5GKC

The crystal structure of the CPS-6 H148A/F122A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.

Lin, J.L.Wu, C.C.Yang, W.Z.Yuan, H.S.

(2016) Nucleic Acids Res. 44: 10480-10490

  • DOI: 10.1093/nar/gkw931
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endonuclease G (EndoG) is an evolutionarily conserved mitochondrial protein in eukaryotes that digests nucleus chromosomal DNA during apoptosis and paternal mitochondrial DNA during embryogenesis. Under oxidative stress, homodimeric EndoG becomes oxi ...

    Endonuclease G (EndoG) is an evolutionarily conserved mitochondrial protein in eukaryotes that digests nucleus chromosomal DNA during apoptosis and paternal mitochondrial DNA during embryogenesis. Under oxidative stress, homodimeric EndoG becomes oxidized and converts to monomers with diminished nuclease activity. However, it remains unclear why EndoG has to function as a homodimer in DNA degradation. Here, we report the crystal structure of the Caenorhabditis elegans EndoG homologue, CPS-6, in complex with single-stranded DNA at a resolution of 2.3 Å. Two separate DNA strands are bound at the ββα-metal motifs in the homodimer with their nucleobases pointing away from the enzyme, explaining why CPS-6 degrades DNA without sequence specificity. Two obligatory monomeric CPS-6 mutants (P207E and K131D/F132N) were constructed, and they degrade DNA with diminished activity due to poorer DNA-binding affinity as compared to wild-type CPS-6. Moreover, the P207E mutant exhibits predominantly 3'-to-5' exonuclease activity, indicating a possible endonuclease to exonuclease activity change. Thus, the dimer conformation of CPS-6 is essential for maintaining its optimal DNA-binding and endonuclease activity. Compared to other non-specific endonucleases, which are usually monomeric enzymes, EndoG is a unique dimeric endonuclease, whose activity hence can be modulated by oxidation to induce conformational changes.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endonuclease G, mitochondrial
A, B
252Caenorhabditis elegansMutation(s): 2 
Gene Names: cps-6
EC: 3.1.30.-
Find proteins for Q95NM6 (Caenorhabditis elegans)
Go to UniProtKB:  Q95NM6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.614α = 90.00
b = 45.630β = 103.20
c = 80.988γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-04 
  • Released Date: 2016-11-23 
  • Deposition Author(s): Lin, J.L., Yuan, H.S.

Funding OrganizationLocationGrant Number
Academia Sinica and the National Science Council, Taiwan, R.O.CTaiwan--

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references, Derived calculations