3GPM

Structure of the trimeric form of the E113G PCNA mutant protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions.

Freudenthal, B.D.Gakhar, L.Ramaswamy, S.Washington, M.T.

(2009) Acta Crystallogr D Biol Crystallogr 65: 560-566

  • DOI: https://doi.org/10.1107/S0907444909011329
  • Primary Citation of Related Structures:  
    3GPM, 3GPN

  • PubMed Abstract: 

    Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form of the protein. In this nontrimeric form, domain A of one PCNA monomer interacts with domain A of a neighboring monomer, while domain B of this monomer interacts with domain B of a different neighboring monomer. The B-B interface is stabilized by an antiparallel beta-sheet and appears to be structurally similar to the A-B interface observed in the trimeric form of PCNA. The A-A interface, in contrast, is primarily stabilized by hydrophobic interactions. Because the E113G substitution is located on this hydrophobic surface, the A-A interface should be less favorable in the case of the wild-type protein. This suggests that the side chain of Glu113 promotes trimer formation by destabilizing these possible alternate subunit interactions.


  • Organizational Affiliation

    Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen258Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: POL30YBR0811YBR088C
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15873
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.093α = 90
b = 122.093β = 90
c = 122.093γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description