4ED2

Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 7.2 (Na+ HEPES) with 1 Ca2+ ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Watching DNA polymerase eta make a phosphodiester bond

Nakamura, T.Zhao, Y.Yamagata, Y.Hua, Y.J.Yang, W.

(2012) Nature 487: 196-201

  • DOI: 10.1038/nature11181
  • Primary Citation of Related Structures:  
    4ED0, 4ED1, 4ECQ, 4ED2, 4ECZ, 4ECR, 4ED3, 4ECS, 4ECT, 4ECU

  • PubMed Abstract: 
  • DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase η, DNA and dATP were co-crystallized at pH 6 ...

    DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase η, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.



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*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')T12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8N/A
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP
      Query on DTP

      Download Ideal Coordinates CCD File 
      P
      2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      A
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      A
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.71 Å
      • R-Value Free: 0.206 
      • R-Value Work: 0.170 
      • R-Value Observed: 0.172 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.786α = 90
      b = 98.786β = 90
      c = 82.431γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-07-11
        Type: Initial release
      • Version 1.1: 2012-07-25
        Changes: Database references