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PDBsum entry 2ipr
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DNA binding protein
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PDB id
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2ipr
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References listed in PDB file
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Key reference
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Title
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Structure of the origin-Binding domain of simian virus 40 large t antigen bound to DNA.
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Authors
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E.Bochkareva,
D.Martynowski,
A.Seitova,
A.Bochkarev.
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Ref.
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EMBO J, 2006,
25,
5961-5969.
[DOI no: ]
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PubMed id
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Abstract
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The large T antigen (T-ag) protein binds to and activates DNA replication from
the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we
determined the crystal structures of the T-ag origin-binding domain (OBD) in apo
form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA
palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were
shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1
loop), a combination of a DNA-binding helix and loop (His203-Asn210), and
Asn227. The A1 loop traveled back-and-forth along the major groove and accounted
for most of the sequence-determining contacts with the DNA. Unexpectedly, in
both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make
direct protein-protein contacts. The T-ag OBD was also captured bound to a
non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our
observations taken together with the known biochemical and structural features
of the T-ag-origin interaction suggest a model for origin unwinding.
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Figure 4.
Figure 4 Structural details of T-ag interaction with DNA bases
in the PEN-2 and PEN-4 structures. (A) Sequence-specific
interaction of Arg 154 with G1 (the first G in the GAGGC
pentamer) in the PEN-4 structure. A representative electron
density map (shown in blue) is superimposed on the model. (B)
Nonspecific interaction of Arg 154 with A1 (A in position of G1)
in the PEN-2 structure. A representative electron density is
superimposed on Arg 154. (C) Sequence-specific interaction of
Ser 152 with A2. (D) Nonspecific interaction of Ser 152 with the
T2 in the PEN-2 structure. Sequence-specific interactions, which
involve (E) the G3 and Asn 153, (F) the G4 and Asn 153, and (G)
the G (complementary to C5) with Arg 204. The protein and DNA
are shown as stick models and colored by atom type; yellow for
carbon, blue for nitrogen, red for oxygen, and purple for
phosphorus. A representative electron density as captured from
2F[o]-F[c] map is shown with contours drawn at the 1.25  level.
Hydrogen bonds are indicated with red dashed lines, and the
length of the bonds is indicated in Å.
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Figure 5.
Figure 5 Molecular model of an initial step in the SV40 DNA
replication. The PEN-4 structure is shown in black, two
hexameric helicase domains are in blue (PDB Id: 1N25), modeled
DNA is shown as a stick model and colored per atom type (carbon
in yellow, oxygen in red, nitrogen in blue, and phosphorus in
purple). Position of the initially melted 8 nt fragment of EP
with respect to the PEN box is highlighted with a yellow
rectangle. Relative positions of the C-terminus in the OBD (aa
253) and N-terminus in the helicase domain (aa 266) are
indicated. See text for more detail.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
5961-5969)
copyright 2006.
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