1wtd
From Proteopedia
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|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1wte|1WTE]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtd OCA], [http://www.ebi.ac.uk/pdbsum/1wtd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wtd RCSB]</span> | ||
}} | }} | ||
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[[Category: Shichijo, N.]] | [[Category: Shichijo, N.]] | ||
[[Category: Shimizu, T.]] | [[Category: Shimizu, T.]] | ||
| - | [[Category: GOL]] | ||
[[Category: dna-free from]] | [[Category: dna-free from]] | ||
[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:40:43 2008'' |
Revision as of 21:40, 30 March 2008
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| , resolution 2.401Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Related: | 1WTE
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form
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 Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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:15590682
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