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: 52.14 kDa 
• Atom Count: 3,446 
• Modelled Residue Count: 352 
• Deposited Residue Count: 374 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1U0D

Y33H Mutant of Homing endonuclease I-CreI

• PDB DOI: 10.2210/pdb1U0D/pdb
• NDB: PD0562

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


• Deposited: 2004-07-13 Released: 2004-11-02 
• Deposition Author(s): Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R., Stoddard, B.L., Seligman, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.242 

Literature

Isolation and characterization of new homing endonuclease specificities at individual target site positions.

Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R., Stoddard, B.L., Seligman, L.M.

(2004) J Mol Biol 342: 31-41

• PubMed: 15313605 
• DOI: 10.1016/j.jmb.2004.07.031
• Primary Citation of Related Structures:  
  1U0C, 1U0D


• PubMed Abstract: 
  

Homing endonucleases are highly specific DNA endonucleases, encoded within mobile introns or inteins, that induce targeted recombination, double-strand repair and gene conversion of their cognate target sites. Due to their biological function and high level of target specificity, these enzymes are under intense investigation as tools for gene targeting. These studies require that naturally occurring enzymes be redesigned to recognize novel target sites. Here, we report studies in which the homodimeric LAGLIDADG homing endonuclease I-CreI is altered at individual side-chains corresponding to contact points to distinct base-pairs in its target site. The resulting enzyme constructs drive specific elimination of selected DNA targets in vivo and display shifted specificities of DNA binding and cleavage in vitro. Crystal structures of two of these constructs demonstrate that substitution of individual side-chain/DNA contact patterns can occur with almost no structural deformation or rearrangement of the surrounding complex, facilitating an isolated, modular redesign strategy for homing endonuclease activity and specificity.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025 Seattle, WA 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): 5  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*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'	A [auth C]	24	N/A

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

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1U0D	Kd: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.242 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.838	α = 90.28
b = 70.331	β = 89.94
c = 88.016	γ = 98.78

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-02 
Deposition Author(s): Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R., Stoddard, B.L., Seligman, L.M.

Revision History  

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance