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PDBsum entry 2f5p

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Hydrolase/DNA PDB id
2f5p
Jmol
Contents
Protein chain
254 a.a.
DNA/RNA
Metals
_ZN
Waters ×166

References listed in PDB file
Key reference
Title Structure of a DNA glycosylase searching for lesions.
Authors A.Banerjee, W.L.Santos, G.L.Verdine.
Ref. Science, 2006, 311, 1153-1157. [DOI no: 10.1126/science.1120288]
PubMed id 16497933
Abstract
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.
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).
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.
The above figures are reprinted by permission from the AAAs: Science (2006, 311, 1153-1157) copyright 2006.
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