1R7M

The homing endonuclease I-SceI bound to its DNA recognition region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity

Moure, C.M.Gimble, F.S.Quiocho, F.A.

(2003) J Mol Biol 334: 685-695

  • DOI: 10.1016/j.jmb.2003.09.068
  • Primary Citation of Related Structures:  
    1R7M

  • PubMed Abstract: 
  • The I-SceI homing endonuclease enhances gene targeting by introducing double-strand breaks at specific chromosomal loci, thereby increasing the recombination frequency. Here, we report the crystal structure of the enzyme complexed to its DNA substrat ...

    The I-SceI homing endonuclease enhances gene targeting by introducing double-strand breaks at specific chromosomal loci, thereby increasing the recombination frequency. Here, we report the crystal structure of the enzyme complexed to its DNA substrate and Ca(2+) determined at 2.25A resolution. The structure shows the prototypical beta-saddle of LAGLIDADG homing endonucleases that is contributed by two pseudo-symmetric domains. The high specificity of I-SceI is explained by the large number of protein-DNA contacts, many that are made by a long beta-hairpin loop that reaches into the major groove of the DNA. The DNA minor groove is compressed at the catalytic center, bringing the two scissile phosphodiester bonds into close proximity. The protein-Ca(2+)-DNA structure shows the protein bound to its DNA substrate in a pre-reactive state that is defined by the presence of two asymmetric active sites, one of which appears poised to first cleave the DNA bottom strand.


    Organizational Affiliation

    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-encoded endonuclease I-SceIAB235Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SECY
EC: 3.1
Find proteins for P03882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03882 
Go to UniProtKB:  P03882
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3'C, E25N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3'D, F25N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B, C, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.6α = 90
b = 90.7β = 90
c = 115.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance