Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

Gabriela Garcia Rodriguez; Yana Girardin; Oleksandr Volkov; Ranjan Kumar Singh; Gopinath Muruganandam; Jeroen Van Dyck; Frank Sobott; Wim Versées; Daniel Charlier; Remy Loris

doi:10.1107/S2059798321004873

Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

Gabriela Garcia Rodriguez, Yana Girardin, Oleksandr Volkov, Ranjan Kumar Singh, Gopinath Muruganandam, Jeroen Van Dyck, Frank Sobott, Wim Versées, Daniel Charlier, Remy Loris

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

101 Downloads (Pure)

Abstract

ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA binding domain followed by an intrinsically disordered ParE-neutralizing domain. In absence of the C-terminal IDP domain, VcParD2 crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open 10-mer or 12-mer, likely as a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows for an extended operator to wrap around the VcParD2 oligomer.

Original language	English
Pages (from-to)	904-920
Number of pages	17
Journal	Acta Crystallographica Section D: Structural Biology (2016- )
Volume	77
Issue number	Pt 7
DOIs	https://doi.org/10.1107/S2059798321004873
Publication status	Published - 18 Jun 2021

Keywords

Toxin-Antitoxin module
DNA binding
Transcription regulation
Intrinsicallydisordered protein
Protein oligomerization
X-ray crystallography
SAXS
Oligomer interface
Protein-DNA interaction
Quaternary structure

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10.1107/S2059798321004873Licence: CC BY

67773259Final published version, 2.95 MBLicence: CC BY

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1 Active
2 Finished

FWOAL967: Structural and thermodynamic dissection of fuzzy protein-DNA interactions in a prokaryotic transcription factor
Loris, R.
1/01/20 → 31/12/23
Project: Fundamental
FWOTM961: Mechanism of Gyrase-poisoning by ParE and its rejuvenation by ParD
Loris, R. & Girardin, Y.
1/11/19 → 31/10/21
Project: Fundamental
FWOAL831: Regulation of persistence by the paaAR-paaA2-parE2 and cog4197-duf1019 operons from E. coli O157
Loris, R.
1/01/17 → 31/12/20
Project: Fundamental

3 Citations
1 Article
1 PhD Thesis

Prokaryote toxin-antitoxin modules: complex regulation of an unclear function
De Bruyn, P., Girardin, Y. & Loris, R., Jun 2021, In: Protein Sci. 30, 6, p. 1103-1113 11 p.
Research output: Contribution to journal › Article › peer-review

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10 Citations (Scopus)

115 Downloads (Pure)
Regulatory mechanisms behind the activities of bacterial HEPN ribonuclease RnlA and ParE2 gyrase poison
Garcia Rodriguez, G., 2020
Research output: Thesis › PhD Thesis

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Cite this

Garcia Rodriguez, Gabriela ; Girardin, Yana ; Volkov, Oleksandr ; Singh, Ranjan Kumar ; Muruganandam, Gopinath ; Van Dyck, Jeroen ; Sobott, Frank ; Versées, Wim ; Charlier, Daniel ; Loris, Remy. / Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin. In: Acta Crystallographica Section D: Structural Biology (2016- ). 2021 ; Vol. 77, No. Pt 7. pp. 904-920.

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abstract = "ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA binding domain followed by an intrinsically disordered ParE-neutralizing domain. In absence of the C-terminal IDP domain, VcParD2 crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open 10-mer or 12-mer, likely as a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows for an extended operator to wrap around the VcParD2 oligomer.",

keywords = "Toxin-Antitoxin module, DNA binding, Transcription regulation, Intrinsicallydisordered protein, Protein oligomerization, X-ray crystallography, SAXS, Oligomer interface, Protein-DNA interaction, Quaternary structure",

author = "{Garcia Rodriguez}, Gabriela and Yana Girardin and Oleksandr Volkov and Singh, {Ranjan Kumar} and Gopinath Muruganandam and {Van Dyck}, Jeroen and Frank Sobott and Wim Vers{\'e}es and Daniel Charlier and Remy Loris",

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Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin. / Garcia Rodriguez, Gabriela; Girardin, Yana ; Volkov, Oleksandr ; Singh, Ranjan Kumar; Muruganandam, Gopinath; Van Dyck, Jeroen; Sobott, Frank; Versées, Wim ; Charlier, Daniel ; Loris, Remy.

In: Acta Crystallographica Section D: Structural Biology (2016- ), Vol. 77, No. Pt 7, 18.06.2021, p. 904-920.

Research output: Contribution to journal › Article › peer-review

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AU - Garcia Rodriguez, Gabriela

AU - Girardin, Yana

AU - Volkov, Oleksandr

AU - Singh, Ranjan Kumar

AU - Muruganandam, Gopinath

AU - Van Dyck, Jeroen

AU - Sobott, Frank

AU - Versées, Wim

AU - Charlier, Daniel

AU - Loris, Remy

PY - 2021/6/18

Y1 - 2021/6/18

N2 - ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA binding domain followed by an intrinsically disordered ParE-neutralizing domain. In absence of the C-terminal IDP domain, VcParD2 crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open 10-mer or 12-mer, likely as a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows for an extended operator to wrap around the VcParD2 oligomer.

AB - ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA binding domain followed by an intrinsically disordered ParE-neutralizing domain. In absence of the C-terminal IDP domain, VcParD2 crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open 10-mer or 12-mer, likely as a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows for an extended operator to wrap around the VcParD2 oligomer.

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KW - DNA binding

KW - Transcription regulation

KW - Intrinsicallydisordered protein

KW - Protein oligomerization

KW - X-ray crystallography

KW - SAXS

KW - Oligomer interface

KW - Protein-DNA interaction

KW - Quaternary structure

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SP - 904

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JO - Acta Crystallographica Section D: Structural Biology (2016- )

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SN - 0907-4449

IS - Pt 7

ER -

Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

Abstract

Keywords

Access to Document

Fingerprint

Projects

FWOAL967: Structural and thermodynamic dissection of fuzzy protein-DNA interactions in a prokaryotic transcription factor

FWOTM961: Mechanism of Gyrase-poisoning by ParE and its rejuvenation by ParD

FWOAL831: Regulation of persistence by the paaAR-paaA2-parE2 and cog4197-duf1019 operons from E. coli O157

Research output

Prokaryote toxin-antitoxin modules: complex regulation of an unclear function

Regulatory mechanisms behind the activities of bacterial HEPN ribonuclease RnlA and ParE2 gyrase poison

Equipment

X-Ray Generator

Cite this