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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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Structure comparison of apo-XerA and Cre bound to DNA monomers.apo-XerA (grey) and Cre (green) complexed to DNA (gold) are superimposed by their catalytic domains. The XerA catalytic Tyr (Y261) is extruded from the catalytic site. The variable C-terminal αMN helices of XerA are in orange and the C-terminal αMN helices of Cre are in blue. The two N-terminal domains differ in their orientations by about 45°, but exhibit approximately the same concave accessible surface openness.
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pone-0063010-g002: Structure comparison of apo-XerA and Cre bound to DNA monomers.apo-XerA (grey) and Cre (green) complexed to DNA (gold) are superimposed by their catalytic domains. The XerA catalytic Tyr (Y261) is extruded from the catalytic site. The variable C-terminal αMN helices of XerA are in orange and the C-terminal αMN helices of Cre are in blue. The two N-terminal domains differ in their orientations by about 45°, but exhibit approximately the same concave accessible surface openness.

Mentions: The XerA dimer differs from DNA bound dimers formed by other Tyr-recombinases. Within the XerA dimer the catalytic domains are related to one another by 180 degrees instead of about 90 degrees in the Cre Holliday junction intermediate (Figure S1). In addition, upon superimposition of the C-terminal domains of XerA and Cre bound to DNA, the N-terminal domain of each XerA monomer deviates by 45° (Figure 2). This deviation suggests that upon DNA binding the XerA N-terminal domain could relocate to clamp DNA, thus repositioning above the C-terminal domain as it is observed for Cre and other Tyr-recombinases (Figure 2).


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)

Structure comparison of apo-XerA and Cre bound to DNA monomers.apo-XerA (grey) and Cre (green) complexed to DNA (gold) are superimposed by their catalytic domains. The XerA catalytic Tyr (Y261) is extruded from the catalytic site. The variable C-terminal αMN helices of XerA are in orange and the C-terminal αMN helices of Cre are in blue. The two N-terminal domains differ in their orientations by about 45°, but exhibit approximately the same concave accessible surface openness.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0063010-g002: Structure comparison of apo-XerA and Cre bound to DNA monomers.apo-XerA (grey) and Cre (green) complexed to DNA (gold) are superimposed by their catalytic domains. The XerA catalytic Tyr (Y261) is extruded from the catalytic site. The variable C-terminal αMN helices of XerA are in orange and the C-terminal αMN helices of Cre are in blue. The two N-terminal domains differ in their orientations by about 45°, but exhibit approximately the same concave accessible surface openness.
Mentions: The XerA dimer differs from DNA bound dimers formed by other Tyr-recombinases. Within the XerA dimer the catalytic domains are related to one another by 180 degrees instead of about 90 degrees in the Cre Holliday junction intermediate (Figure S1). In addition, upon superimposition of the C-terminal domains of XerA and Cre bound to DNA, the N-terminal domain of each XerA monomer deviates by 45° (Figure 2). This deviation suggests that upon DNA binding the XerA N-terminal domain could relocate to clamp DNA, thus repositioning above the C-terminal domain as it is observed for Cre and other Tyr-recombinases (Figure 2).

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