5UGP

DNA polymerase beta complex with a 1nt gap and dCMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.955 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction.

Shock, D.D.Freudenthal, B.D.Beard, W.A.Wilson, S.H.

(2017) Nat. Chem. Biol. 13: 1074-1080

  • DOI: 10.1038/nchembio.2450
  • Primary Citation of Related Structures:  5UGN, 5UGO

  • PubMed Abstract: 
  • DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleos ...

    DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleoside triphosphates. Because pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that this reaction was limited by a nonchemical step. Use of a pyrophosphate analog, in which the bridging oxygen is replaced with an imido group (PNP), increased the rate of the reverse reaction and displayed a large thio-elemental effect, indicating that chemistry was now rate determining. Time-lapse crystallography with PNP captured structures consistent with a chemical equilibrium favoring the reverse reaction. These results highlight the importance of the bridging atom between the β- and γ-phosphates of the incoming nucleotide in reaction chemistry, enzyme conformational changes, and overall reaction equilibrium.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo sapiensGene 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
DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')P10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T16synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
8CP
Query on 8CP

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine
C9 H17 N4 O12 P3
ICHPBSCTWPZUQK-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.955 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.784α = 90.00
b = 79.966β = 107.68
c = 55.454γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesES024431

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Author supporting evidence
  • Version 1.2: 2017-08-16
    Type: Database references
  • Version 1.3: 2017-10-04
    Type: Database references