4ECY

Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 6.0 (Na+ MES) with 1 Ca2+ ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.943 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 

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:  

  • 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 we ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase eta
A
435Homo sapiensMutation(s): 0 
Gene Names: POLH (RAD30, RAD30A, XPV)
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Go to Gene View: POLH
Go to UniProtKB:  Q9Y253
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')T12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')P8N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.943 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.786α = 90.00
b = 98.786β = 90.00
c = 82.431γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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