3OR3

Restriction endonuclease HPY188I in complex with product DNA

Summary for 3OR3

• Entry DOI: 10.2210/pdb3or3/pdb
• Related: 1MK0 1YD1 2WSH 3MX1 3MX4 3NIC 3OQG
• Descriptor: RESTRICTION ENDONUCLEASE HPY188I, 5'-D(*GP*AP*TP*CP*T)-3', 5'-D(*GP*TP*TP*CP*A)-3', ... (8 entities in total)
• Functional Keywords: endonuclease-dna complex, restriction enzyme, hpy188i, intercalation, giy-yig nuclease, catalytic mechanism, pseudopalindrome, hydrolase-dna complex, restriction endonuclease, dna, hydrolase/dna
• Biological source: Helicobacter pylori (Campylobacter pylori); More
• Total number of polymer chains: 6
• Total formula weight: 47902.91

Authors

Sokolowska, M.,Czapinska, H.,Bochtler, M. (deposition date: 2010-09-06, release date: 2010-10-20, Last modification date: 2023-12-06)

Primary citation

Sokolowska, M.,Czapinska, H.,Bochtler, M.
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Nucleic Acids Res., 39:1554-1564, 2011

PubMed 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 ββα-Me nucleases.

PubMed: 20935048
DOI: 10.1093/nar/gkq821

Experimental method

X-RAY DIFFRACTION (1.95 Å)