The structure of the E. coli recA protein monomer and polymer

Story, Randall M.; Weber, Irene T.; Steitz, Thomas A.

doi:10.1038/355318a0

Cited by 735 publications

(745 citation statements)

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“…This observation remained puzzling until 2002, when the application of systematically mutated aromatic residues in RecA allowed a threedimensional model to be constructed for the aqueous solution structures of RecA-dsDNA and RecA-ssDNA (Morimatsu et al 2002). From LD results combined with crystal data for RecA (Story et al 1992), a model emerged in which the DNA was accommodated in an ordered way inside a helical arrangement of RecA monomers allowing the bases to be perpendicular (Morimatsu et al 2002). A later crystal structure of RecA-dsDNA and RecA-ssDNA confirmed our conclusion: a near perpendicular nucleobase orientation and clustering of triplets of bases stacked approximately as in B-form DNA (Chen et al 2008) (Fig.…”

Section: Introductionmentioning

confidence: 99%

A stretched conformation of DNA with a biological role?

Bosaeus

Reymer

Beke‐Somfai

et al. 2017

Quart. Rev. Biophys.

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Abstract. We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair) −1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3′−3′ strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51. Despite vital importance to all biological organisms for survival, genome maintenance and evolution, the recombination reaction is not yet understood at atomic level. We here propose that the structural distortion represented by Σ-DNA, which is thus physically inherent to the nucleic acid, is related to how recombination proteins mediate recognition of sequence homology and execute strand exchange. Our hypothesis is that a homogeneously stretched DNA undergoes a 'disproportionation' into an inhomogeneous Σ-form consisting of triplets of locally B-like perpendicularly stacked bases. This structure may ensure improved fidelity of base-pair recognition and promote rejection in case of mismatch during homologous recombination reaction. Because a triplet is the length of a gene codon, we speculate that the structural physics of nucleic acids may have biased the evolution of recombinase proteins to exploit triplet base stacks and also the genetic code.

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Section: Introductionmentioning

confidence: 99%

A stretched conformation of DNA with a biological role?

Bosaeus

Reymer

Beke‐Somfai

et al. 2017

Quart. Rev. Biophys.

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“…An examination of the crystal structure of RecA (Story et al 1992), shows that residue 129 is present in an amphipathic a-helix which is designated helix E. This a-helix is predicted to be involved in interactions which form the protein-protein interface (Story et al 1992). When monomers pack against one another to form the nucleoprotein filament, the a-helix E and bsheet 3 of one monomer pack against the a-helix A and b-sheet 0 of the monomer below (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…These residues are situated 4.1 Å (I141), 3.55 Å (V143) and 4.3 Å (L189) from the sulphur group of C129. Loops 1 and 2, which are connected to b-sheets 4 and 5, respectively, project into the filament core and may be involved in DNA binding (Story et al 1992). I141 and V143 are located within one of the two highly conserved Walker motifs (Walker et al 1982)-motif B-which corresponds to residues 140-144, the most highly conserved region among all the RecA protein homologues studied to date (Karlin et al 1995;Karlin & Brocchieri 1996).…”

Section: Discussionmentioning

confidence: 99%

“…The numbers 1-5 indicate b-sheets 1-5. The numbering system and letter designations used are those of Story & Steitz (Story et al 1992). The large white arrow indicates the orientation of the view used to generate of residue M129.…”

Section: Characterization Of Reca1332mentioning

confidence: 99%

“…Alpha helix E has been proposed to be involved in forming one side of the subunit interface (Story et al 1992). The C129M mutation occurs on the hydrophobic face of a-helix E, which is opposite to that of the subunit interface.…”

Section: Characterization Of Reca1332mentioning

confidence: 99%

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Characterization of RecA1332 in vivo and in vitro. A role for α‐helix E as a liaison between the subunit–subunit interface and the DNA and ATP binding domains of RecA protein

Bianco¹,

Weinstock²

1998

Genes to Cells

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Background: The RecA protein of Escherichia coli is essential for homologous recombination and induction of the SOS response. RecA has three cysteines located at positions 90, 116 and 129. Chemical modification of these residues abolishes ATP hydrolysis and repressor cleavage, and causes a reduction in the DNA strand exchange and DNA strand annealing activities. Several mutants at each of these positions were isolated and partially characterized. One of these, recA1332, replaces cysteine 129 with methionine. Although this is a relatively conservative mutation based on hydrophobicity, recA1332 was completely defective for DNA repair but the purified protein was active for ATPase in vitro.

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Structural trees for protein superfamilies

Ефимов

1997

Proteins

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Structural trees for large protein superfamilies, such as beta proteins with the aligned beta sheet packing, beta proteins with the orthogonal packing of alpha helices, two-layer and three-layer alpha/beta proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of alpha helices and/or beta strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for alpha helices to be packed in alpha-helical layers and beta strands in beta layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of alpha helices and/or beta strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold.

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The structure of the E. coli recA protein monomer and polymer

Cited by 735 publications

References 65 publications

A stretched conformation of DNA with a biological role?

A stretched conformation of DNA with a biological role?

Characterization of RecA1332 in vivo and in vitro. A role for α‐helix E as a liaison between the subunit–subunit interface and the DNA and ATP binding domains of RecA protein

Structural trees for protein superfamilies

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