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Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion

Two critical steps controlling serine recombinase activity are the remodeling of dimers into the chemically active synaptic tetramer and the regulation of subunit rotation during DNA exchange. We identify a set of hydrophobic residues within the oligomerization helix that controls these steps by the...

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Autores principales: Chang, Yong, Johnson, Reid C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513852/
https://www.ncbi.nlm.nih.gov/pubmed/26056171
http://dx.doi.org/10.1093/nar/gkv565
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author Chang, Yong
Johnson, Reid C.
author_facet Chang, Yong
Johnson, Reid C.
author_sort Chang, Yong
collection PubMed
description Two critical steps controlling serine recombinase activity are the remodeling of dimers into the chemically active synaptic tetramer and the regulation of subunit rotation during DNA exchange. We identify a set of hydrophobic residues within the oligomerization helix that controls these steps by the Hin DNA invertase. Phe105 and Met109 insert into hydrophobic pockets within the catalytic domain of the same subunit to stabilize the inactive dimer conformation. These rotate out of the catalytic domain in the dimer and into the subunit rotation interface of the tetramer. About half of residue 105 and 109 substitutions gain the ability to generate stable synaptic tetramers and/or promote DNA chemistry without activation by the Fis/enhancer element. Phe106 replaces Phe105 in the catalytic domain pocket to stabilize the tetramer conformation. Significantly, many of the residue 105 and 109 substitutions support subunit rotation but impair ligation, implying a defect in rotational pausing at the tetrameric conformer poised for ligation. We propose that a ratchet-like surface involving Phe105, Met109 and Leu112 within the rotation interface functions to gate the subunit rotation reaction. Hydrophobic residues are present in analogous positions in other serine recombinases and likely perform similar functions.
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spelling pubmed-45138522015-07-27 Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion Chang, Yong Johnson, Reid C. Nucleic Acids Res Nucleic Acid Enzymes Two critical steps controlling serine recombinase activity are the remodeling of dimers into the chemically active synaptic tetramer and the regulation of subunit rotation during DNA exchange. We identify a set of hydrophobic residues within the oligomerization helix that controls these steps by the Hin DNA invertase. Phe105 and Met109 insert into hydrophobic pockets within the catalytic domain of the same subunit to stabilize the inactive dimer conformation. These rotate out of the catalytic domain in the dimer and into the subunit rotation interface of the tetramer. About half of residue 105 and 109 substitutions gain the ability to generate stable synaptic tetramers and/or promote DNA chemistry without activation by the Fis/enhancer element. Phe106 replaces Phe105 in the catalytic domain pocket to stabilize the tetramer conformation. Significantly, many of the residue 105 and 109 substitutions support subunit rotation but impair ligation, implying a defect in rotational pausing at the tetrameric conformer poised for ligation. We propose that a ratchet-like surface involving Phe105, Met109 and Leu112 within the rotation interface functions to gate the subunit rotation reaction. Hydrophobic residues are present in analogous positions in other serine recombinases and likely perform similar functions. Oxford University Press 2015-07-27 2015-06-08 /pmc/articles/PMC4513852/ /pubmed/26056171 http://dx.doi.org/10.1093/nar/gkv565 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Nucleic Acid Enzymes
Chang, Yong
Johnson, Reid C.
Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title_full Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title_fullStr Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title_full_unstemmed Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title_short Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion
title_sort controlling tetramer formation, subunit rotation and dna ligation during hin-catalyzed dna inversion
topic Nucleic Acid Enzymes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513852/
https://www.ncbi.nlm.nih.gov/pubmed/26056171
http://dx.doi.org/10.1093/nar/gkv565
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