6WK6

Crystal structure of human polymerase eta complexed with Xanthine containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report



Literature

Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase.

Jung, H.Hawkins, M.Lee, S.

(2020) Biochem J 

  • DOI: 10.1042/BCJ20200800
  • Primary Citation of Related Structures:  
    6WK6, 6MQ8

  • PubMed Abstract: 
  • The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively ...

    The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e., xanthine) forms three Watson-Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson-Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.


    Organizational Affiliation

    The University of Texas at Austin, Austin, Texas, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase etaA432Homo sapiensMutation(s): 0 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
NIH Common Fund Data Resources
PHAROS  Q9Y253
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*TP*(3ZO)P*CP*TP*CP*AP*CP*AP*CP*T)-3')T12Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')P8Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      0KX
      Query on 0KX

      Download Ideal Coordinates CCD File 
      A
      2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
      C9 H17 N4 O12 P3
      STYMTWKSQLVXJN-SHYZEUOFSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.35 Å
      • R-Value Free: 0.238 
      • R-Value Work: 0.189 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.93α = 90
      b = 98.93β = 90
      c = 81.552γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      MOLREPphasing

      Structure Validation

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      Entry History 

      Deposition Data

      • Deposited Date: 2020-04-15 
      • Released Date: 2021-01-06 
      • Deposition Author(s): Jung, H., Lee, S.

      Revision History 

      • Version 1.0: 2021-01-06
        Type: Initial release