6K19

Crystal structure of EXD2 exonuclease domain soaked in Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1093/nar/gkz454
  • Primary Citation of Related Structures:  
    6K17, 6K18, 6K19, 6K1A, 6K1B, 6K1C, 6K1D, 6K1E

  • 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 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

    Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exonuclease 3'-5' domain-containing protein 2
A, B
220Homo sapiensMutation(s): 0 
Gene Names: EXD2C14orf114EXDL2
EC: 3.1.11.1 (PDB Primary Data), 3.1.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVH0 (Homo sapiens)
Explore Q9NVH0 
Go to UniProtKB:  Q9NVH0
PHAROS:  Q9NVH0
GTEx:  ENSG00000081177 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVH0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.347α = 90
b = 74.107β = 90
c = 133.477γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description