6HVO

Crystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The p12 subunit of human polymerase delta uses an atypical PIP box for molecular recognition of proliferating cell nuclear antigen (PCNA).

Gonzalez-Magana, A.Ibanez de Opakua, A.Romano-Moreno, M.Murciano-Calles, J.Merino, N.Luque, I.Rojas, A.L.Onesti, S.Blanco, F.J.De Biasio, A.

(2019) J.Biol.Chem. 294: 3947-3956

  • DOI: 10.1074/jbc.RA118.006391

  • PubMed Abstract: 
  • Human DNA polymerase δ is essential for DNA replication and acts in conjunction with the processivity factor proliferating cell nuclear antigen (PCNA). Besides its catalytic subunit (p125), pol δ comprises three regulatory subunits (p50, p68, and p12 ...

    Human DNA polymerase δ is essential for DNA replication and acts in conjunction with the processivity factor proliferating cell nuclear antigen (PCNA). Besides its catalytic subunit (p125), pol δ comprises three regulatory subunits (p50, p68, and p12). PCNA interacts with all of these subunits, but only the interaction with p68 has been structurally characterized. Here, we report solution NMR-, isothermal titration calorimetry-, and X-ray crystallography-based analyses of the p12-PCNA interaction, which takes part in the modulation of the rate and fidelity of DNA synthesis by pol δ. We show that p12 binds with micromolar affinity to the classical PIP-binding pocket of PCNA via a highly atypical PIP-box located at the p12 N terminus. Unlike the canonical PIP-box of p68, the PIP-box of p12 lacks the conserved glutamine, binds through a 2-fork plug made of an isoleucine and a tyrosine residue at +3 and +8 positions, respectively, and is stabilized by an aspartate at +6 position, which creates a network of intra-molecular hydrogen bonds. These findings add to growing evidence that PCNA can bind a diverse range of protein sequences that may be broadly grouped as PIP-like motifs as has been previously suggested.


    Organizational Affiliation

    CIC bioGUNE, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, B, C
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 4
D, F, E
19Homo sapiensMutation(s): 0 
Gene Names: POLD4 (POLDS)
Find proteins for Q9HCU8 (Homo sapiens)
Go to Gene View: POLD4
Go to UniProtKB:  Q9HCU8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.965α = 90.00
b = 83.888β = 90.00
c = 154.982γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainCTQ2017-83810-R

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references
  • Version 1.2: 2019-03-27
    Type: Data collection, Database references