3MX1: The Structure Of Giy-Yig Endonuclease R.Eco29ki

Citation:
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 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.
PDB ID: 3MX1Download
MMDB ID: 84675
PDB Deposition Date: 2010/5/6
Updated in MMDB: 2010/10
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Similar Structures:
Biological Unit for 3MX1: dimeric; determined by author and by software (PISA)
Molecular Components in 3MX1
Label Count Molecule
Proteins (2 molecules)
2
Eco29kir
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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