3TBL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    3TBL

  • 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 synthesis (TLS) polymerases with replication polymerases ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenA, B, C261Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS:  P12004
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinD, E76Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
Find proteins for P62979 (Homo sapiens)
Explore P62979 
Go to UniProtKB:  P62979
NIH Common Fund Data Resources
PHAROS:  P62979
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.055α = 90
b = 161.055β = 90
c = 97.357γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Database references
  • Version 1.2: 2013-09-25
    Changes: Derived calculations
  • Version 1.3: 2020-01-29
    Changes: Derived calculations