Structure
Volume 18, Issue 10, 13 October 2010, Pages 1321-1331
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Article
Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI

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Summary

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.

Highlights

► The GIY-YIG endonuclease family now has a representative structure bound to DNA ► The structure demonstrates how the GIY-YIG motif can recognize a specific DNA target ► Recognition of the DNA target by R.Eco29kI follows an unusual minimalistic strategy ► Minimal elaboration of the core fold permits site-specific target recognition

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Present address: Seattle Children's Research Institute C9S-6, 1900 9th Avenue, Seattle, WA 98101, USA