2F03

Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


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:  

  • 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 tet ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Type II restriction enzyme SfiI
A, C
269Streptomyces fimbriatusMutation(s): 0 
Gene Names: sfiIR
EC: 3.1.21.4
Find proteins for O52512 (Streptomyces fimbriatus)
Go to UniProtKB:  O52512
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')E,G21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')F,H21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.241 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.600α = 90.00
b = 85.600β = 90.00
c = 418.700γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-09-09
    Type: Version format compliance