5DB8

Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.547 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.

Kou, Y.Koag, M.C.Lee, S.

(2015) J.Am.Chem.Soc. 137: 14067-14070

  • DOI: 10.1021/jacs.5b10172
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methy ...

    N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polĪ²-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polĪ²-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.


    Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo 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*GP*TP*CP*GP*CP*AP*TP*AP*AP*GP*C)-3')T16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*(FMG)P*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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FMG
Query on FMG
P
DNA linkingC11 H16 F N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.547 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.149α = 90.00
b = 78.904β = 105.39
c = 54.751γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-08-21 
  • Released Date: 2015-11-11 
  • Deposition Author(s): Koag, M.C., Lee, S.

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references