4P2H

Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.987 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine.

Koag, M.C.Kou, Y.Ouzon-Shubeita, H.Lee, S.

(2014) Nucleic Acids Res. 42: 8755-8766

  • DOI: 10.1093/nar/gku554
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG ...

    N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2'-fluoro-m7dG (Fm7dG), by human DNA polymerase β (polβ) and solved three X-ray structures of polβ in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows polβ catalysis ∼ 300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson-Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the polβ-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by polβ. In addition, the polβ-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7-methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that polβ catalysis across m7dG is slow, yet highly accurate.


    Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA SeongminLee@austin.utexas.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
326Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*AP*CP*(FMG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3')P10Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
1FZ
Query on 1FZ

Download SDF File 
Download CCD File 
A
5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
C10 H18 N3 O13 P3
YRKUYVYMPXAOAT-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FMG
Query on FMG
T
DNA linkingC11 H16 F N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.987 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.767α = 90.00
b = 79.167β = 106.18
c = 54.982γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-03-04 
  • Released Date: 2014-06-25 
  • Deposition Author(s): Lee, S., Koag, M.C.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesES23101

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2015-01-07
    Type: Database references
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.5: 2017-09-27
    Type: Refinement description