EcoRI

EcoRI
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 helices into fragments at specific
sites. It is also a part of the restriction
modification system.
EcoRI
EcoRI crystal structure. Dimer bound to DNA (PDB

1ckq)
Identifiers
Symbol EcoRI
Pfam PF02963
InterPro IPR004221
SCOPe 1na6
SUPERFAMILY 1na6
CDD 79lll
Available protein structures:
Pfam structures
PDB RCSB PDB ; PDBe ;
PDBj
PDBsum structure summary
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.
Structure
Primary structure
EcoRI contains the PD..D/EXK motif within

its active site like many restriction
endonucleases.
Tertiary and quaternary

structure
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.[1][2]
EcoRI recognition site with cutting pattern indicated by

a green line
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.[1] In the complex, two α-
helices from each subunit come together
to form a four-helix bundle.[3] 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.[4]
Uses
Restriction enzymes, such as EcoRI, are
used in a wide variety of molecular
genetics techniques including cloning,
DNA screening and deleting sections of
DNA in vitro. Restriction enzymes, like
EcoRI, that generate sticky ends of DNA
are often used to cut DNA prior to ligation,
as the sticky ends make the ligation
reaction more efficient. EcoRI can exhibit
non-site-specific cutting, known as star
activity, depending on the conditions
present in the reaction. Conditions that
can induce star activity when using EcoRI
include low salt concentration, high
glycerol concentration, excessive amounts
of enzyme present in the reaction, high pH
and contamination with certain organic
solvents. The cut made by the Eco RI
enzyme produces sticky ends on the
vector mainly plasmids or viral DNA's.[5]
See also
EcoRII, another nuclease enzyme from
E. coli.
EcoRV, another nuclease enzyme from
E. coli.
References
1. Pingoud A, Jeltsch A (September
2001). "Structure and function of type
II restriction endonucleases" . Nucleic
Acids Research. 29 (18): 3705–27.
doi:10.1093/nar/29.18.3705 .
PMC 55916 . PMID 11557805 .
2. Kurpiewski MR, Engler LE, Wozniak LA,
Kobylanska A, Koziolkiewicz M, Stec
WJ, Jen-Jacobson L (October 2004).
"Mechanisms of coupling between
DNA recognition specificity and
catalysis in EcoRI endonuclease".
Structure. 12 (10): 1775–88.
doi:10.1016/j.str.2004.07.016 .
PMID 15458627 .
3. Bitinaite J, Wah DA, Aggarwal AK,
Schildkraut I (September 1998). "FokI
dimerization is required for DNA
cleavage" . Proceedings of the
National Academy of Sciences of the
United States of America. 95 (18):
10570–5.
doi:10.1073/pnas.95.18.10570 .
PMC 27935 . PMID 9724744 .
4. Kim YC, Grable JC, Love R, Greene PJ,
Rosenberg JM (September 1990).
"Refinement of Eco RI endonuclease
crystal structure: a revised protein
chain tracing". Science. 249 (4974):
1307–9.
doi:10.1126/science.2399465 .
PMID 2399465 .
5. http://www.neb.com/nebecomm/prod
ucts/faqproductR0101.asp#1
External links
Eco-RI at the US National Library of
Medicine Medical Subject Headings
(MeSH)
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title=EcoRI&oldid=876413653"
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EcoRI (pronounced "eco R one") is a

EcoRI crystal structure. Dimer bound to DNA (PDB

Available protein structures:

PDBsum structure summary

In molecular biology it is used as a

EcoRI contains the PD..D/EXK motif within

Tertiary and quaternary

The enzyme is a homodimer of a 31

EcoRI recognition site with cutting pattern indicated by

EcoRI has been cocrystallized with the

Last edited 4 months ago by BattyBot

Content is available under CC BY-SA 3.0 unless

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