2EZV

Crystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 

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This is version 1.3 of the entry. See complete history


Literature

A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA

Vanamee, E.S.Viadiu, H.Kucera, R.Dorner, L.Picone, S.Schildkraut, I.Aggarwal, A.K.

(2005) EMBO J 24: 4198-4208

  • DOI: 10.1038/sj.emboj.7600880
  • Primary Citation of Related Structures:  
    2EZV, 2F03

  • PubMed Abstract: 
  • Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex with cognate DNA ...

    Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex with cognate DNA. The structures reveal two different binding states of SfiI: one with both DNA-binding sites fully occupied and the other with fully and partially occupied sites. These two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC), and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between the two enzymes, their modes of DNA recognition are unusually similar.


    Related Citations: 
    • Crystallization of restriction endonuclease SfiI in complex with DNA.
      Viadiu, H., Vanamee, E.S., Jacobson, E.M., Schildkraut, I., Aggarwal, A.K.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1493

    Organizational Affiliation

    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Type II restriction enzyme SfiIC [auth A], D [auth B]269N/AMutation(s): 0 
EC: 3.1.21.4
Find proteins for O52512 (Streptomyces fimbriatus)
Explore O52512 
Go to UniProtKB:  O52512
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'A [auth F]21N/A
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'B [auth G]21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.6α = 90
b = 85.6β = 90
c = 202.4γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary