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Structure. 2010 Oct 13;18(10):1321-31. doi: 10.1016/j.str.2010.07.006. Epub 2010 Aug 26.

Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.

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1
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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.

PMID:
20800503
PMCID:
PMC2955809
DOI:
10.1016/j.str.2010.07.006
[Indexed for MEDLINE]
Free PMC Article
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