6QCG

PCNA complex with Cdt1 N-terminal PIP-box peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2E3 ligase activity to Cdt1.

Hayashi, A.Giakoumakis, N.N.Heidebrecht, T.Ishii, T.Panagopoulos, A.Caillat, C.Takahara, M.Hibbert, R.G.Suenaga, N.Stadnik-Spiewak, M.Takahashi, T.Shiomi, Y.Taraviras, S.von Castelmur, E.Lygerou, Z.Perrakis, A.Nishitani, H.

(2018) Life Sci Alliance 1: e201800238-e201800238

  • DOI: 10.26508/lsa.201800238
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The CRL4 <sup>Cdt2 </sup> ubiquitin ligase complex is an essential regulator of cell-cycle progression and genome stability, ubiquitinating substrates such as p21, Set8, and Cdt1, via a display of substrate degrons on proliferating cell nuclear antig ...

    The CRL4 Cdt2 ubiquitin ligase complex is an essential regulator of cell-cycle progression and genome stability, ubiquitinating substrates such as p21, Set8, and Cdt1, via a display of substrate degrons on proliferating cell nuclear antigens (PCNAs). Here, we examine the hierarchy of the ligase and substrate recruitment kinetics onto PCNA at sites of DNA replication. We demonstrate that the C-terminal end of Cdt2 bears a PCNA interaction protein motif (PIP box, Cdt2 PIP ), which is necessary and sufficient for the binding of Cdt2 to PCNA. Cdt2 PIP binds PCNA directly with high affinity, two orders of magnitude tighter than the PIP box of Cdt1. X-ray crystallographic structures of PCNA bound to Cdt2 PIP and Cdt1 PIP show that the peptides occupy all three binding sites of the trimeric PCNA ring. Mutating Cdt2 PIP weakens the interaction with PCNA, rendering CRL4 Cdt2 less effective in Cdt1 ubiquitination and leading to defects in Cdt1 degradation. The molecular mechanism we present suggests a new paradigm for bringing substrates to the CRL4-type ligase, where the substrate receptor and substrates bind to a common multivalent docking platform to enable subsequent ubiquitination.


    Organizational Affiliation

    Department of Physiology, School of Medicine, University of Patras, Patras, Greece.,Department of Biology, School of Medicine, University of Patras, Patras, Greece.,Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of Science, Kyushu University, Fukuoka, Japan.,Graduate School of Life Science, University of Hyogo, Kamigori, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, B, E, D, F
263Homo 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 replication factor Cdt1
I, G, H, J, K, L
14Homo sapiensMutation(s): 0 
Gene Names: CDT1
Find proteins for Q9H211 (Homo sapiens)
Go to Gene View: CDT1
Go to UniProtKB:  Q9H211
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.585α = 90.00
b = 143.173β = 90.00
c = 173.592γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release