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3mx1, resolution 2.30Å ()
Gene: eco29kIR (Escherichia coli)
Activity: Type II site-specific deoxyribonuclease, with EC number
Related: 3mx4

Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml

The structure of GIY-YIG endonuclease R.Eco29kI

Publication Abstract from PubMed

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.

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI., Mak AN, Lambert AR, Stoddard BL, Structure. 2010 Aug 25. PMID:20800503

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3mx1 is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.


  • Mak AN, Lambert AR, Stoddard BL. Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI. Structure. 2010 Aug 25. PMID:20800503 doi:10.1016/j.str.2010.07.006
  • Pertzev AV, Ruban NM, Zakharova MV, Beletzkaja IV, Petrov SI, Kravetz AN, Solonin AS. Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli. Nucleic Acids Res. 1992 Apr 25;20(8):1991. PMID:1579502

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