1I3J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1093/emboj/20.14.3631

  • 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 su ...

    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.


    Organizational Affiliation

    Wadsworth Center, PO Box 509, Albany, NY 12201-0509, USA. vanroey@wadsworth.org




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INTRON-ASSOCIATED ENDONUCLEASE 1
A
116Enterobacteria phage T4Mutation(s): 0 
Gene Names: ITEVIR
EC: 3.1.-.-
Find proteins for P13299 (Enterobacteria phage T4)
Go to UniProtKB:  P13299
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3'B21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*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: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.140α = 90.00
b = 65.210β = 93.10
c = 43.670γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance