1GPP

Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

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This is version 1.3 of the entry. See complete history


Literature

High Resolution Crystal Structure of Domain I of the Saccharomyces Cerevisiae Homing Endonuclease Pi-Scei

Werner, E.Wende, W.Pingoud, A.Heinemann, U.

(2002) Nucleic Acids Res 30: 3962

  • DOI: 10.1093/nar/gkf523
  • Primary Citation of Related Structures:  
    1GPP

  • PubMed Abstract: 
  • The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid se ...

    The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.


    Organizational Affiliation

    Crystallography Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE PI-SCEIA237Saccharomyces cerevisiaeMutation(s): 4 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt), 3.1 (UniProt)
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17255 
Go to UniProtKB:  P17255
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.856α = 90
b = 47.595β = 121.41
c = 60.297γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection