1I3J | pdb_00001i3j

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

• PDB DOI: https://doi.org/10.2210/pdb1I3J/pdb
• NAKB: 1I3J

• Classification: HYDROLASE/DNA
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-02-15 Released: 2001-07-13 
• Deposition Author(s): Van Roey, P., Waddling, C.A., Fox, K.M., Belfort, M., Derbyshire, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.215 (Depositor), 0.232 (DCC) 

Literature

Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.

Van Roey, P., Waddling, C.A., Fox, K.M., Belfort, M., Derbyshire, V.

(2001) EMBO J 20: 3631-3637

• PubMed: 11447104 
• DOI: https://doi.org/10.1093/emboj/20.14.3631
• Primary Citation Related Structures: 
  1I3J


• PubMed Abstract: 
  

  I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target reveals an unusually extended structure composed of three subdomains: a Zn finger, an elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The protein wraps around the DNA, mostly following the minor groove, contacting the phosphate backbone along the full length of the duplex. Surprisingly, while the minor groove-binding helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion site. The multiple base-specific interactions over a long segment of the substrate are consistent with the observed high site specificity in spite of sequence tolerance, while the modular composition of the domain is pertinent to the evolution of homing endonucleases.

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Organizational Affiliation: 
• Wadsworth Center, PO Box 509, Albany, NY 12201-0509, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.19 kDa 
• Atom Count: 1,823 
• Modeled Residue Count: 138 
• Deposited Residue Count: 158 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
INTRON-ASSOCIATED ENDONUCLEASE 1	C [auth A]	116	Tequatrovirus T4	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P13299 (Enterobacteria phage T4) Explore P13299  Go to UniProtKB:  P13299

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3'	A [auth B]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*A)-3'	B [auth C]	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.215 (Depositor), 0.232 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.14	α = 90
b = 65.21	β = 93.1
c = 43.67	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-13 
Deposition Author(s): Van Roey, P., Waddling, C.A., Fox, K.M., Belfort, M., Derbyshire, V.

Revision History  

• Version 1.0: 2001-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Advisory, Data collection, Database references, Derived calculations