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Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approac...

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Autores principales: Felicori, Liza, Jameson, Katie H., Roblin, Pierre, Fogg, Mark J., Garcia-Garcia, Transito, Ventroux, Magali, Cherrier, Mickaël V., Bazin, Alexandre, Noirot, Philippe, Wilkinson, Anthony J., Molina, Franck, Terradot, Laurent, Noirot-Gros, Marie-Françoise
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705661/
https://www.ncbi.nlm.nih.gov/pubmed/26615189
http://dx.doi.org/10.1093/nar/gkv1318
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author Felicori, Liza
Jameson, Katie H.
Roblin, Pierre
Fogg, Mark J.
Garcia-Garcia, Transito
Ventroux, Magali
Cherrier, Mickaël V.
Bazin, Alexandre
Noirot, Philippe
Wilkinson, Anthony J.
Molina, Franck
Terradot, Laurent
Noirot-Gros, Marie-Françoise
author_facet Felicori, Liza
Jameson, Katie H.
Roblin, Pierre
Fogg, Mark J.
Garcia-Garcia, Transito
Ventroux, Magali
Cherrier, Mickaël V.
Bazin, Alexandre
Noirot, Philippe
Wilkinson, Anthony J.
Molina, Franck
Terradot, Laurent
Noirot-Gros, Marie-Françoise
author_sort Felicori, Liza
collection PubMed
description YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.
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spelling pubmed-47056612016-01-11 Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners Felicori, Liza Jameson, Katie H. Roblin, Pierre Fogg, Mark J. Garcia-Garcia, Transito Ventroux, Magali Cherrier, Mickaël V. Bazin, Alexandre Noirot, Philippe Wilkinson, Anthony J. Molina, Franck Terradot, Laurent Noirot-Gros, Marie-Françoise Nucleic Acids Res Structural Biology YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell. Oxford University Press 2016-01-08 2015-11-28 /pmc/articles/PMC4705661/ /pubmed/26615189 http://dx.doi.org/10.1093/nar/gkv1318 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 Structural Biology
Felicori, Liza
Jameson, Katie H.
Roblin, Pierre
Fogg, Mark J.
Garcia-Garcia, Transito
Ventroux, Magali
Cherrier, Mickaël V.
Bazin, Alexandre
Noirot, Philippe
Wilkinson, Anthony J.
Molina, Franck
Terradot, Laurent
Noirot-Gros, Marie-Françoise
Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title_full Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title_fullStr Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title_full_unstemmed Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title_short Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners
title_sort tetramerization and interdomain flexibility of the replication initiation controller yaba enables simultaneous binding to multiple partners
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705661/
https://www.ncbi.nlm.nih.gov/pubmed/26615189
http://dx.doi.org/10.1093/nar/gkv1318
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