1WTD

Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form

Summary for 1WTD

• Entry DOI: 10.2210/pdb1wtd/pdb
• Related: 1WTE
• Descriptor: EcoO109IR, GLYCEROL (3 entities in total)
• Functional Keywords: restriction endonuclease, dna-free from, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 63884.89

Authors

Hashimoto, H.,Shimizu, T.,Imasaki, T.,Kato, M.,Shichijo, N.,Kita, K.,Sato, M. (deposition date: 2004-11-22, release date: 2004-12-14, Last modification date: 2024-03-13)

Primary citation

Hashimoto, H.,Shimizu, T.,Imasaki, T.,Kato, M.,Shichijo, N.,Kita, K.,Sato, M.
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA
J.Biol.Chem., 280:5605-5610, 2005

PubMed Abstract: EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2 mechanism, whereas the other water interacts with the 3'-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.

PubMed: 15590682
DOI: 10.1074/jbc.M411684200

Experimental method

X-RAY DIFFRACTION (2.401 Å)