5EWG

Ternary complex of human DNA polymerase eta inserting rATP opposite an 8-Oxodeoxyguanosine Lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta.

Su, Y.Egli, M.Guengerich, F.P.

(2016) J Biol Chem 291: 3747-3756

  • DOI: 10.1074/jbc.M115.706226
  • Primary Citation of Related Structures:  
    5EWF, 5EWE, 5EWG

  • PubMed Abstract: 
  • Ribonucleotides and 2'-deoxyribonucleotides are the basic units for RNA and DNA, respectively, and the only difference is the extra 2'-OH group on the ribonucleotide sugar. Cellular rNTP concentrations are much higher than those of dNTP. When copying DNA, DNA polymerases not only select the base of the incoming dNTP to form a Watson-Crick pair with the template base but also distinguish the sugar moiety ...

    Ribonucleotides and 2'-deoxyribonucleotides are the basic units for RNA and DNA, respectively, and the only difference is the extra 2'-OH group on the ribonucleotide sugar. Cellular rNTP concentrations are much higher than those of dNTP. When copying DNA, DNA polymerases not only select the base of the incoming dNTP to form a Watson-Crick pair with the template base but also distinguish the sugar moiety. Some DNA polymerases use a steric gate residue to prevent rNTP incorporation by creating a clash with the 2'-OH group. Y-family human DNA polymerase η (hpol η) is of interest because of its spacious active site (especially in the major groove) and tolerance of DNA lesions. Here, we show that hpol η maintains base selectivity when incorporating rNTPs opposite undamaged DNA and the DNA lesions 7,8-dihydro-8-oxo-2'-deoxyguanosine and cyclobutane pyrimidine dimer but with rates that are 10(3)-fold lower than for inserting the corresponding dNTPs. X-ray crystal structures show that the hpol η scaffolds the incoming rNTP to pair with the template base (dG) or 7,8-dihydro-8-oxo-2'-deoxyguanosine with a significant propeller twist. As a result, the 2'-OH group avoids a clash with the steric gate, Phe-18, but the distance between primer end and Pα of the incoming rNTP increases by 1 Å, elevating the energy barrier and slowing polymerization compared with dNTP. In addition, Tyr-92 was identified as a second line of defense to maintain the position of Phe-18. This is the first crystal structure of a DNA polymerase with an incoming rNTP opposite a DNA lesion.


    Organizational Affiliation

    From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146 f.guengerich@vanderbilt.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo 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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')T12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ATP
      Query on ATP

      Download Ideal Coordinates CCD File 
      A
      ADENOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O13 P3
      ZKHQWZAMYRWXGA-KQYNXXCUSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      A
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.75 Å
      • R-Value Free: 0.215 
      • R-Value Work: 0.178 
      • R-Value Observed: 0.180 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 99.024α = 90
      b = 99.024β = 90
      c = 81.571γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing
      ARPmodel building
      Cootmodel building

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR01 ES010375
      National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA160032

      Revision History  (Full details and data files)

      • Version 1.0: 2016-01-13
        Type: Initial release
      • Version 1.1: 2016-01-20
        Changes: Database references
      • Version 1.2: 2016-03-02
        Changes: Database references
      • Version 1.3: 2017-09-13
        Changes: Author supporting evidence, Database references, Derived calculations
      • Version 1.4: 2019-12-04
        Changes: Author supporting evidence