Primase large subunit amino terminal domain from Pyrococcus horikoshii

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.248 

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Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii

Ito, N.Matsui, I.Matsui, E.

(2007) FEBS J 274: 1340-1351

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.05690.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Archaeal/eukaryotic primases form a heterodimer consisting of a small catalytic subunit (PriS) and a large subunit (PriL). The heterodimer complex synthesizes primer oligoribonucleotides that are required for chromosomal replication. Here, we describe crystallographic and biochemical studies of the N-terminal domain (NTD) of PriL (PriL(NTD); residues 1-222) that bind to PriS from a hyperthermophilic archaeon, Pyrococcus horikoshii, at 2.9 A resolution. The PriL(NTD) structure consists of two subdomains, the helix-bundle and twisted-strand domains. The latter is structurally flexible, and is expected to contain a PriS interaction site. Pull-down and surface plasmon resonance analyses of structure-based deletion and alanine scanning mutants showed that the conserved hydrophobic Tyr155-Tyr156-Ile157 region near the flexible region is the PriS-binding site, as the Y155A/Y156A/I157A mutation markedly reduces PriS binding, by 1000-fold. These findings and a structural comparison with a previously reported PriL(NTD)-PriS complex suggest that the presented alternative conformations of the twisted-strand domain facilitate the heterodimer assembly.

  • Organizational Affiliation

    Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
397aa long hypothetical protein
A, B, C
222Pyrococcus horikoshii OT3Mutation(s): 0 
Find proteins for O57935 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57935 
Go to UniProtKB:  O57935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57935
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.248 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.25α = 90
b = 89.25β = 90
c = 252.674γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2007-02-27 
  • Deposition Author(s): Ito, N.

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description