1I3J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 

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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
  • Primary Citation of 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 ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
INTRON-ASSOCIATED ENDONUCLEASE 1C [auth A]116Escherichia virus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
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]21N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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]21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.14α = 90
b = 65.21β = 93.1
c = 43.67γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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