Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

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

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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.

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

Cite this

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title = "Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin",

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 A.N. 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",

year = "2021",

month = jun,

day = "18",

doi = "10.1107/S2059798321004873",

language = "English",

volume = "77",

pages = "904--920",

journal = "Acta Crystallographica Section D: Structural Biology (2016- )",

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publisher = "International Union of Crystallography",

number = "Pt 7",

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T1 - Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

AU - Garcia Rodriguez, Gabriela

AU - Girardin, Yana

AU - Volkov, A.N.

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.

KW - Toxin-Antitoxin module

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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U2 - 10.1107/S2059798321004873

DO - 10.1107/S2059798321004873

M3 - Article

C2 - 34196617

SN - 0907-4449

VL - 77

SP - 904

EP - 920

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

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

IS - Pt 7

ER -

Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

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Entropic pressure controls olgomerization of Vibrio cholerae ParD2 antitoxin

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