6K1B

Crystal structure of EXD2 exonuclease domain soaked in Mn and dGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.605 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.

Park, J.Lee, S.Y.Jeong, H.Kang, M.G.Van Haute, L.Minczuk, M.Seo, J.K.Jun, Y.Myung, K.Rhee, H.W.Lee, C.

(2019) Nucleic Acids Res. 47: 7078-7093

  • DOI: 10.1093/nar/gkz454
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • EXD2 (3'-5' exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3'-5' exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break re ...

    EXD2 (3'-5' exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3'-5' exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central α5-α7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.


    Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.,UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exonuclease 3'-5' domain-containing protein 2
A, B
220Homo sapiensMutation(s): 0 
Gene Names: EXD2 (C14orf114, EXDL2)
EC: 3.1.11.1
Find proteins for Q9NVH0 (Homo sapiens)
Go to Gene View: EXD2
Go to UniProtKB:  Q9NVH0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.605 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.339α = 90.00
b = 73.571β = 90.00
c = 131.951γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-10 
  • Released Date: 2019-05-22 
  • Deposition Author(s): Park, J., Lee, C.

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references