5CNQ

Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA, Mg2+ and Mn2+ ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.602 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.

Liu, Y.Freeman, A.D.Declais, A.C.Wilson, T.J.Gartner, A.Lilley, D.M.

(2015) Cell Rep 13: 2565-2575

  • DOI: 10.1016/j.celrep.2015.11.042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolut ...

    We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.


    Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Center for Gene Regulation and Expression, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: d.m.j.lilley@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease-like protein
A
464Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RYN2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYN2
Entity ID: 2
MoleculeChainsLengthOrganism
RR16Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')H15Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.602 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.582α = 90.00
b = 98.582β = 90.00
c = 119.619γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references