5DB6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/jacs.5b10172
  • Primary Citation of Related Structures:  
    5DB6, 5DB7, 5DB8, 5DB9, 5DBA, 5DBB, 5DBC

  • 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-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polβ-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 polβ-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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase beta335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
GTEx:  ENSG00000070501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')B [auth T]16Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3')C [auth P]10Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*GP*G)-3')5Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.138α = 90
b = 78.828β = 105.92
c = 54.764γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
StructureStudiodata collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy