EcoRI
| EcoRI | |||||||||
|---|---|---|---|---|---|---|---|---|---|
The crystallographic structure of restriction endonuclease EcoRI at 3.3 a in the absence of DNA
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| Identifiers | |||||||||
| Symbol | EcoRI | ||||||||
| Pfam | PF02963 | ||||||||
| InterPro | IPR004221 | ||||||||
| SCOP | 1na6 | ||||||||
| SUPERFAMILY | 1na6 | ||||||||
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| Available protein structures: | |
|---|---|
| Pfam | structures |
| PDB | RCSB PDB; PDBe; PDBj |
| PDBsum | structure summary |
EcoRI (pronounced "eco R one") is a restriction endonuclease enzyme isolated from species E. coli. The Eco part of the enzyme's name originates from the species from which it was isolated, while the R represents the particular strain, in this case RY13. The last part of its name, the I, denotes that it was the first enzyme isolated from this strain. EcoRI is a restriction enzyme that cleaves DNA double helixes into fragments at specific sites. It is also a part of the restriction modification system.
In molecular biology it is used as a restriction enzyme. EcoRI creates 4 nucleotide sticky ends with 5' end overhangs of AATT. The nucleic acid recognition sequence where the enzyme cuts is G/AATTC, which has a palindromic, complementary sequence of CTTAA/G. The / in the sequence indicates which phosphodiester bond the enzyme will break in the DNA molecule. Other restriction enzymes, depending on their cut sites, can also leave 3' overhangs or blunt ends with no overhangs.
EcoRI contains the PD..D/EXK motif within its active site like many restriction endonucleases.
The enzyme is a homodimer of a 31 kilodalton subunit consisting of one globular domain of the α/β architecture. Each subunit contains a loop which sticks out from the globular domain and wraps around the DNA when bound.
EcoRI has been cocrystallized with the sequence it normally cuts. This crystal was used to solve the structure of the complex 1QPS. The solved crystal structure shows that the subunits of the enzyme homodimer interact with the DNA symmetrically. In the complex, two α-helices from each subunit come together to form a four-helix bundle. On the interacting helices are residues Glu144 and Arg145, which interact together, forming a crosstalk ring that is believed to allow the enzyme's two active sites to communicate.
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