From Wikipedia, the free encyclopedia
Restriction enzyme
Eco RII dimer based on
PDB ID
1NA6
Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an
enzyme of
restriction modification system (RM) naturally found in
Escherichia coli , a
Gram-negative bacteria . Its
molecular mass is 45.2
kDa , being composed of 402
amino acids .
[1]
Mode of action
EcoRII is a
bacterial Type IIE
[2]
REase that interacts with two
[3] or
three
[4] copies of the pseudopalindromic
DNA
recognition sequence
5' -
CC W
GG -
3' (W =
A or
T ), one being the actual target of cleavage, the other(s) serving as the
allosteric activator (s). EcoRII cuts the target
DNA sequence CCWGG, generating
sticky ends .
[5]
Cut diagram
Recognition site
Cut results
5' NNCCWGG NN
3' NNGGWCC NN
5' NN CCWGG NN
3' NNGGWCC NN
Structure
The
apo
crystal structure of EcoRII
mutant R88A (
PDB :
1NA6 )
[6] has been solved at 2.1
Å
resolution . The EcoRII
monomer has two
domains ,
N-terminal and
C-terminal , linked through a
hinge
loop .
Effector-binding domain
The N-terminal
effector -
binding domain has an archetypal DNA-binding pseudobarrel fold (
SCOP
101936 ) with a prominent
cleft .
Structural superposition showed it is evolutionarily related to:
Catalytic domain
The C-terminal
catalytic domain has a typical
[10] restriction endonuclease-like fold (
SCOP
52979 ) and belongs to the large (more than 30 members)
restriction endonuclease superfamily (
SCOP
52980 ).
Autoinhibition/activation mechanism
Structure-based sequence alignment and
site-directed mutagenesis identified the putative PD..D/EXK
active sites of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.
[6]
See also
External links
EcoRII in Restriction Enzyme Database
REBASE
References
^ Richard J. Roberts.
"EcoRII" . REBASE - The Restriction Enzyme Database . Retrieved 2008-03-23 .
^ Roberts RJ, Belfort M, Bestor T, et al. (2003).
"A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes" . Nucleic Acids Res . 31 (7): 1805–12.
doi :
10.1093/nar/gkg274 .
PMC
152790 .
PMID
12654995 .
PDF [
dead link ]
^ Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M (2000).
"Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage" . J. Biol. Chem . 275 (39): 30631–7.
doi :
10.1074/jbc.M003904200 .
PMID
10903314 .
PDF [
permanent dead link ]
^ Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL (2007). "Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy". Biochemistry . 46 (39): 11128–36.
doi :
10.1021/bi701123u .
PMID
17845057 .
S2CID
27800123 .
^ Griffiths, Anthony J. F. (1999). An Introduction to genetic analysis . San Francisco: W.H. Freeman.
ISBN
978-0-7167-3520-5 .
^
a
b Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L (2004). "Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold". J. Mol. Biol . 335 (1): 307–19.
doi :
10.1016/j.jmb.2003.10.030 .
PMID
14659759 .
^ Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S (2004).
"Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1" . Plant Cell . 16 (12): 3448–59.
doi :
10.1105/tpc.104.026112 .
PMC
535885 .
PMID
15548737 .
PDF
^ Richard J. Roberts.
"BfiI" . REBASE - The Restriction Enzyme Database . Retrieved 2008-03-23 .
^ Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V (2005).
"Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease" (PDF) . Proc. Natl. Acad. Sci. U.S.A . 102 (44): 15797–802.
Bibcode :
2005PNAS..10215797G .
doi :
10.1073/pnas.0507949102 .
PMC
1266039 .
PMID
16247004 .
PDF
^ Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA (2007).
"Topology of Type II REases revisited; structural classes and the common conserved core" . Nucleic Acids Research . 35 (7): 2227–37.
doi :
10.1093/nar/gkm045 .
PMC
1874628 .
PMID
17369272 .
Basic Concept Recognition sequence 4bp Recognition sequence 5bp Recognition sequence 6bp Recognition sequence 8bp
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