PDBsum entry 1aa3

Double-stranded DNA binding domain

PDB id: 1aa3

Contents

Protein chain

63 a.a. *

* Residue conservation analysis

PDB id:

1aa3

Name:

Double-stranded DNA binding domain

Title:

C-terminal domain of the e. Coli reca, nmr, minimized average structure

Structure:

Reca. Chain: a. Fragment: c-terminal domain

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12

NMR struc:

1 models

Authors:

H.Aihara,Y.Ito,H.Kurumizaka,T.Terada,S.Yokoyama,T.Shibata,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

H.Aihara et al. (1997). An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing. J Mol Biol, 274, 213-221. PubMed id: 9398528 DOI: 10.1006/jmbi.1997.1403

Date:

22-Jan-97 Release date: 23-Jul-97

Protein chain

P0A7G6  (RECA_ECOLI) -  Protein RecA from Escherichia coli (strain K12)

Seq: 353 a.a.

Struc: 63 a.a.

DOI no: 10.1006/jmbi.1997.1403

J Mol Biol 274:213-221 (1997)

PubMed id: 9398528

An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing.

H.Aihara, Y.Ito, H.Kurumizaka, T.Terada, S.Yokoyama, T.Shibata.

ABSTRACT

RecA protein and its homologs catalyze homologous pairing of dsDNA and ssDNA, a critical reaction in homologous genetic recombination in various organisms from a virus, microbes to higher eukaryotes. In this reaction, RecA protein forms a nucleoprotein filament on ssDNA, which in turn binds to naked dsDNA for homology search. We suggested that the C-terminal domain of RecA protein plays a role in capturing the dsDNA. Here, we isolated the C-terminal domain as a soluble form and determined the solution structure by NMR spectroscopy. The overall folding of the NMR structure agrees with that of the corresponding part of the reported crystal structure, but a remarkable difference was found in a solvent-exposed region due to intermolecular contacts in the crystal. Then, we studied the interaction between the C-terminal domain and DNA, and found that significant chemical shift changes were induced in a specific region by titration with dsDNA. SsDNA induced a much smaller chemical shift perturbation. The difference of DNA concentrations to give the half-saturation of the chemical shift change showed a higher affinity of the C-terminal region toward dsDNA. Combined with our previous results, these provide direct evidence that the defined region in the C-terminal domain furnishes a binding surface for DNA.

Selected figure(s)

Figure 2.

Figure 3.
Figure 3. Superposition of backbone traces of the energy minimized average structure derived from NMR (shown in cyan) and the X-ray structure (shown in red) around Gly 295. The structures were superimposed to give the lowest deviations in the C^α positions of residues 270 to 322. The largest deviation occurs at Gly295. Side-chains which might be involved in electrostatic interactions with the adjacent molecule (green) in the crystal (distance between N and O atoms is less than 4 Å) are shown in white. Plausible hydrogen bonds or salt bridges are indicated by broken lines, with distances in angstroms. The crystal structure is that of [Story et al 1992]. This Figure was drawn using MidasPlus [Ferrin et al 1988].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 274, 213-221) copyright 1997.

Figures were selected by an automated process.