PDBsum entry 3cmu

Recombination/DNA

PDB id: 3cmu

Contents

Protein chain

1937 a.a.

DNA/RNA

Ligands

ALF ×6

ADP ×6

Metals

_MG ×6

PDB id:

3cmu

Name:

Recombination/DNA

Title:

Mechanism of homologous recombination from the reca-ssdna/dsdna structures

Structure:

DNA (5'- d( Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dt p Dt)-3'). Chain: b. Engineered: yes. Protein reca. Chain: a. Synonym: recombinase a. Engineered: yes

Source:

Synthetic: yes. Escherichia coli

Resolution:

4.20Å R-factor: 0.276 R-free: 0.298

Authors:

N.P.Pavletich

Key ref:

Z.Chen et al. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453, 489-484. PubMed id: 18497818 DOI: 10.1038/nature06971

Date:

24-Mar-08 Release date: 20-May-08

Protein chain

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

Seq: 353 a.a.

Struc: 1937 a.a.*

* PDB and UniProt seqs differ at 18 residue positions (black crosses)

DNA/RNA chain

T-T-T-T-T-T-T-T-T-T-T-T-T-T-T 15 bases

DOI no: 10.1038/nature06971

Nature 453:489-484 (2008)

PubMed id: 18497818

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.

Z.Chen, H.Yang, N.P.Pavletich.

ABSTRACT

The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex. Here we have solved the crystal structures of the Escherichia coli RecA-ssDNA and RecA-heteroduplex filaments. They show that ssDNA and ATP bind to RecA-RecA interfaces cooperatively, explaining the ATP dependency of DNA binding. The ATP gamma-phosphate is sensed across the RecA-RecA interface by two lysine residues that also stimulate ATP hydrolysis, providing a mechanism for DNA release. The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The complementary strand interacts primarily through base pairing, making heteroduplex formation strictly dependent on complementarity. The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling.

Selected figure(s)

Figure 1.
Figure 1: Structure of the presynaptic nucleoprotein filament. a, Structure of the RecA[6]–(ADP-AlF[4]-Mg)[6]–(dT)[18] complex. The six RecA protomers are numbered from the N-terminal RecA of the fusion protein and are coloured pink, brown, green, cyan, purple and magenta, respectively. Only 15 of the 18 nucleotides are ordered (red). The DNA backbone is traced by a red coil. The six ADP-AlF[4]-Mg molecules are coloured gold. The five individual rotation/translation axes that relate adjacent RecA protomers are shown as grey vertical lines. b, The L1 and L2 loop regions and the F and G helices that bind to ssDNA are coloured and numbered as in a, with the rest of each RecA structure omitted for clarity. The ssDNA is numbered starting with the 5'-most nucleotide in each nucleotide triplet. The 5'-most and 3'-most nucleotide triplets have only two and one ordered nucleotides, respectively. Portions of the L1 and L2 loops of the C-terminal RecA are disordered (dashed lines).

Figure 4.
Figure 4: Structure of the postsynaptic nucleoprotein filament. a, Structure of the RecA[5]–(ADP-AlF[4]-Mg)[5]–(dT)[15]–(dA)[12] complex. The five RecA protomers are coloured as the first five protomers of Fig. 1a. The primary (dT)[15] strand (red) has 13 ordered nucleotides, and the complementary (dA)[12] strand (magenta) has 10 ordered nucleotides. b, View of the heteroduplex looking down the filament axis, showing the three central base-pair triplets (of RecA^2, RecA^3 and RecA^4).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 453, 489-484) copyright 2008.

Figures were selected by the author.