1LWS

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

• PDB DOI: https://doi.org/10.2210/pdb1LWS/pdb
• NAKB: 1LWS

• Classification: HYDROLASE/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-06-03 Released: 2002-09-27 
• Deposition Author(s): Moure, C.M., Gimble, F.S., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.287 

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 Biol 9: 764-770

• PubMed: 12219083 
• DOI: https://doi.org/10.1038/nsb840
• Primary Citation of Related Structures:  
  1LWS, 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, 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.23 kDa 
• Atom Count: 4,756 
• Modelled Residue Count: 495 
• Deposited Residue Count: 528 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDONUCLEASE PI-SCEI	C [auth A]	454	Saccharomyces cerevisiae	Mutation(s): 8  Gene Names: VMA1 EC: 3.1
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17255  Go to UniProtKB:  P17255

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PI-SceI DNA recognition region top strand	A [auth B]	37	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
PI-SceI DNA recognition region bottom strand	B [auth C]	37	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	C [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.287 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123	α = 90
b = 123	β = 90
c = 211.7	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-27 
Deposition Author(s): Moure, C.M., Gimble, F.S., Quiocho, F.A.

Revision History  

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