Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.68 kDa 
• Atom Count: 1010 
• Modelled Residue Count: 97 
• Deposited Residue Count: 97 
• Unique protein chains: 1

1MK0

catalytic domain of intron endonuclease I-TevI, E75A mutant

• PDB DOI: 10.2210/pdb1MK0/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia virus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-08-28 Released: 2002-10-30 
• Deposition Author(s): Van Roey, P., Meehan, L., Kowalski, J.C., Belfort, M., Derbyshire, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.216 
• R-Value Work: 0.197 

Literature

Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.

Van Roey, P., Meehan, L., Kowalski, J.C., Belfort, M., Derbyshire, V.

(2002) Nat Struct Biol 9: 806-811

• PubMed: 12379841 
• DOI: 10.1038/nsb853
• Primary Citation of Related Structures:  
  1LN0, 1MK0


• PubMed Abstract: 
  

I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically widespread catalytic cartridge that is often associated with mobile genetic elements. The crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Similarities in the three-dimensional arrangement of the catalytically important residues and the cation-binding site with those of the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among these different families of homing endonucleases despite completely different folds.

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Organizational Affiliation: 

Wadsworth Center, New York State Department Health, Albany, New York 12201-0509, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intron-associated endonuclease 1	A	97	Escherichia virus T4	Mutation(s): 1  Gene Names: ITEVIR EC: 3.1
UniProt
Find proteins for P13299 (Enterobacteria phage T4) Explore P13299  Go to UniProtKB:  P13299

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.216 
• R-Value Work: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.36	α = 90
b = 39.43	β = 90
c = 97.42	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-28 
• Released Date: 2002-10-30 
Deposition Author(s): Van Roey, P., Meehan, L., Kowalski, J.C., Belfort, M., Derbyshire, V.

Revision History  

• Version 1.0: 2002-10-30
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations