3E54

Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

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This is version 1.2 of the entry. See complete history


Literature

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases

Nomura, N.Nomura, Y.Sussman, D.Klein, D.Stoddard, B.L.

(2008) Nucleic Acids Res 36: 6988-6998

  • DOI: 10.1093/nar/gkn846
  • Primary Citation of Related Structures:  
    3E54

  • PubMed Abstract: 
  • The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA t ...

    The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea and in eukarya, by LAGLIDADG and His-Cys box homing endonucleases, respectively. The bases encoded by this target include a universally conserved ribosomal structure, termed helix 69 (H69) in the large ribosomal subunit. This region forms the 'B2a' intersubunit bridge to the small ribosomal subunit, contacts bound tRNA in the A- and P-sites, and acts as a trigger for ribosome disassembly through its interactions with ribosome recycling factor. We have determined the DNA-bound structure and specificity profile of an archaeal LAGLIDADG homing endonuclease (I-Vdi141I) that recognizes this target site, and compared its specificity with the analogous eukaryal His-Cys box endonuclease I-PpoI. These homodimeric endonuclease scaffolds have arrived at similar specificity profiles across their common biological target and analogous solutions to the problem of accommodating conserved asymmetries within the DNA sequence, but with differences at individual base pairs that are fine-tuned to the sequence conservation of archaeal versus eukaryal ribosomes.


    Organizational Affiliation

    Iwata Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Kyoto, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RRNA intron-encoded endonucleaseAB169Vulcanisaeta distributaMutation(s): 2 
Gene Names: 23S rRNA intron (Vdi141.L1927)
EC: 3.1
Find proteins for Q6L703 (Vulcanisaeta distributa)
Explore Q6L703 
Go to UniProtKB:  Q6L703
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')C13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')D9N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')E13N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')F9N/A
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          EOH
          Query on EOH

          Download CCD File 
          D, E, F
          ETHANOL
          C2 H6 O
          LFQSCWFLJHTTHZ-UHFFFAOYSA-N
           Ligand Interaction
          MG
          Query on MG

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

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.50 Å
          • R-Value Free: 0.250 
          • R-Value Work: 0.231 
          • R-Value Observed: 0.231 
          • Space Group: P 61
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 66.58α = 90
          b = 66.58β = 90
          c = 217.91γ = 120
          Software Package:
          Software NamePurpose
          CNSrefinement
          PDB_EXTRACTdata extraction
          HKL-2000data reduction
          SCALEPACKdata scaling
          SOLVEphasing

          Structure Validation

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          Entry History 

          Deposition Data

          Revision History 

          • Version 1.0: 2008-12-30
            Type: Initial release
          • Version 1.1: 2011-07-13
            Changes: Version format compliance
          • Version 1.2: 2014-03-12
            Changes: Derived calculations