3OGU

DNA Polymerase beta mutant 5P20 complexed with 6bp of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.845 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Human DNA polymerase beta mutations allowing efficient abasic site bypass.

Gieseking, S.Bergen, K.Di Pasquale, F.Diederichs, K.Welte, W.Marx, A.

(2011) J.Biol.Chem. 286: 4011-4020

  • DOI: 10.1074/jbc.M110.176826

  • PubMed Abstract: 
  • The DNA of every cell in the human body gets damaged more than 50,000 times a day. The most frequent damages are abasic sites. This kind of damage blocks proceeding DNA synthesis by several DNA polymerases that are involved in DNA replication and rep ...

    The DNA of every cell in the human body gets damaged more than 50,000 times a day. The most frequent damages are abasic sites. This kind of damage blocks proceeding DNA synthesis by several DNA polymerases that are involved in DNA replication and repair. The mechanistic basis for the incapability of these DNA polymerases to bypass abasic sites is not clarified. To gain insights into the mechanistic basis, we intended to identify amino acid residues that govern for the pausing of DNA polymerase β when incorporating a nucleotide opposite to abasic sites. Human DNA polymerase β was chosen because it is a well characterized DNA polymerase and serves as model enzyme for studies of DNA polymerase mechanisms. Moreover, it acts as the main gap-filling enzyme in base excision repair, and human tumor studies suggest a link between DNA polymerase β and cancer. In this study we employed high throughput screening of a library of more than 11,000 human DNA polymerase β variants. We identified two mutants that have increased ability to incorporate a nucleotide opposite to an abasic site. We found that the substitutions E232K and T233I promote incorporation opposite the lesion. In addition to this feature, the variants have an increased activity and a lower fidelity when processing nondamaged DNA. The mutations described in this work are located in well characterized regions but have not been reported before. A crystallographic structure of one of the mutants was obtained, providing structural insights.


    Organizational Affiliation

    Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78464 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo sapiensMutation(s): 4 
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
5'-D(*CP*AP*TP*CP*TP*G)-3'T6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(P*CP*AP*GP*AP*TP*G)-3'P6N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, P
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.845 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 175.474α = 90.00
b = 56.782β = 90.00
c = 47.602γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XDSdata scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description