1T2T

Crystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.

Edgell, D.R.Derbyshire, V.Van Roey, P.LaBonne, S.Stanger, M.J.Li, Z.Boyd, T.M.Shub, D.A.Belfort, M.

(2004) Nat.Struct.Mol.Biol. 11: 936-944

  • DOI: 10.1038/nsmb823

  • PubMed Abstract: 
  • Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless alleles, at the so-called homing sites. Here, we describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron o ...

    Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless alleles, at the so-called homing sites. Here, we describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron of phage T4. This site is an operator that overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the operator and homing sites with equal affinity, and functions as a transcriptional autorepressor. Distinct sequence and spacing requirements of the catalytic domain result in reduced cleavage activity on operator DNA. Crystallographic studies showed that the overall interactions of the DNA-binding domain with the operator and homing sites are similar, but have some different hydrogen-bonding contacts. We present a model in which the flexibility in protein-DNA interactions allows I-TevI to bind variant intronless alleles to promote intron mobility while facilitating its function in autorepression, and thereby persistence in its host.


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Center for Medical Sciences, 150 New Scotland Avenue, Albany, New York 12208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Intron-associated endonuclease 1
A
116Enterobacteria phage T4Gene Names: ITEVIR
EC: 3.1.-.-
Find proteins for P13299 (Enterobacteria phage T4)
Go to UniProtKB:  P13299
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*GP*TP*AP*GP*GP*AP*CP*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*T)-3'B21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3'C21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.660α = 90.00
b = 64.890β = 90.48
c = 42.810γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance