1wtd

[[Image:1wtd.jpg|left|200px]]<br /><applet load="1wtd" size="450" color="white" frame="true" align="right" spinBox="true"

caption="1wtd, resolution 2.401&Aring;" />

'''Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form'''<br />

==Overview==

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.

==About this Structure==

1WTD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with GOL as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WTD OCA].

 

Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA., Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo N, Kita K, Sato M, J Biol Chem. 2005 Feb 18;280(7):5605-10. Epub 2004 Dec 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15590682 15590682]

[[Category: Single protein]]

[[Category: Type II site-specific deoxyribonuclease]]

[[Category: Hashimoto, H.]]

[[Category: Imasaki, T.]]

[[Category: Kato, M.]]

[[Category: Kita, K.]]

[[Category: Sato, M.]]

[[Category: Shichijo, N.]]

[[Category: Shimizu, T.]]