Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

Paul Murphy; Yingqi Xu; Sarah L.  Rouse; Ellis G. Jaffray; Anna Plechanovova; Steve J. Matthews; J. Carlos Penedo; Ronald Hay

doi:10.1038/s41467-020-17647-x

Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

Paul Murphy, Yingqi Xu, Sarah L. Rouse, Ellis G. Jaffray, Anna Plechanovova, Steve J. Matthews, J. Carlos Penedo, Ronald Hay (Lead / Corresponding author)

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Abstract

The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2~Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction.
Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.

Original language	English
Article number	3807
Number of pages	13
Journal	Nature Communications
Volume	11
DOIs	https://doi.org/10.1038/s41467-020-17647-x
Publication status	Published - 30 Jul 2020

Keywords

Enzyme mechanisms
Molecular conformation
Solution-state NMR
Ubiquitylation

ASJC Scopus subject areas

General Physics and Astronomy
General Chemistry
General Biochemistry,Genetics and Molecular Biology

Access to Document

10.1038/s41467-020-17647-xLicence: CC BY

Final Published VersionFinal published version, 3.14 MBLicence: CC BY

Cite this

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title = "Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer",

abstract = "The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2\textasciitilde{}Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction. Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function. ",

keywords = "Enzyme mechanisms, Molecular conformation, Solution-state NMR, Ubiquitylation",

author = "Paul Murphy and Yingqi Xu and Rouse, \{Sarah L.\} and Jaffray, \{Ellis G.\} and Anna Plechanovova and Matthews, \{Steve J.\} and Penedo, \{J. Carlos\} and Ronald Hay",

note = "This work was supported by the following grants: Wellcome Trust Investigator Award (098391/Z/12/Z) to R.T.H., Wellcome Trust Studentship (109113/Z/15/Z) to P.M., Wellcome Trust Collaborative Award (215539) and multiuser equipment grant (104833) to S.J.M. Additionally J.C.P. thanks the Scottish Universities Physics Alliance (SUPA) and the University of St. Andrews for financial support. We would also like to thank Michael Tatham for his contribution to data analysis and Federico Pelisch for his feedback on the manuscript. In addition, we would like to acknowledge Professor Takeshi Urano (Shimane University School of Medicine, Japan) for kindly providing the monoclonal antibody to RNF4. ",

year = "2020",

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doi = "10.1038/s41467-020-17647-x",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

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T1 - Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

AU - Murphy, Paul

AU - Xu, Yingqi

AU - Rouse, Sarah L.

AU - Jaffray, Ellis G.

AU - Plechanovova, Anna

AU - Matthews, Steve J.

AU - Penedo, J. Carlos

AU - Hay, Ronald

N1 - This work was supported by the following grants: Wellcome Trust Investigator Award (098391/Z/12/Z) to R.T.H., Wellcome Trust Studentship (109113/Z/15/Z) to P.M., Wellcome Trust Collaborative Award (215539) and multiuser equipment grant (104833) to S.J.M. Additionally J.C.P. thanks the Scottish Universities Physics Alliance (SUPA) and the University of St. Andrews for financial support. We would also like to thank Michael Tatham for his contribution to data analysis and Federico Pelisch for his feedback on the manuscript. In addition, we would like to acknowledge Professor Takeshi Urano (Shimane University School of Medicine, Japan) for kindly providing the monoclonal antibody to RNF4.

PY - 2020/7/30

Y1 - 2020/7/30

N2 - The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2~Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction. Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.

AB - The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2~Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction. Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.

KW - Enzyme mechanisms

KW - Molecular conformation

KW - Solution-state NMR

KW - Ubiquitylation

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DO - 10.1038/s41467-020-17647-x

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VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 3807

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Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

Abstract

Keywords

ASJC Scopus subject areas

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Harnessing the PML-SUMO-RNF4 Axis for Cancer Therapy (Programme Grant)

Wellcome Trust PhD Studentship

Determining the Role and Mechanism of Action of SUMO Targeted Ubiquitin Ligase RNF4 in Maintaining Genome Integrity (Senior Investigator Award)