4FLY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.jmb.2012.07.025
  • Primary Citation of Related Structures:  
    4FLT, 4FLU, 4FLV, 4FLW, 4FLX, 4FLY, 4FLZ, 4FM0, 4FM1, 4FM2

  • 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 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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase 1C [auth A]793Pyrococcus abyssi GE5Mutation(s): 1 
Gene Names: polIpolPYRAB17200PAB1128
EC: 2.7.7.7
UniProt
Find proteins for P0CL77 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore P0CL77 
Go to UniProtKB:  P0CL77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL77
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
Template strandA [auth T]13synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Primer strandB [auth P]8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.1α = 90
b = 114.34β = 90
c = 128.58γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description