3MX1

The structure of GIY-YIG endonuclease R.Eco29kI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.

Mak, A.N.Lambert, A.R.Stoddard, B.L.

(2010) Structure 18: 1321-1331

  • DOI: 10.1016/j.str.2010.07.006
  • Primary Citation of Related Structures:  3MX4, 3NIC

  • PubMed Abstract: 
  • The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its t ...

    The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC.


    Related Citations: 
    • Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.
      Pertzev, A.V.,Ruban, N.M.,Zakharova, M.V.,Beletzkaja, I.V.,Petrov, S.I.,Kravetz, A.N.,Solonin, A.S.
      (1992) Nucleic Acids Res. 20: 1991


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eco29kIR
A
235Escherichia coliGene Names: eco29kIR
EC: 3.1.21.4
Find proteins for Q46944 (Escherichia coli)
Go to UniProtKB:  Q46944
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 87.906α = 90.00
b = 90.074β = 90.00
c = 88.850γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXphasing
ADSCdata collection
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance