5V7K

PCNA mutant D41A/D42A Protein Defective in Gene Silencing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring.

Kondratick, C.M.Litman, J.M.Shaffer, K.V.Washington, M.T.Dieckman, L.M.

(2018) PLoS ONE 13: e0193333-e0193333

  • DOI: 10.1371/journal.pone.0193333
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chap ...

    Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro. Three of these mutant forms of PCNA, encoded by the pol30-6, pol30-8, and the pol30-79 alleles, direct the synthesis of PCNA proteins with the amino acid substitutions D41A/D42A, R61A/D63A, and L126A/I128A, respectively. Interestingly, these double alanine substitutions are located far away from each other within the PCNA protein. To understand the structural basis of the interaction between PCNA and CAF-1 and how disruption of this interaction leads to reduced gene silencing, we determined the X-ray crystal structures of each of these mutant PCNA proteins. All three of the substitutions caused disruptions of a surface cavity on the front face of the PCNA ring, which is formed in part by three loops comprised of residues 21-24, 41-44, and 118-134. We suggest that this cavity is a novel binding pocket required for the interaction between PCNA and CAF-1, and that this region in PCNA also represents a potential binding site for other PCNA-binding proteins.


    Organizational Affiliation

    Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America.,Department of Chemistry, Creighton University, Omaha, NE, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A
265Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: POL30
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P15873
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 122.323α = 90.00
b = 122.323β = 90.00
c = 122.323γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
d*TREKdata reduction
Force Field Xrefinement
Cootmodel building
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM081433
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP20-GM103427

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release