1A74

I-PPOL HOMING ENDONUCLEASE/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.

Flick, K.E.Jurica, M.S.Monnat Jr., R.J.Stoddard, B.L.

(1998) Nature 394: 96-101

  • DOI: 10.1038/27952
  • Primary Citation of Related Structures:  1A73, 1IPP
  • Also Cited By: 3FC3, 3GOX

  • PubMed Abstract: 
  • Homing endonucleases are a diverse collection of proteins that are encoded by genes with mobile, self-splicing introns. They have also been identified in self-splicing inteins (protein introns). These enzymes promote the movement of the DNA sequences ...

    Homing endonucleases are a diverse collection of proteins that are encoded by genes with mobile, self-splicing introns. They have also been identified in self-splicing inteins (protein introns). These enzymes promote the movement of the DNA sequences that encode them from one chromosome location to another; they do this by making a site-specific double-strand break at a target site in an allele that lacks the corresponding mobile intron. The target sites recognized by these small endonucleases are generally long (14-44 base pairs). Four families of homing endonucleases have been identified, including the LAGLIDADG, the His-Cys box, the GIY-YIG and the H-N-H endonucleases. The first identified His-Cys box homing endonuclease was I-PpoI from the slime mould Physarum polycephalum. Its gene resides in one of only a few nuclear introns known to exhibit genetic mobility. Here we report the structure of the I-PpoI homing endonuclease bound to homing-site DNA determined to 1.8 A resolution. I-PpoI displays an elongated fold of dimensions 25 x 35 x 80 A, with mixed alpha/beta topology. Each I-PpoI monomer contains three antiparallel beta-sheets flanked by two long alpha-helices and a long carboxy-terminal tail, and is stabilized by two bound zinc ions 15 A apart. The enzyme possesses a new zinc-bound fold and endonuclease active site. The structure has been determined in both uncleaved substrate and cleaved product complexes.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Studies of I-Ppoi: A Nuclear, Intron- Encoded Homing Endonuclease from Physarum Polycephalum
      Flick, K.E.,Mchugh, D.,Heath, J.D.,Stephens, K.M.,Monnat Junior, R.J.,Stoddard, B.L.
      (1997) Protein Sci. 6: 2677


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center, University of Washington, Seattle 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTRON-ENCODED ENDONUCLEASE I-PPOI
A, B
163Physarum polycephalumEC: 3.1.-.-
Find proteins for Q94702 (Physarum polycephalum)
Go to UniProtKB:  Q94702
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*A P*GP*TP*CP*A)-3')C,D21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.400α = 90.00
b = 113.400β = 90.00
c = 88.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
PHASESphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-22
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance