Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Wei-Wei Kung; Sarath Ramachandran; Nikolai Makukhin; Elvira Bruno; Alessio Ciulli

doi:10.1038/s41467-019-10190-4

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Wei-Wei Kung, Sarath Ramachandran, Nikolai Makukhin, Elvira Bruno, Alessio Ciulli (Lead / Corresponding author)

Biological Chemistry and Drug Discovery

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

31 Citations (Scopus)

213 Downloads (Pure)

Abstract

The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2 ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.

Original language	English
Article number	2534
Pages (from-to)	1-14
Number of pages	14
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-10190-4
Publication status	Published - 10 Jun 2019

Keywords

Crystallography, X-Ray
Humans
Phosphotyrosine/chemistry
Polymorphism, Single Nucleotide
Protein Conformation
Receptors, Erythropoietin/chemistry
Receptors, Somatotropin/chemistry
Sequence Alignment
Substrate Specificity
Suppressor of Cytokine Signaling Proteins/chemistry
Ubiquitin-Protein Ligases/chemistry
Ubiquitination

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41467-019-10190-4Licence: CC BY

Final Published VersionFinal published version, 2.68 MBLicence: CC BY

Cite this

@article{4d14951731be468ea5cee08e8616d46b,

title = "Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase",

abstract = "The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2 ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 {\AA} and 2.69 {\AA}, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.",

keywords = "Crystallography, X-Ray, Humans, Phosphotyrosine/chemistry, Polymorphism, Single Nucleotide, Protein Conformation, Receptors, Erythropoietin/chemistry, Receptors, Somatotropin/chemistry, Sequence Alignment, Substrate Specificity, Suppressor of Cytokine Signaling Proteins/chemistry, Ubiquitin-Protein Ligases/chemistry, Ubiquitination",

author = "Wei-Wei Kung and Sarath Ramachandran and Nikolai Makukhin and Elvira Bruno and Alessio Ciulli",

note = "This project has received funding from the European Research Council (ERC) under the European Union{\textquoteright}s Seventh Framework Programme (FP7/2007-2013) as a Starting Grant to A.C. (grant agreement No. ERC-2012-StG-311460 DrugE3CRLs). Biophysics and drug discovery activities at Dundee are supported by Wellcome Trust strategic awards (100476/Z/12/Z and 094090/Z/10/Z, respectively). W.K. was supported by a PhD Scholarship by the School of Life Sciences at the University of Dundee",

year = "2019",

month = jun,

day = "10",

doi = "10.1038/s41467-019-10190-4",

language = "English",

volume = "10",

pages = "1--14",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

TY - JOUR

T1 - Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

AU - Kung, Wei-Wei

AU - Ramachandran, Sarath

AU - Makukhin, Nikolai

AU - Bruno, Elvira

AU - Ciulli, Alessio

N1 - This project has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) as a Starting Grant to A.C. (grant agreement No. ERC-2012-StG-311460 DrugE3CRLs). Biophysics and drug discovery activities at Dundee are supported by Wellcome Trust strategic awards (100476/Z/12/Z and 094090/Z/10/Z, respectively). W.K. was supported by a PhD Scholarship by the School of Life Sciences at the University of Dundee

PY - 2019/6/10

Y1 - 2019/6/10

N2 - The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2 ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.

AB - The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2 ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.

KW - Crystallography, X-Ray

KW - Humans

KW - Phosphotyrosine/chemistry

KW - Polymorphism, Single Nucleotide

KW - Protein Conformation

KW - Receptors, Erythropoietin/chemistry

KW - Receptors, Somatotropin/chemistry

KW - Sequence Alignment

KW - Substrate Specificity

KW - Suppressor of Cytokine Signaling Proteins/chemistry

KW - Ubiquitin-Protein Ligases/chemistry

KW - Ubiquitination

UR - http://www.scopus.com/inward/record.url?scp=85067182103&partnerID=8YFLogxK

U2 - 10.1038/s41467-019-10190-4

DO - 10.1038/s41467-019-10190-4

M3 - Article

C2 - 31182716

SN - 2041-1723

VL - 10

SP - 1

EP - 14

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2534

ER -

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)

A Translational Engine for Biomedical Discoveries (Strategic Grant)

Cite this

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Projects

DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)

A Translational Engine for Biomedical Discoveries (Strategic Grant)

Cite this