PDBsum entry 2f5o

Hydrolase/DNA

PDB id: 2f5o

Contents

Protein chain

252 a.a. *

DNA/RNA

Ligands

GOL

Metals

_ZN

Waters ×142

* Residue conservation analysis

PDB id:

2f5o

Name:

Hydrolase/DNA

Title:

Mutm crosslinked to undamaged DNA sampling g:c base pair ic3

Structure:

5'-d( Ap Gp Gp Tp Ap Gp Ap Tp Cp Cp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d( Tp Gp C Gp Tp Cp Cp Gp Gp Ap Tp Cp Tp Ap Cp C)-3'. Chain: c. Engineered: yes. Formamidopyrimidine-DNA glycosidase. Chain: a. Synonym: mutm.

Source:

Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA with a backbone modification containiing a dsulfide linker. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.05Å R-factor: 0.203 R-free: 0.240

Authors:

A.Banerjee,W.L.Santos,G.L.Verdine

Key ref:

A.Banerjee et al. (2006). Structure of a DNA glycosylase searching for lesions. Science, 311, 1153-1157. PubMed id: 16497933 DOI: 10.1126/science.1120288

Date:

26-Nov-05 Release date: 07-Mar-06

Protein chain

P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase from Geobacillus stearothermophilus

Seq: 274 a.a.

Struc: 252 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-G-G-T-A-G-A-T-C-C-G-G-A-C 14 bases

G-T-C-C-G-G-A-T-C-T-A-C-C 13 bases

Enzyme reactions

• Enzyme class 1: E.C.3.2.2.23 - DNA-formamidopyrimidine glycosylase.
• Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
• Enzyme class 2: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1126/science.1120288

Science 311:1153-1157 (2006)

PubMed id: 16497933

Structure of a DNA glycosylase searching for lesions.

A.Banerjee, W.L.Santos, G.L.Verdine.

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.

Selected figure(s)

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.

Figures were selected by an automated process.