3OR3: Restriction endonuclease HPY188I in complex with product DNA

Citation:
Abstract
The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It is found in the eukaryotic flap endonuclease and Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision repair proteins UvrC and Cho, and in proteins of 'selfish' genetic elements. Here we present the structures of the ternary pre- and post-cleavage complexes of the type II GIY-YIG restriction endonuclease Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a single substitution reaction. They are consistent with a previous proposal that a tyrosine residue (which we expect to occur in its phenolate form) acts as a general base for the attacking water molecule. In contrast to the earlier proposal, our data identify the general base with the GIY and not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in trans in Hpy188I) anchors a single metal cation in the active site. This metal ion contacts the phosphate proS oxygen atom and the leaving group 3'-oxygen atom, presumably to facilitate its departure. Taken together, our data reveal striking analogy in the absence of homology between GIY-YIG and betabetaalpha-Me nucleases.
PDB ID: 3OR3Download
MMDB ID: 85660
PDB Deposition Date: 2010/9/6
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.95  Å
Source Organism:
Helicobacter pylori 118
Similar Structures:
Biological Unit for 3OR3: hexameric; determined by author and by software (PISA)
Molecular Components in 3OR3
Label Count Molecule
Proteins (2 molecules)
2
Restriction Endonuclease Hpy188i
Molecule annotation
Nucleotides(4 molecules)
1
5'-d(*gp*ap*tp*cp*t)-3'
Molecule annotation
1
5'-d(*gp*tp*tp*cp*a)-3'
Molecule annotation
1
5'-d(p*gp*ap*ap*c)-3'
Molecule annotation
1
5'-d(p*gp*ap*tp*c)-3'
Molecule annotation
Chemicals (7 molecules)
1
3
2
4
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.