1CYQ

INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel endonuclease mechanism directly visualized for I-PpoI.

Galburt, E.A.Chevalier, B.Tang, W.Jurica, M.S.Flick, K.E.Monnat Jr., R.J.Stoddard, B.L.

(1999) Nat.Struct.Mol.Biol. 6: 1096-1099

  • DOI: 10.1038/70027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the previously visualized product complex. This enzyme employs a unique si ...

    A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the previously visualized product complex. This enzyme employs a unique single metal mechanism. A magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule is activated by a histidine residue for an in-line attack on the scissile phosphate. A strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the reaction.


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center and the Graduate Programs in Molecular and Cell Biology and Biomolecular Structure and Design, University of Washington, 1100 Fairview Ave. N. A3-023, Seattle, Washington 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI
A, B
162Physarum polycephalumMutation(s): 1 
EC: 3.1.-.-
Find proteins for Q94702 (Physarum polycephalum)
Go to UniProtKB:  Q94702
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'C,D21N/A
Small Molecules
Ligands 2 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
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.866α = 90.00
b = 113.866β = 90.00
c = 89.040γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance