Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1

Structure. 2004 Dec;12(12):2209-19. doi: 10.1016/j.str.2004.09.018.


Human Proliferating Cellular Nuclear Antigen (hPCNA), a member of the sliding clamp family of proteins, makes specific protein-protein interactions with DNA replication and repair proteins through a small peptide motif termed the PCNA-interacting protein, or PIP-box. We solved the structure of hPCNA bound to PIP-box-containing peptides from the p66 subunit of the human replicative DNA polymerase-delta (452-466) at 2.6 A and of the flap endonuclease (FEN1) (331-350) at 1.85 A resolution. Both structures demonstrate that the pol-delta p66 and FEN1 peptides interact with hPCNA at the same site shown to bind the cdk-inhibitor p21(CIP1). Binding studies indicate that peptides from the p66 subunit of the pol-delta holoenzyme and FEN1 bind hPCNA from 189- to 725-fold less tightly than those of p21. Thus, the PIP-box and flanking regions provide a small docking peptide whose affinities can be readily adjusted in accord with biological necessity to mediate the binding of DNA replication and repair proteins to hPCNA.

MeSH terms

  • Calorimetry
  • Crystallization
  • DNA Polymerase III / metabolism*
  • Flap Endonucleases / metabolism*
  • Humans
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism*
  • Proliferating Cell Nuclear Antigen / chemistry*
  • Proliferating Cell Nuclear Antigen / metabolism
  • Protein Structure, Tertiary
  • Thermodynamics


  • Peptide Fragments
  • Proliferating Cell Nuclear Antigen
  • POLD3 protein, human
  • DNA Polymerase III
  • Flap Endonucleases

Associated data

  • PDB/1U76
  • PDB/1U7B