1VRR

Crystal structure of the restriction endonuclease BstYI complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Implications for Switching Restriction Enzyme Specificities from the Structure of BstYI Bound to a BglII DNA Sequence.

Townson, S.A.Samuelson, J.C.Xu, S.Y.Aggarwal, A.K.

(2005) Structure 13: 791-801

  • DOI: 10.1016/j.str.2005.02.018
  • Primary Citation of Related Structures:  
    1VRR

  • PubMed Abstract: 
  • The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like ...

    The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.


    Organizational Affiliation

    Structural Biology Program, Department of Physiology & Biophysics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, New York 10029, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BstYIC [auth A], D [auth B]203Geobacillus stearothermophilusMutation(s): 0 
Gene Names: bstYIR
EC: 3.1.21.4
UniProt
Find proteins for Q84AF2 (Geobacillus stearothermophilus)
Explore Q84AF2 
Go to UniProtKB:  Q84AF2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3'A [auth C], B [auth D]14N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.267 
    • R-Value Work: 0.230 
    • R-Value Observed: 0.233 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.58α = 90
    b = 110.91β = 107.17
    c = 80.08γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    CNSrefinement
    HKL-2000data reduction
    CNSphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2005-06-07
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-04-18
      Changes: Data collection