6EHT

Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

p15PAF binding to PCNA modulates the DNA sliding surface.

De March, M.Barrera-Vilarmau, S.Crespan, E.Mentegari, E.Merino, N.Gonzalez-Magana, A.Romano-Moreno, M.Maga, G.Crehuet, R.Onesti, S.Blanco, F.J.De Biasio, A.

(2018) Nucleic Acids Res 46: 9816-9828

  • DOI: 10.1093/nar/gky723
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the ...

    p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF-PCNA-DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η-PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.


    Related Citations: 
    • Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.
      De Biasio, A., de Opakua, A.I., Mortuza, G.B., Molina, R., Cordeiro, T.N., Castillo, F., Villate, M., Merino, N., Delgado, S., Gil-Carton, D., Luque, I., Diercks, T., Bernado, P., Montoya, G., Blanco, F.J.
      (2015) Nat Commun 6: 6439
    • Structural basis of human PCNA sliding on DNA.
      De March, M., Merino, N., Barrera-Vilarmau, S., Crehuet, R., Onesti, S., Blanco, F.J., De Biasio, A.
      (2017) Nat Commun 8: 13935

    Organizational Affiliation

    Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, B
254Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
C
256Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PCNA-associated factor
D, E
20Homo sapiensMutation(s): 0 
Gene Names: PCLAFKIAA0101NS5ATP9PAFL5
Find proteins for Q15004 (Homo sapiens)
Go to UniProtKB:  Q15004
NIH Common Fund Data Resources
PHAROS  Q15004
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')F10Homo sapiens
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')G10Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.264 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.993α = 90
b = 42.3β = 102.7
c = 141.827γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references