5J0R

Binary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.

Batra, V.K.Beard, W.A.Pedersen, L.C.Wilson, S.H.

(2016) Structure 24: 1863-1875

  • DOI: 10.1016/j.str.2016.08.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the┬ápolymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic s ...

    High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709-12233, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
Template StrandT16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Primer StrandP10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
Downstream Primer StrandD5synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.590α = 90.00
b = 79.490β = 105.58
c = 55.000γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
CNSphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references