4FLT

Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.

Gouge, J.Ralec, C.Henneke, G.Delarue, M.

(2012) J.Mol.Biol. 423: 315-336

  • DOI: 10.1016/j.jmb.2012.07.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination ...

    Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3Å and 2.9Å resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5.


    Organizational Affiliation

    Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase 1
A
793Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 1 
Gene Names: polI (pol)
EC: 2.7.7.7
Find proteins for P0CL77 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P0CL77
Entity ID: 2
MoleculeChainsLengthOrganism
Primer strandP11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
Template strandT13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 2.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.930α = 90.00
b = 114.400β = 90.00
c = 128.580γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
DNAdata collection
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-15 
  • Released Date: 2012-08-29 
  • Deposition Author(s): Gouge, J., Delarue, M.

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Database references