1LWS

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.287 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.

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

(2002) Nat.Struct.Mol.Biol. 9: 764-770

  • DOI: 10.1038/nsb840
  • Primary Citation of Related Structures:  1LWT

  • PubMed Abstract: 
  • The first X-ray structures of an intein-DNA complex, that of the two-domain homing endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, ...

    The first X-ray structures of an intein-DNA complex, that of the two-domain homing endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50 degree bend in the endonuclease domain and a minor 22 degree bend in the splicing domain region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two cleavage sites in the catalytic center. DNA binding induces changes in the protein conformation. The two overlapping non-identical active sites in the endonucleolytic center contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis indicates that the top strand may be cleaved first.


    Related Citations: 
    • Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity
      Duan, X.,Gimble, F.S.,Quiocho, F.A.
      (1997) Cell 89: 555


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ENDONUCLEASE PI-SCEI
A
454Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: VMA1 (CLS8, TFP1)
EC: 3.1.-.-, 3.6.3.14
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17255
Entity ID: 1
MoleculeChainsLengthOrganism
PI-SceI DNA recognition region top strandB37N/A
Entity ID: 2
MoleculeChainsLengthOrganism
PI-SceI DNA recognition region bottom strandC37N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.287 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.000α = 90.00
b = 123.000β = 90.00
c = 211.700γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance