4E3S

RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.

Xia, S.Christian, T.D.Wang, J.Konigsberg, W.H.

(2012) Biochemistry 51: 4343-4353

  • DOI: 10.1021/bi300416z
  • Primary Citation of Related Structures:  
    4E3S, 4DU1, 4DU3, 4DU4

  • PubMed Abstract: 
  • Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension ...

    Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n - 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA903Escherichia phage RB69Mutation(s): 3 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA templateB [auth T]17N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA primerC [auth P]13N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      QTP (Subject of Investigation/LOI)
      Query on QTP

      Download Ideal Coordinates CCD File 
      D [auth A]3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine
      C12 H18 N3 O12 P3
      LSFMZRZQGVHWHK-IVZWLZJFSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.04 Å
      • R-Value Free: 0.219 
      • R-Value Work: 0.180 
      • R-Value Observed: 0.182 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 78.166α = 90
      b = 118.509β = 90
      c = 130.667γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      AMoREphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-05-23
        Type: Initial release
      • Version 1.1: 2012-08-15
        Changes: Database references