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PDBsum entry 2f5o
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Hydrolase/DNA
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PDB id
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2f5o
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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 a DNA glycosylase searching for lesions.
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Authors
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A.Banerjee,
W.L.Santos,
G.L.Verdine.
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Ref.
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Science, 2006,
311,
1153-1157.
[DOI no: ]
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PubMed id
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Abstract
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DNA glycosylases must interrogate millions of base pairs of undamaged DNA in
order to locate and then excise one damaged nucleobase. The nature of this
search process remains poorly understood. Here we report the use of disulfide
cross-linking (DXL) technology to obtain structures of a bacterial DNA
glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0
angstrom resolution, reveal the nature of the search process: The protein
inserts a probe residue into the helical stack and severely buckles the target
base pair, which remains intrahelical. MutM therefore actively interrogates the
intact DNA helix while searching for damage.
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Figure 2.
Fig. 2. Schematic representation of MutM-DNA complexes. (A) The
MutM LRC used as the basis for the design of the cross-linking
system. (B to D) Interrogation complexes showing the positioning
of MutM over the DNA duplex, with the target base pair in aqua.
The side chain of the helix-probe residue Phe^114 is indicated.
The numbering system for the base pairs and backbone phosphates
is as indicated. The curved green line denotes the thiol-bearing
tether engaged in a cross-link to Cys166. Each blue box
indicates the site of tether attachment to DNA, the position of
the target base pair, and the separation between them, here
referred to as the register. Dashed blue lines indicate the lack
of order in the oxoG recognition loop. (E and F) Overall view of
complexes CC1 (E) and IC1 (F). CC1 is a lesion recognition
complex (LRC) formed by disulfide cross-linking between MutM and
oxoG-containing DNA. IC1 is the corresponding interrogation
complex having MutM cross-linked to non-lesion-containing DNA.
Blue box denotes the target base pair, which is disrupted in (E)
and intact but buckled in (F).
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Figure 4.
Fig. 4. Direct and water-mediated interactions between MutM and
the DNA backbone in the control LRC CC2 (A) and interrogation
complexes IC1 (B) and IC2 (C). Dashed lines indicate hydrogen
bonding interactions among backbone phosphates in DNA, ordered
waters (red spheres), and residues in MutM. The side chains of
amino acid residues are shown in green with the numbers colored
according to which moiety on the amino acid is involved in the
contact: green, side chain; blue, backbone amide NH; red,
backbone amide carbonyl; gray, no contact in that particular
complex.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2006,
311,
1153-1157)
copyright 2006.
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