Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.34 kDa 
• Atom Count: 8,523 
• Modelled Residue Count: 933 
• Deposited Residue Count: 933 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 4E3S

RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT

• PDB DOI: 10.2210/pdb4E3S/pdb
• NDB: NA1686

• Classification: Transferase/DNA
• Organism(s): Escherichia phage RB69
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-03-10 Released: 2012-05-23 
• Deposition Author(s): Xia, S., Wang, J., Konigsberg, W.H.

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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 

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

• PubMed: 22571765 
• DOI: 10.1021/bi300416z
• Primary Citation of Related Structures:  
  4DU1, 4DU3, 4DU4, 4E3S


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	903	Escherichia phage RB69	Mutation(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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA template	B [auth T]	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA primer	C [auth P]	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QTP	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
CA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 78.166	α = 90
b = 118.509	β = 90
c = 130.667	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Xia, S., Wang, J., Konigsberg, W.H.

Revision History  

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