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PDBsum entry 2odh
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* Residue conservation analysis
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DOI no:
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J Mol Biol
369:722-734
(2007)
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PubMed id:
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Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA.
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M.Sokolowska,
M.Kaus-Drobek,
H.Czapinska,
G.Tamulaitis,
R.H.Szczepanowski,
C.Urbanke,
V.Siksnys,
M.Bochtler.
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ABSTRACT
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Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG
(S stands for C or G, / designates a cleavage position) to generate staggered
products with single nucleotide 5'-overhangs. Here, we show that BcnI functions
as a monomer that interacts with its target DNA in 1:1 molar ratio and report
crystal structures of BcnI in the absence and in the presence of DNA. In the
complex with DNA, BcnI makes specific contacts with all five bases of the target
sequence and not just with a half-site, as the protomer of a typical dimeric
restriction endonuclease. Our data are inconsistent with BcnI dimerization and
suggest that the enzyme introduces double-strand breaks by sequentially nicking
individual DNA strands, although this remains to be confirmed by kinetic
experiments. BcnI is remotely similar to the DNA repair protein MutH and shares
approximately 20% sequence identity with the restriction endonuclease MvaI,
which is specific for the related sequence CC/WGG (W stands for A or T). As
expected, BcnI is structurally similar to MvaI and recognizes conserved bases in
the target sequence similarly but not identically. BcnI has a unique machinery
for the recognition of the central base-pair.
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Selected figure(s)
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Figure 4.
Figure 4. Apo-BcnI versus BcnI in complex with DNA. (a) A
stereo diagram of the superimposed structures. Apo-BcnI is shown
in grey, and the BcnI from the cocrystals with DNA is colored as
in Figure 3. (b) The C^α trace of apo-BcnI color-ramped
according to B-factor. (c) The C^α trace of BcnI from the
cocrystals with DNA color-ramped according to B-factor. In the
protein region, the correspondence between B-factor and color is
identical in (b) and (c). Residues with the lowest B-factors are
blue, and residues with the highest B-factors are yellow. DNA is
presented in a smoothed representation and colored as in Figure
3.
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Figure 6.
Figure 6. Stereo diagram of the BcnI active site in complex
with DNA. BcnI active site residues are shown in all-atom
representation, metal ions are presented as black and grey
spheres, and some key water molecules are shown as red spheres.
The 5′-end of the DNA is on the right and the 3′-end is on
the left. The 2F[o]–F[c] density was contoured at 1.5 σ and
is shown only around the DNA and the nucleophilic water
molecule. The assignment of the metal ion that is shown without
detailed coordination is very uncertain.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
369,
722-734)
copyright 2007.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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F.Chen,
Z.Yang,
M.Yan,
J.B.Alvarado,
G.Wang,
and
S.A.Benner
(2011).
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
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Nucleic Acids Res,
39,
3949-3961.
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G.Kostiuk,
G.Sasnauskas,
G.Tamulaitiene,
and
V.Siksnys
(2011).
Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.
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Nucleic Acids Res,
39,
3744-3753.
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M.Firczuk,
M.Wojciechowski,
H.Czapinska,
and
M.Bochtler
(2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
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Nucleic Acids Res,
39,
744-754.
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PDB code:
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W.Yang
(2011).
Nucleases: diversity of structure, function and mechanism.
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Q Rev Biophys,
44,
1.
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I.Stier,
and
A.Kiss
(2010).
The type II restriction endonuclease MvaI has dual specificity.
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Nucleic Acids Res,
38,
8231-8238.
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M.Zaremba,
A.Owsicka,
G.Tamulaitis,
G.Sasnauskas,
L.S.Shlyakhtenko,
A.Y.Lushnikov,
Y.L.Lyubchenko,
N.Laurens,
B.van den Broek,
G.J.Wuite,
and
V.Siksnys
(2010).
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
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Nucleic Acids Res,
38,
7142-7154.
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T.Raskó,
A.Dér,
E.Klement,
K.Slaska-Kiss,
E.Pósfai,
K.F.Medzihradszky,
D.R.Marshak,
R.J.Roberts,
and
A.Kiss
(2010).
BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
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Nucleic Acids Res,
38,
7155-7166.
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K.L.Sanders,
L.E.Catto,
S.R.Bellamy,
and
S.E.Halford
(2009).
Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.
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Nucleic Acids Res,
37,
2105-2115.
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D.Daujotyte,
Z.Liutkeviciūte,
G.Tamulaitis,
and
S.Klimasauskas
(2008).
Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
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Nucleic Acids Res,
36,
e57.
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G.Gasiunas,
G.Sasnauskas,
G.Tamulaitis,
C.Urbanke,
D.Razaniene,
and
V.Siksnys
(2008).
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
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Nucleic Acids Res,
36,
938-949.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
