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The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.

Serre MC, El Arnaout T, Brooks MA, Durand D, Lisboa J, Lazar N, Raynal B, van Tilbeurgh H, Quevillon-Cheruel S - PLoS ONE (2013)

Bottom Line: Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates.Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis.We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

View Article: PubMed Central - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France. marie-claude.serre@igmors.u-psud.fr

ABSTRACT
Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

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Predicted molecular switches leading to XerA activation.Two monomers of XerA are represented in grey and green. The catalytic Tyr is in red, the sulfate ion in cyan and the αMN helices in orange or blue. The structure of a double stranded DNA is represented in gold. Equilibrium between monomer and dimer conformations is represented by a two-way arrow. The DNA binding step is represented by a single arrow. Two angles of view are represented for each step, showing the switch of αN helices from one subunit to the other. αN helices are not involved in stabilisation of the XerA apo-dimer whereas they are essential to stabilise subunits within the synaptic complex. The αN helices switch from the cis to the trans position induces active site assembly. The last step is illustrated by the X-ray structure of Cre bound to DNA (cartooned at the bottom left with the same colour code). The XerA dimer bound to DNA was inferred from the AB Cre dimer.
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pone-0063010-g009: Predicted molecular switches leading to XerA activation.Two monomers of XerA are represented in grey and green. The catalytic Tyr is in red, the sulfate ion in cyan and the αMN helices in orange or blue. The structure of a double stranded DNA is represented in gold. Equilibrium between monomer and dimer conformations is represented by a two-way arrow. The DNA binding step is represented by a single arrow. Two angles of view are represented for each step, showing the switch of αN helices from one subunit to the other. αN helices are not involved in stabilisation of the XerA apo-dimer whereas they are essential to stabilise subunits within the synaptic complex. The αN helices switch from the cis to the trans position induces active site assembly. The last step is illustrated by the X-ray structure of Cre bound to DNA (cartooned at the bottom left with the same colour code). The XerA dimer bound to DNA was inferred from the AB Cre dimer.

Mentions: The cis packing observed for the XerA αMN helices could correspond to a dormant state of the enzyme. Binding to the DNA substrate would induce a switch of these helices towards the catalytic pocket thus initiating the catalytic cycle (Figure 9). Interestingly, the switch would not require dimer dissociation to occur as the XerA dimer interface can accommodate the required αMN helices movement.


The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.

Serre MC, El Arnaout T, Brooks MA, Durand D, Lisboa J, Lazar N, Raynal B, van Tilbeurgh H, Quevillon-Cheruel S - PLoS ONE (2013)

Predicted molecular switches leading to XerA activation.Two monomers of XerA are represented in grey and green. The catalytic Tyr is in red, the sulfate ion in cyan and the αMN helices in orange or blue. The structure of a double stranded DNA is represented in gold. Equilibrium between monomer and dimer conformations is represented by a two-way arrow. The DNA binding step is represented by a single arrow. Two angles of view are represented for each step, showing the switch of αN helices from one subunit to the other. αN helices are not involved in stabilisation of the XerA apo-dimer whereas they are essential to stabilise subunits within the synaptic complex. The αN helices switch from the cis to the trans position induces active site assembly. The last step is illustrated by the X-ray structure of Cre bound to DNA (cartooned at the bottom left with the same colour code). The XerA dimer bound to DNA was inferred from the AB Cre dimer.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646895&req=5

pone-0063010-g009: Predicted molecular switches leading to XerA activation.Two monomers of XerA are represented in grey and green. The catalytic Tyr is in red, the sulfate ion in cyan and the αMN helices in orange or blue. The structure of a double stranded DNA is represented in gold. Equilibrium between monomer and dimer conformations is represented by a two-way arrow. The DNA binding step is represented by a single arrow. Two angles of view are represented for each step, showing the switch of αN helices from one subunit to the other. αN helices are not involved in stabilisation of the XerA apo-dimer whereas they are essential to stabilise subunits within the synaptic complex. The αN helices switch from the cis to the trans position induces active site assembly. The last step is illustrated by the X-ray structure of Cre bound to DNA (cartooned at the bottom left with the same colour code). The XerA dimer bound to DNA was inferred from the AB Cre dimer.
Mentions: The cis packing observed for the XerA αMN helices could correspond to a dormant state of the enzyme. Binding to the DNA substrate would induce a switch of these helices towards the catalytic pocket thus initiating the catalytic cycle (Figure 9). Interestingly, the switch would not require dimer dissociation to occur as the XerA dimer interface can accommodate the required αMN helices movement.

Bottom Line: Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates.Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis.We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

View Article: PubMed Central - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France. marie-claude.serre@igmors.u-psud.fr

ABSTRACT
Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

Show MeSH
Related in: MedlinePlus