Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.89 kDa 
• Atom Count: 3,890 
• Modelled Residue Count: 352 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1G9Y

HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM

• PDB DOI: 10.2210/pdb1G9Y/pdb
• NDB: PD0189

• Classification: HYDROLASE/DNA
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-11-28 Released: 2001-04-02 
• Deposition Author(s): Chevalier, B., Monnat, R.J., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.260 
• R-Value Work: 0.207 

Literature

The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.

Chevalier, B.S., Monnat Jr., R.J., Stoddard, B.L.

(2001) Nat Struct Biol 8: 312-316

• PubMed: 11276249 
• DOI: 10.1038/86181
• Primary Citation of Related Structures:  
  1G9Y, 1G9Z


• PubMed Abstract: 
  

Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target sites. The cleavage mechanism(s) utilized by LAGLIDADG endonucleases have been difficult to elucidate; their active sites are divergent, and only one low resolution cocrystal structure has been determined. Here we report two high resolution structures of the dimeric I-CreI homing endonuclease bound to DNA: a substrate complex with calcium and a product complex with magnesium. The bound metals in both complexes are verified by manganese anomalous difference maps. The active sites are positioned close together to facilitate cleavage across the DNA minor groove; each contains one metal ion bound between a conserved aspartate (Asp 20) and a single scissile phosphate. A third metal ion bridges the two active sites. This divalent cation is bound between aspartate residues from the active site of each subunit and is in simultaneous contact with the scissile phosphates of both DNA strands. A metal-bound water molecule acts as the nucleophile and is part of an extensive network of ordered water molecules that are positioned by enzyme side chains. These structures illustrate a unique variant of a two-metal endonuclease mechanism is employed by the highly divergent LAGLIDADG enzyme family.

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Organizational Affiliation: 

Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave. N. A3-023, Seattle, Washington 98109, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ENDONUCLEASE I-CREI	C [auth A], D [auth B]	152	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: CR.LSU INTRON OF CHOROPLAST 23S RRNA GENE EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3'	A [auth C]	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3'	B [auth D]	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth C], F [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.260 
• R-Value Work: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.2	α = 90
b = 67.8	β = 91.6
c = 88.3	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-02 
Deposition Author(s): Chevalier, B., Monnat, R.J., Stoddard, B.L.

Revision History  

• Version 1.0: 2001-04-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance