DSSR-PyMOL cartoon-block schematics: PDB entry 3nic

PDB-id

3nic; DSSR-derived features in text and JSON formats

Class

hydrolase-DNA

Method

X-ray (2.8 Å)

Summary

DNA binding and cleavage by the giy-yig endonuclease r.eco29ki inactive variant y49f

Reference

Mak AN, Lambert AR, Stoddard BL (2010): "Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI." Structure, 18, 1321-1331. doi: 10.1016/j.str.2010.07.006.

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.