Pyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala): orthorhombic form

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 

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This is version 1.4 of the entry. See complete history


Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA

Matsumiya, S.Ishino, S.Ishino, Y.Morikawa, K.

(2003) Protein Sci 12: 823-831

  • DOI: https://doi.org/10.1110/ps.0234503
  • Primary Citation of Related Structures:  
    1IZ4, 1IZ5

  • PubMed Abstract: 

    Two mutant proliferating cell nuclear antigens from the hyperthermophilic archaeon Pyrococcus furiosus, PfuPCNA(D143A) and PfuPCNA(D143A/D147A), were prepared by site-specific mutagenesis. The results from gel filtration showed that mutations at D143 and D147 drastically affect the stability of the trimeric structure of PfuPCNA. The PfuPCNA(D143A) still retained the activity to stimulate the DNA polymerase reaction, but PfuPCNA(D143A/D147A) lost the activity. Crystal structures of the mutant PfuPCNAs were determined. Although the wild-type PCNA forms a toroidal trimer with intermolecular hydrogen bonds between the N- and C-terminal domains, the mutant PfuPCNAs exist as V-shaped dimers through intermolecular hydrogen bonds between the two C-terminal domains in the crystal. Because the mutated residues are involved in the intermolecular ion pairs through their side chains in the wild-type PfuPCNA, these ion pairs seem to play a key role in maintaining the toroidal structure of the PfuPCNA trimer. The comparison of the crystal structures revealed intriguing conformational flexibility of each domain in the PfuPCNA subunit. This structural versatility of PCNA may be involved in the mechanisms for ring opening and closing.

  • Organizational Affiliation

    Department of Structural Biology, Biomolecular Engineering Research Institute, Osaka 565-0874, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
A, B
249Pyrococcus furiosusMutation(s): 3 
Find proteins for O73947 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore O73947 
Go to UniProtKB:  O73947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO73947
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.289α = 90
b = 85.348β = 90
c = 118.03γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description