3C0W

I-SceI in complex with a bottom nicked DNA substrate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.268 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.

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

(2008) Nucleic Acids Res 36: 3287-3296

  • DOI: https://doi.org/10.1093/nar/gkn178
  • Primary Citation of Related Structures:  
    3C0W, 3C0X

  • PubMed Abstract: 

    • I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage ...

    I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.

    Organizational Affiliation: 

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. mmoure@bcm.tmc.edu



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-encoded endonuclease I-SceID [auth A]235Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCEI, OMEGA, SECY
EC: 3.1
UniProt
Find proteins for P03882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03882 
Go to UniProtKB:  P03882
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03882
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DAP*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3')A [auth B]24N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DT)-3')B [auth C]15N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3')C [auth D]9N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth B],
F [auth A],
H [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.61α = 90
b = 80.61β = 90
c = 127.09γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description