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 
  • R-Value Observed: 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 Biol 6: 1096-1099

  • DOI: 10.1038/70027
  • Primary Citation of Related Structures:  
    1CYQ, 1CZ0

  • 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 single metal mechanism ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INTRON-ENCODED HOMING ENDONUCLEASE I-PPOIC [auth A], D [auth B]162Physarum polycephalumMutation(s): 1 
EC: 3.1
UniProt
Find proteins for Q94702 (Physarum polycephalum)
Explore Q94702 
Go to UniProtKB:  Q94702
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'A [auth C], B [auth D]21N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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