5ZKJ

Human EXOG-H140A in complex with RNA/DNA hybrid duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.

Wu, C.C.Lin, J.L.J.Yang-Yen, H.F.Yuan, H.S.

(2019) Nucleic Acids Res 47: 5405-5419

  • DOI: 10.1093/nar/gkz241
  • Primary Citation of Related Structures:  
    5ZKI, 5ZKJ, 6IID

  • PubMed Abstract: 
  • Replication of sufficient mitochondrial DNA (mtDNA) is essential for maintaining mitochondrial functions in mammalian cells. During mtDNA replication, RNA primers must be removed before the nascent circular DNA strands rejoin. This process involves m ...

    Replication of sufficient mitochondrial DNA (mtDNA) is essential for maintaining mitochondrial functions in mammalian cells. During mtDNA replication, RNA primers must be removed before the nascent circular DNA strands rejoin. This process involves mitochondrial RNase H1, which removes most of the RNA primers but leaves two ribonucleotides attached to the 5' end of nascent DNA. A subsequent 5'-exonuclease is required to remove the residual ribonucleotides, however, it remains unknown if any mitochondrial 5'-exonuclease could remove two RNA nucleotides from a hybrid duplex DNA. Here, we report that human mitochondrial Exonuclease G (ExoG) may participate in this particular process by efficiently cleaving at RNA-DNA junctions to remove the 5'-end RNA dinucleotide in an RNA/DNA hybrid duplex. Crystal structures of human ExoG bound respectively with DNA, RNA/DNA hybrid and RNA-DNA chimeric duplexes uncover the underlying structural mechanism of how ExoG specifically recognizes and cleaves at RNA-DNA junctions of a hybrid duplex with an A-form conformation. This study hence establishes the molecular basis of ExoG functioning as a unique 5'-exonuclease to mediate the flap-independent RNA primer removal process during mtDNA replication to maintain mitochondrial genome integrity.


    Organizational Affiliation

    Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclease EXOG, mitochondrialAB348Homo sapiensMutation(s): 1 
Gene Names: EXOGENDOGL1ENDOGL2ENGL
EC: 3.1.30
Find proteins for Q9Y2C4 (Homo sapiens)
Explore Q9Y2C4 
Go to UniProtKB:  Q9Y2C4
NIH Common Fund Data Resources
PHAROS  Q9Y2C4
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3')C, E12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')D, F12synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CL
      Query on CL

      Download CCD File 
      B
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A, C
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.227 
      • R-Value Work: 0.181 
      • R-Value Observed: 0.183 
      • Space Group: H 3
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 167.576α = 90
      b = 167.576β = 90
      c = 105.438γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2019-04-03
        Type: Initial release
      • Version 1.1: 2019-04-17
        Changes: Data collection, Database references
      • Version 1.2: 2019-06-19
        Changes: Data collection, Database references