Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

Ramasubramanian Sundaramoorthy; Amanda L Hughes; Hassane El-Mkami; David G Norman; Helder Ferreira; Tom Owen-Hughes

doi:10.7554/eLife.35720

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

Ramasubramanian Sundaramoorthy, Amanda L Hughes, Hassane El-Mkami, David G Norman, Helder Ferreira, Tom Owen-Hughes

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

Abstract

ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.

Original language	English
Article number	e35720
Number of pages	28
Journal	eLife
Volume	7
DOIs	https://doi.org/10.7554/eLife.35720
Publication status	Published - 6 Aug 2018

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10.7554/eLife.35720Licence: CC BY

Sundaramoorthy_2018_eLife_Chd1_CC
Copyright. © 2018, Sundaramoorthy et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Final published version, 8 MBLicence: CC BY

State of the art pulse EPR instrumentati: State of the art pulse EPR instrumentation for long range distance measurements in biomacromolecules
Smith, G. M. (PI), Bode, B. E. (CoI), Naismith, J. (CoI), Schiemann, O. (CoI) & White, M. (CoI)
The Wellcome Trust
1/09/12 → 31/08/17
Project: Standard

Helder Ferreira
- hcf2st-andrews.acuk
Person: Academic

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosom (PDB dataset)
Sundaramoorthy, R. (Creator), Hughes, A. L. (Creator), El Mkami, H. (Creator), Norman, D. G. (Creator), Ferreira, H. C. (Creator) & Owen-Hughes, T. (Creator), EMBL-EBI, 22 Aug 2018
https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-4318 and one more link, https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-4336 (show fewer)
Dataset

Cite this

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title = "Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome",

abstract = "ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.",

author = "Ramasubramanian Sundaramoorthy and Hughes, {Amanda L} and Hassane El-Mkami and Norman, {David G} and Helder Ferreira and Tom Owen-Hughes",

note = "This work was funded by Wellcome Senior Fellowship 095062, Wellcome Trust grants 094090, 099149 and 097945. ALH was funded by an EMBO long term fellowship ALTF 380–2015 co-funded by the European Commission (LTFCOFUND2013, GA-2013–609409).",

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AU - Hughes, Amanda L

AU - El-Mkami, Hassane

AU - Norman, David G

AU - Ferreira, Helder

AU - Owen-Hughes, Tom

N1 - This work was funded by Wellcome Senior Fellowship 095062, Wellcome Trust grants 094090, 099149 and 097945. ALH was funded by an EMBO long term fellowship ALTF 380–2015 co-funded by the European Commission (LTFCOFUND2013, GA-2013–609409).

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Y1 - 2018/8/6

N2 - ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.

AB - ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.

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Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

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State of the art pulse EPR instrumentati: State of the art pulse EPR instrumentation for long range distance measurements in biomacromolecules

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Helder Ferreira

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Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosom (PDB dataset)

Cite this