3C2M

Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.

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

(2008) Mol Cell 30: 315-324

  • DOI: 10.1016/j.molcel.2008.02.025
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substit ...

    We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substituting Mn(2+) for Mg(2+) significantly decreases the fidelity of DNA synthesis. The structures reveal that the enzyme is in a closed conformation like that observed with a matched Watson-Crick base pair. The incorrect dAMPCPP binds in a conformation identical to that observed with the correct nucleotide. To accommodate the incorrect nucleotide and closed protein conformation, the template strand in the vicinity of the active site has shifted upstream over 3 A, removing the coding base from the active site and generating an abasic templating pocket. The primer terminus rotates as its complementary template base is repositioned. This rotation moves O3' of the primer terminus away from the alpha-phosphate of the incoming nucleotide, thereby deterring misincorporation.

    Organizational Affiliation: 

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335N/AMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06746 (Homo sapiens)
Go to UniProtKB:  P06746
NIH Common Fund Data Resources
PHAROS  P06746
GTEx  ENSG00000070501
Protein Feature View
  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DGP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3')T16N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3')P10N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DTP*DCP*DGP*DG)-3')D5N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F2A
Query on F2A
Download CCD File 
A
2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
C11 H18 N5 O11 P3
XETARULVTCYJAN-XLPZGREQSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
A, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download CCD File 
A, T
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download CCD File 
A, P, T
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F2AKi:  5000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.75α = 90
b = 78.37β = 113.36
c = 55.17γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance