1CYQ

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

• PDB DOI: https://doi.org/10.2210/pdb1CYQ/pdb
• NAKB: 1CYQ

• Classification: HYDROLASE/DNA
• Organism(s): Physarum polycephalum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-08-31 Released: 1999-11-19 
• Deposition Author(s): Galburt, E.A., Chevalier, B., Jurica, M.S., Flick, K.E., Stoddard, B.L.

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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 

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

• PubMed: 10581547 
• DOI: https://doi.org/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 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.41 kDa 
• Atom Count: 3,680 
• Modelled Residue Count: 366 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INTRON-ENCODED HOMING ENDONUCLEASE I-PPOI	C [auth A], D [auth B]	162	Physarum polycephalum	Mutation(s): 1  EC: 3.1
UniProt
Find proteins for Q94702 (Physarum polycephalum) Explore Q94702  Go to UniProtKB:  Q94702

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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]	21	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth C], F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 113.866	α = 90
b = 113.866	β = 90
c = 89.04	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-19 
Deposition Author(s): Galburt, E.A., Chevalier, B., Jurica, M.S., Flick, K.E., Stoddard, B.L.

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
• Version 1.3: 2021-11-03
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection