3QQY | pdb_00003qqy

Crystal structure of a novel LAGLIDADG homing endonuclease, I-OnuI (from Ophiostoma novo-ulmi subsp. americana)

• PDB DOI: https://doi.org/10.2210/pdb3QQY/pdb
• NAKB: 3QQY

• Classification: HYDROLASE/DNA
• Organism(s): Ophiostoma novo-ulmi subsp. americana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-16 Released: 2011-07-20 
• Deposition Author(s): Takeuchi, R., Stoddard, B.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Tapping natural reservoirs of homing endonucleases for targeted gene modification.

Takeuchi, R., Lambert, A.R., Mak, A.N., Jacoby, K., Dickson, R.J., Gloor, G.B., Scharenberg, A.M., Edgell, D.R., Stoddard, B.L.

(2011) Proc Natl Acad Sci U S A 108: 13077-13082

• PubMed: 21784983 
• DOI: https://doi.org/10.1073/pnas.1107719108
• Primary Citation Related Structures: 
  3QQY, 3R7P


• PubMed Abstract: 
  

  Homing endonucleases mobilize their own genes by generating double-strand breaks at individual target sites within potential host DNA. Because of their high specificity, these proteins are used for "genome editing" in higher eukaryotes. However, alteration of homing endonuclease specificity is quite challenging. Here we describe the identification and phylogenetic analysis of over 200 naturally occurring LAGLIDADG homing endonucleases (LHEs). Biochemical and structural characterization of endonucleases from one clade within the phylogenetic tree demonstrates strong conservation of protein structure contrasted against highly diverged DNA target sites and indicates that a significant fraction of these proteins are sufficiently stable and active to serve as engineering scaffolds. This information was exploited to create a targeting enzyme to disrupt the endogenous monoamine oxidase B gene in human cells. The ubiquitous presence and diversity of LHEs described in this study may facilitate the creation of many tailored nucleases for genome editing.

---

Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North A3-025, Seattle, WA 98109, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.17 kDa 
• Atom Count: 3,553 
• Modeled Residue Count: 351 
• Deposited Residue Count: 359 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein 3/homing endonuclease-like protein fusion	A	307	Ophiostoma novo-ulmi subsp. americana	Mutation(s): 0  Gene Names: rps3/HEG fusion
UniProt
Find proteins for Q4VWW5 (Ophiostoma novo-ulmi subsp. americana) Explore Q4VWW5  Go to UniProtKB:  Q4VWW5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	B	26	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	C	26	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.948	α = 90
b = 73.933	β = 90
c = 166.93	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Takeuchi, R., Stoddard, B.L.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-08-10
  Changes: Database references
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description