3E54

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


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

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RRNA intron-encoded endonuclease
A, B
169Vulcanisaeta distributaMutation(s): 2 
Find proteins for Q6L703 (Vulcanisaeta distributa)
Go to UniProtKB:  Q6L703
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')C13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')D9N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')E13N/A
Entity ID: 5
MoleculeChainsLengthOrganism
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
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
D, E, F
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.231 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 66.580α = 90.00
b = 66.580β = 90.00
c = 217.910γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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