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: 52.19 kDa 
• Atom Count: 3,623 
• Modelled Residue Count: 350 
• Deposited Residue Count: 374 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1T9J

I-CreI(Q47E)/DNA complex

• PDB DOI: 10.2210/pdb1T9J/pdb
• NDB: PD0548

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


• Deposited: 2004-05-17 Released: 2004-11-16 
• Deposition Author(s): Chevalier, B., Sussman, D., Otis, C., Boudreau, D., Turmel, M., Lemieux, C., Stephens, K., Monnat Jr., R.J., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease.

Chevalier, B., Sussman, D., Otis, C., Noel, A.J., Turmel, M., Lemieux, C., Stephens, K., Monnat Jr., R.J., Stoddard, B.L.

(2004) Biochemistry 43: 14015-14026

• PubMed: 15518550 
• DOI: 10.1021/bi048970c
• Primary Citation of Related Structures:  
  1T9I, 1T9J


• PubMed Abstract: 
  

The LAGLIDADG homing endonucleases include free-standing homodimers, pseudosymmetric monomers, and related enzyme domains embedded within inteins. DNA-bound structures of homodimeric I-CreI and monomeric I-SceI indicate that three catalytic divalent metal ions are distributed across a pair of overlapping active sites, with one shared metal participating in both strand cleavage reactions. These structures differ in the precise position and binding interactions of the metals. We have studied the metal dependence for the I-CreI homodimer using site-directed mutagenesis of active site residues and assays of binding affinity and cleavage activity. We have also reassessed the binding of a nonactivating metal ion (calcium) in the wild-type enzyme-substrate complex, and determined the DNA-bound structure of two inactive enzyme mutants. The conclusion of these studies is that the catalytic mechanism of symmetric LAGLIDADG homing endonucleases, and probably many of their monomeric cousins, involves a canonical two-metal mechanism in each of two active sites, which are chemically and structurally tethered to one another by a shared metal ion. Failure to occupy the shared metal site, as observed in the presence of calcium or when the metal-binding side chain from the LAGLIDADG motif (Asp 20) is mutated to asparagine, prevents cleavage by the enzyme.

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Organizational Affiliation: 

Graduate Program in Molecular and Cellular Biology, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North A3-025, 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]	163	Chlamydomonas reinhardtii	Mutation(s): 1  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(*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'	A [auth C]	24	N/A

Entity ID: 2
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'	B [auth D]	24	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1T9J	Kd: 0.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.11	α = 90
b = 67.86	β = 91.55
c = 87.65	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-16 
Deposition Author(s): Chevalier, B., Sussman, D., Otis, C., Boudreau, D., Turmel, M., Lemieux, C., Stephens, K., Monnat Jr., R.J., Stoddard, B.L.

Revision History  

• Version 1.0: 2004-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-07
  Changes: Experimental preparation
• Version 1.4: 2021-10-27
  Changes: Database references