4RJF

Crystal structure of the human sliding clamp at 2.0 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0072 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

p21 Exploits Residue Tyr151 as a Tether for High-Affinity PCNA Binding.

Kroker, A.J.Bruning, J.B.

(2015) Biochemistry 54: 3483-3493

  • DOI: 10.1021/acs.biochem.5b00241

  • PubMed Abstract: 
  • Proliferating cell nuclear antigen (PCNA, processivity factor, sliding clamp) is a ring-shaped protein that tethers proteins to DNA in processes, including DNA replication, DNA repair, and cell-cycle control. Often used as a marker for cell prolifera ...

    Proliferating cell nuclear antigen (PCNA, processivity factor, sliding clamp) is a ring-shaped protein that tethers proteins to DNA in processes, including DNA replication, DNA repair, and cell-cycle control. Often used as a marker for cell proliferation, PCNA is overexpressed in cancer cells, making it an appealing pharmaceutical target. PCNA interacts with proteins through a PCNA interacting protein (PIP)-box, an eight-amino acid consensus sequence; different binding partners display a wide range of affinities based on function. Of all biological PIP-boxes, p21 has the highest known affinity for PCNA, allowing for inhibition of DNA replication and cell growth under cellular stress. As p21 is one of the few PIP-box sequences to contain a tyrosine rather than a phenylalanine in the eighth conserved position, we probed the significance of the hydroxyl group at this position using a mutational approach. Here we present the cocrystal structure of PCNA bound to a mutant p21 PIP-box peptide, p21Tyr151Phe, with associated isothermal titration calorimetry data. The p21Tyr151Phe peptide showed a 3-fold difference in affinity, as well as differences in entropy and enthalpy of binding. These differences can be attributed to a loss of hydrogen bonding capacity, as well as structural plasticity in the PCNA interdomain connector loop and the hydrophobic cavity of PCNA to which p21 binds. Thus, the hydroxyl group of Tyr151 in p21 acts as a tethering point for ideal packing and surface recognition of the peptide interface, increasing the binding affinity of p21 for PCNA.


    Organizational Affiliation

    School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, E
261Homo 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
Cyclin-dependent kinase inhibitor 1
B, D, F
22Homo sapiensMutation(s): 1 
Gene Names: CDKN1A (CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1)
Find proteins for P38936 (Homo sapiens)
Go to Gene View: CDKN1A
Go to UniProtKB:  P38936
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0072 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 142.970α = 90.00
b = 142.970β = 90.00
c = 41.410γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release