Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62271.25 
• Atom Count: 3996 
• Residue Count: 520 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

5GKP

Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A in complex with DNA

• DOI: 10.2210/pdb5GKP/pdb
• NDB: 5GKP

• Classification: HYDROLASE/DNA
• Organism(s): unidentified, Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2016-07-05 Released: 2016-11-23 
• Deposition Author(s): Lin, J.L., Yuan, H.S.
• Funding Organization(s): Academia Sinica and the National Science Council, Taiwan 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.173 

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

• PubMed: 27738134 
• DOI: 10.1093/nar/gkw931
• Primary Citation of Related Structures:  
  5GKC


• 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 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.

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Related Citations: 

• StructuralInsightsintoApoptoticDNADegradationbyCED-3 ProteaseSuppressor-6(CPS-6)fromCaenorhabditiselegans
  Lin, J.L.,Yuan, H.S.
  (2012) J.BIOL.CHEM. 287: 7110




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Endonuclease G, mitochondrial	A, B	252	Caenorhabditis elegans	Mutation(s): 2  Gene Names: cps-6 EC: 3.1.30.-
Find proteins for Q95NM6 (Caenorhabditis elegans) Go to UniProtKB:  Q95NM6

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*TP*TP*TP*T)-3')	C,D	8	unidentified

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.672	α = 90.00
b = 72.562	β = 90.00
c = 127.914	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-07-05 
• Released Date: 2016-11-23 
• Deposition Author(s): Lin, J.L., Yuan, H.S.

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Funding Organization	Location	Grant Number
Academia Sinica and the National Science Council, Taiwan	Taiwan	--

Revision History 

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