5DMP

Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.793 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for DNA strand displacement by NHEJ repair polymerases.

Bartlett, E.J.Brissett, N.C.Plocinski, P.Carlberg, T.Doherty, A.J.

(2016) Nucleic Acids Res. 44: 2173-2186

  • DOI: 10.1093/nar/gkv965
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates ...

    The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair.


    Organizational Affiliation

    Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
169Methanocella paludicola (strain DSM 17711 / JCM 13418 / NBRC 101707 / SANAE)Mutation(s): 0 
Find proteins for D1Z0H7 (Methanocella paludicola (strain DSM 17711 / JCM 13418 / NBRC 101707 / SANAE))
Go to UniProtKB:  D1Z0H7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
VN4
Query on VN4

Download SDF File 
Download CCD File 
A
oxido(dioxo)vanadium
O3 V
ALTWGIIQPLQAAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.793 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.070α = 90.00
b = 57.070β = 90.00
c = 105.041γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom(BB/J018643/1)

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references