Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair

Cell. 2004 Jan 9;116(1):39-50. doi: 10.1016/s0092-8674(03)01036-5.


Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the molecular basis of FEN-1 specificity and PCNA activation, we report here structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with fluorescence resonance energy transfer (FRET) and mutational results. FEN-1 binds the unpaired 3' DNA end (3' flap), opens and kinks the DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5' cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular beta sheet interface that directly links adjacent PCNA and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1 activity. The DNA and protein conformational changes, composite complex structures, FRET, and mutational results support enzyme-PCNA alignments and a kinked DNA pivot point that appear suitable to coordinate rotary handoffs of kinked DNA intermediates among enzymes localized by the three PCNA binding sites.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Archaeoglobus
  • Binding Sites / physiology
  • Catalytic Domain / physiology
  • DNA / genetics
  • DNA / metabolism
  • DNA Repair / genetics*
  • DNA Replication / genetics*
  • Flap Endonucleases / chemistry*
  • Flap Endonucleases / metabolism*
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Conformation
  • Proliferating Cell Nuclear Antigen / chemistry
  • Proliferating Cell Nuclear Antigen / metabolism*
  • Protein Binding / physiology
  • Protein Structure, Secondary / physiology
  • Protein Structure, Tertiary / physiology
  • Saccharomyces cerevisiae
  • Substrate Specificity / physiology


  • Macromolecular Substances
  • Proliferating Cell Nuclear Antigen
  • DNA
  • Flap Endonucleases

Associated data

  • PDB/1RWZ
  • PDB/1RXC
  • PDB/1RXV
  • PDB/1RXW