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PDBsum entry 2f03
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Hydrolase/DNA
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PDB id
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2f03
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References listed in PDB file
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Key reference
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Title
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A view of consecutive binding events from structures of tetrameric endonuclease sfii bound to DNA.
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Authors
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E.S.Vanamee,
H.Viadiu,
R.Kucera,
L.Dorner,
S.Picone,
I.Schildkraut,
A.K.Aggarwal.
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Ref.
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EMBO J, 2005,
24,
4198-4208.
[DOI no: ]
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PubMed id
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Abstract
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Many reactions in cells proceed via the sequestration of two DNA molecules in a
synaptic complex. SfiI is a member of a growing family of restriction enzymes
that can bind and cleave two DNA sites simultaneously. We present here the
structures of tetrameric SfiI in complex with cognate DNA. The structures reveal
two different binding states of SfiI: one with both DNA-binding sites fully
occupied and the other with fully and partially occupied sites. These two states
provide details on how SfiI recognizes and cleaves its target DNA sites, and
gives insight into sequential binding events. The SfiI recognition sequence
(GGCCNNNN[downward arrow]NGGCC) is a subset of the recognition sequence of BglI
(GCCNNNN[downward arrow]NGGC), and both enzymes cleave their target DNAs to
leave 3-base 3' overhangs. We show that even though SfiI is a tetramer and BglI
is a dimer, and there is little sequence similarity between the two enzymes,
their modes of DNA recognition are unusually similar.
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Figure 5.
Figure 5 Change in loop E conformation. (A) Loop E enters the
DNA major groove in the native complex (blue), but in the C/D
dimer of the Se-Met complex (red) it packs away from the DNA.
Black spheres mark the position of Arg 213. (B) View of C/D
dimer looking down the DNA axis. In the native complex (blue),
loop E's bracket the DNA and help to hold it in place, while in
the Se-Met complex (red) the loops are positioned away from the
DNA.
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Figure 6.
Figure 6 The active sites of SfiI (left) and BglI (right). The
DNA and the active site residues of SfiI (Asp 79, Asp100, and
Lys102) and BglI (Asp116, Asp142, and Lys144) are shown in
'stick' representation. The scissile phosphodiester is indicated
by arrows. The Ca^2+ ions are shown as nonbonded spheres and
colored aqua, water molecules are not shown. In SfiI, the second
Ca^2+ is missing and the scissile phosphodiester is  3
Å further away than in BglI, indicating that the enzyme is in an
inactive state.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2005,
24,
4198-4208)
copyright 2005.
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