1T2T | pdb_00001t2t

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.274 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1T2T

This is version 1.3 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: https://doi.org/10.1038/nsmb823
  • Primary Citation Related Structures: 
    1T2T

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 26.19 kDa 
  • Atom Count: 1,697 
  • Modeled Residue Count: 138 
  • Deposited Residue Count: 158 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Intron-associated endonuclease 1C [auth A]116Tequatrovirus T4Mutation(s): 0 
Gene Names: ITEVIR
EC: 3.1
UniProt
Find proteins for P13299 (Enterobacteria phage T4)
Explore P13299 
Go to UniProtKB:  P13299
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13299
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*TP*GP*TP*AP*GP*GP*AP*CP*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*T)-3'A [auth B]21N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3'B [auth C]21N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.66α = 90
b = 64.89β = 90.48
c = 42.81γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description