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Purser N, Tripathi-Giesgen I, Li J, Scott DC, Horn-Ghetko D, Baek K, Schulman BA, Alpi AF, Kleiger G. Catalysis of non-canonical protein ubiquitylation by the ARIH1 ubiquitin ligase. Biochem J 2023; 480:1817-1831. [PMID: 37870100 PMCID: PMC10657180 DOI: 10.1042/bcj20230373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Protein ubiquitylation typically involves isopeptide bond formation between the C-terminus of ubiquitin to the side-chain amino group on Lys residues. However, several ubiquitin ligases (E3s) have recently been identified that ubiquitylate proteins on non-Lys residues. For instance, HOIL-1 belongs to the RING-in-between RING (RBR) class of E3s and has an established role in Ser ubiquitylation. Given the homology between HOIL-1 and ARIH1, an RBR E3 that functions with the large superfamily of cullin-RING E3 ligases (CRLs), a biochemical investigation was undertaken, showing ARIH1 catalyzes Ser ubiquitylation to CRL-bound substrates. However, the efficiency of ubiquitylation was exquisitely dependent on the location and chemical environment of the Ser residue within the primary structure of the substrate. Comprehensive mutagenesis of the ARIH1 Rcat domain identified residues whose mutation severely impacted both oxyester and isopeptide bond formation at the preferred site for Ser ubiquitylation while only modestly affecting Lys ubiquitylation at the physiological site. The results reveal dual isopeptide and oxyester protein ubiquitylation activities of ARIH1 and set the stage for physiological investigations into this function of emerging importance.
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Affiliation(s)
- Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Daniel C. Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Arno F. Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
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Wang XS, Cotton TR, Trevelyan SJ, Richardson LW, Lee WT, Silke J, Lechtenberg BC. The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family. Nat Commun 2023; 14:168. [PMID: 36631489 PMCID: PMC9834252 DOI: 10.1038/s41467-023-35871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
The RING-between-RING (RBR) E3 ubiquitin ligase family in humans comprises 14 members and is defined by a two-step catalytic mechanism in which ubiquitin is first transferred from an E2 ubiquitin-conjugating enzyme to the RBR active site and then to the substrate. To define the core features of this catalytic mechanism, we here structurally and biochemically characterise the two RBRs HOIL-1 and RNF216. Crystal structures of both enzymes in their RBR/E2-Ub/Ub transthiolation complexes capturing the first catalytic step, together with complementary functional experiments, reveal the defining features of the RBR catalytic mechanism. RBRs catalyse ubiquitination via a conserved transthiolation complex structure that enables efficient E2-to-RBR ubiquitin transfer. Our data also highlight a conserved RBR allosteric activation mechanism by distinct ubiquitin linkages that suggests RBRs employ a feed-forward mechanism. We finally identify that the HOIL-1 RING2 domain contains an unusual Zn2/Cys6 binuclear cluster that is required for catalytic activity and substrate ubiquitination.
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Affiliation(s)
- Xiangyi S Wang
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Thomas R Cotton
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Sarah J Trevelyan
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Lachlan W Richardson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Wei Ting Lee
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - John Silke
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Bernhard C Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Wu Q, Koliopoulos MG, Rittinger K, Stieglitz B. Structural basis for ubiquitylation by HOIL-1. Front Mol Biosci 2023; 9:1098144. [PMID: 36685275 PMCID: PMC9853177 DOI: 10.3389/fmolb.2022.1098144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
The linear ubiquitin chain assembly complex synthesises linear Ub chains which constitute a binding and activation platform for components of the TNF signalling pathway. One of the components of LUBAC is the ubiquitin ligase HOIL-1 which has been shown to generate oxyester linkages on several proteins and on linear polysaccharides. We show that HOIL-1 activity requires linear tetra-Ub binding which enables HOIL-1 to mono-ubiquitylate linear Ub chains and polysaccharides. Furthermore, we describe the crystal structure of a C-terminal tandem domain construct of HOIL-1 comprising the IBR and RING2 domains. Interestingly, the structure reveals a unique bi-nuclear Zn-cluster which substitutes the second zinc finger of the canonical RING2 fold. We identify the C-terminal histidine of this bi-nuclear Zn-cluster as the catalytic base required for the ubiquitylation activity of HOIL-1. Our study suggests that the unique zinc-coordinating architecture of RING2 provides a binding platform for ubiquitylation targets.
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Affiliation(s)
- Qilong Wu
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Marios G. Koliopoulos
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom,*Correspondence: Katrin Rittinger, ; Benjamin Stieglitz,
| | - Benjamin Stieglitz
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom,*Correspondence: Katrin Rittinger, ; Benjamin Stieglitz,
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Stieglitz B. HHARI in motion reveals an unexpected substrate recognition site for RBR ligases. Structure 2022; 30:1221-1223. [PMID: 36055221 DOI: 10.1016/j.str.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Capturing the enzymatic activity of RBR ligases in molecular detail is challenging due to their inherent dynamic behavior. In this issue of Structure, Reiter and colleagues tackle this problem using a multidisciplinary approach. They show that activation of the ubiquitin ligase HHARI by phosphorylation induces a major conformational rearrangement, which reveals an unexpected substrate binding site.
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Affiliation(s)
- Benjamin Stieglitz
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, Blizard Institute, 4 Newark Street, London E1 2AT, UK.
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