2GB7

Metal-depleted Ecl18kI in complex with uncleaved, modified DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease

Bochtler, M., Szczepanowski, R.H., Tamulaitis, G., Grazulis, S., Czapinska, H., Manakova, E., Siksnys, V.

(2006) EMBO J 25: 2219-2229

  • DOI: 10.1038/sj.emboj.7601096
  • Primary Citation of Related Structures:  
    2FQZ, 2GB7

  • PubMed Abstract: 

    • Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs ...

    Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.

    Related Citations: 
    • Alternative arrangements of catalytic residues at the active sites of restriction enzymes.
      Tamulaitis, G., Solonin, A.S., Siksnys, V.
      (2002) FEBS Lett 518: 17
    • The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.
      Denjmukhametov, M.M., Brevnov, M.G., Zakharova, M.V., Repyk, A.V., Solonin, A.S., Petrauskene, O.V., Gromova, E.S.
      (1998) FEBS Lett 433: 233
    Organizational Affiliation: 

    International Institute of Molecular and Cell Biology, Warsaw, Poland. MBochtler@iimcb.gov.pl



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
R.Ecl18kIE [auth A],
F [auth B],
G [auth C],
H [auth D]		305Enterobacter cloacaeMutation(s): 1 
Gene Names: ecl18kIR
UniProt
Find proteins for O87963 (Enterobacter cloacae)
Explore O87963 
Go to UniProtKB:  O87963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87963
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA STRAND 1A [auth E],
C [auth G]		9N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA STRAND 2B [auth F],
D [auth H]		9N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.697α = 90
b = 96.739β = 90
c = 192.012γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
GETAXphasing
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references