5VBN

Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit.

Baranovskiy, A.G.Gu, J.Babayeva, N.D.Kurinov, I.Pavlov, Y.I.Tahirov, T.H.

(2017) J. Biol. Chem. 292: 15717-15730

  • DOI: 10.1074/jbc.M117.792705

  • PubMed Abstract: 
  • The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polϵ, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subun ...

    The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polϵ, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polϵ B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polϵ contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 Å2 Comparative structural analysis of p59-p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polϵ. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.


    Organizational Affiliation

    From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon subunit 2
A, E
527Homo sapiensMutation(s): 0 
Gene Names: POLE2 (DPE2)
EC: 2.7.7.7
Find proteins for P56282 (Homo sapiens)
Go to Gene View: POLE2
Go to UniProtKB:  P56282
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon catalytic subunit A
B, F
145Homo sapiensMutation(s): 0 
Gene Names: POLE (POLE1)
EC: 2.7.7.7
Find proteins for Q07864 (Homo sapiens)
Go to Gene View: POLE
Go to UniProtKB:  Q07864
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.260α = 90.00
b = 201.459β = 90.00
c = 78.336γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

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 StatesGM101167
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
National Institutes of Health/National Cancer InstituteUnited StatesCA036727

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence
  • Version 1.3: 2017-10-04
    Type: Database references