bound UTP and Mn(2+) provides insights into the mechanism of nucleotide synthesis by primase. Substitution of conserved residues involved in either metal or nucleotide binding alter nucleotide binding affinities, and yeast strains containing the corresponding Pri1p substitutions are not viable. Our results reveal that two residues (S160 and H166) in direct contact with the nucleotide were previously unrecognized as critical to the human primase active site. Comparing p48 structures to those of similar polymerases in different states of action suggests changes that would be required to attain a catalytically competent conformation capable of initiating dinucleotide synthesis.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit392Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens)
Explore P49642 
Go to UniProtKB:  P49642
PHAROS:  P49642
GTEx:  ENSG00000198056 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49642
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.346α = 90
b = 79.346β = 90
c = 148.2γ = 90
Software Package:
Software NamePurpose
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: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations