1CZ0

INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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 Biol 6: 1096-1099

  • DOI: 10.1038/70027
  • Structures With Same Primary Citation

  • 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): 0 
EC: 3.1
Find proteins for Q94702 (Physarum polycephalum)
Go to UniProtKB:  Q94702
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (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 CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.866α = 90
b = 113.866β = 90
c = 89.04γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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