6P7E

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.001 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.

Foster, B.M.Rosenberg, D.Salvo, H.Stephens, K.L.Bintz, B.J.Hammel, M.Ellenberger, T.Gainey, M.D.Wallen, J.R.

(2019) Biochemistry 58: 4466-4479

  • DOI: 10.1021/acs.biochem.9b00525

  • PubMed Abstract: 
  • Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA bindi ...

    Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri 63110 , United States.,Graduate Group in Biophysics , University of California, Berkeley , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed DNA polymerase
A, B, C, D
704Escherichia phage T7Mutation(s): 2 
EC: 2.7.7.7, 3.1.11.-
Find proteins for P00581 (Escherichia phage T7)
Go to UniProtKB:  P00581
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TrxA
E, F, G, H
109Escherichia coliMutation(s): 0 
Gene Names: trxA
Find proteins for Q14F07 (Escherichia coli)
Go to UniProtKB:  Q14F07
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ASP-THR-ASP-PHE peptide
U, V
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
THR-ASP-PHE peptide
W
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*CP*TP*TP*GP*CP*CP*GP*GP*TP*GP*A)-3')I,K,M,O21Escherichia phage T7
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (25-MER)J,L,N,P25Escherichia phage T7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download SDF File 
Download CCD File 
A, B, C, D
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.001 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 100.724α = 91.36
b = 102.698β = 96.83
c = 148.885γ = 113.11
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM055390

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release