5DG9

CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dGMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N6-ETHENODEOXYADENOSINE LESION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta.

Patra, A.Su, Y.Zhang, Q.Johnson, K.M.Guengerich, F.P.Egli, M.

(2016) J Biol Chem 291: 14134-14145

  • DOI: https://doi.org/10.1074/jbc.M116.732487
  • Primary Citation of Related Structures:  
    5DG7, 5DG8, 5DG9, 5DGA, 5DGB

  • PubMed Abstract: 

    1,N(6)-Ethenodeoxyadenosine (1,N(6)-ϵdA) is the major etheno lesion formed in the reaction of DNA with epoxides substituted with good leaving groups (e.g. vinyl chloride epoxide). This lesion is also formed endogenously in DNA from lipid oxidation. Recombinant human DNA polymerase η (hpol η) can replicate oligonucleotide templates containing 1,N(6)-ϵdA. In steady-state kinetic analysis, hpol η preferred to incorporate dATP and dGTP, compared with dTTP. Mass spectral analysis of incorporation products also showed preferred purine (A, G) incorporation and extensive -1 frameshifts, suggesting pairing of the inserted purine and slippage before further replication. Five x-ray crystal structures of hpol η ternary complexes were determined, three at the insertion and two at the extension stage. Two insertion complexes revealed incoming non-hydrolyzable dATP or dGTP analogs not pairing with but instead in a staggered configuration relative to 1,N(6)-ϵdA in the anti conformation, thus opposite the 5'-T in the template, explaining the proclivity for frameshift misincorporation. In another insertion complex, dTTP was positioned opposite 1,N(6)-ϵdA, and the adduct base was in the syn conformation, with formation of two hydrogen bonds. At the extension stage, with either an incorporated dA or dT opposite 1,N(6)-ϵdA and 2'-deoxythymidine-5'-[(α,β)-imido]triphosphate opposite the 5'-A, the 3'-terminal nucleoside of the primer was disordered, consistent with the tendency not to incorporate dTTP opposite 1,N(6)-ϵdA. Collectively, the results show a preference for purine pairing opposite 1,N(6)-ϵdA and for -1 frameshifts.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase eta435Homo sapiensMutation(s): 0 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253
GTEx:  ENSG00000170734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y253
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*TP*(EDA)P*AP*TP*GP*AP*CP*GP*CP*T)-3')B [auth T]12synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')C [auth P]8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.929α = 90
b = 98.929β = 90
c = 81.712γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references
  • Version 1.3: 2019-01-16
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description