3C25

Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.

Lambert, A.R.Sussman, D.Shen, B.Maunus, R.Nix, J.Samuelson, J.Xu, S.Y.Stoddard, B.L.

(2008) Structure 16: 558-569

  • DOI: https://doi.org/10.1016/j.str.2008.01.017
  • Primary Citation of Related Structures:  
    3BVQ, 3C25

  • PubMed Abstract: 

    The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp target 5'-GCGGCCGC-3', has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65 kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys4 motif. This domain positions nearby protein elements for DNA recognition, and serves a structural role. While recognition of the central six base pairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral base pairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.


  • Organizational Affiliation

    Graduate Program in Biomolecular Structure and Design, University of Washington, Seattle, WA 98195, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NotI restriction endonucleaseC [auth A],
D [auth B]
383Nocardia otitidiscaviarumMutation(s): 0 
Gene Names: notIR
UniProt
Find proteins for Q2I6W2 (Nocardia otitidiscaviarum)
Explore Q2I6W2 
Go to UniProtKB:  Q2I6W2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2I6W2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3')A [auth C]22N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3')B [auth D]22N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.89α = 90
b = 81.712β = 99.51
c = 73.583γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description