3TBL

Structure of Mono-ubiquitinated PCNA: Implications for DNA Polymerase Switching and Okazaki Fragment Maturation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.903 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of monoubiquitinated PCNA: Implications for DNA polymerase switching and Okazaki fragment maturation.

Zhang, Z.Zhang, S.Lin, S.H.Wang, X.Wu, L.Lee, E.Y.Lee, M.Y.

(2012) Cell Cycle 11: 2128-2136

  • DOI: 10.4161/cc.20595

  • PubMed Abstract: 
  • Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion s ...

    Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA. Zhongtao_zhang@nymc.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, B, C
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
Ubiquitin
D, E
76Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.903 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 161.055α = 90.00
b = 161.055β = 90.00
c = 97.357γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-3000data collection
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Derived calculations