5KFK

Human DNA polymerase eta-DNA ternary complex: reaction with 10 mM Mn2+ for 300s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Capture of a third Mg2+ is essential for catalyzing DNA synthesis.

Gao, Y.Yang, W.

(2016) Science 352: 1334-1337

  • DOI: 10.1126/science.aad9633
  • Primary Citation of Related Structures:  
    5L9X, 5KFI, 5KFH, 5KFK, 5KFJ, 5KFM, 5KFL, 5KFO, 5KG0, 5KFN

  • PubMed Abstract: 
  • It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound ...

    It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. wei.yang@nih.gov.



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
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  • 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')T12Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')P9Homo sapiens
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.210 
      • R-Value Work: 0.172 
      • R-Value Observed: 0.175 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.27α = 90
      b = 98.27β = 90
      c = 82.01γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XSCALEdata scaling
      PDB_EXTRACTdata extraction
      XDSdata reduction
      MOLREPphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2016-06-12 
      • Released Date: 2016-06-22 
      • Deposition Author(s): Gao, Y., Yang, W.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesIntramural DK036146-08

      Revision History  (Full details and data files)

      • Version 1.0: 2016-06-22
        Type: Initial release
      • Version 1.1: 2017-09-20
        Changes: Author supporting evidence, Database references, Derived calculations
      • Version 1.2: 2019-12-25
        Changes: Author supporting evidence