1
|
Collins JC, Magaziner SJ, English M, Hassan B, Chen X, Balanda N, Anderson M, Lam A, Fernandez-Pol S, Kwong B, Greenberg PL, Terrier B, Likhite ME, Kosmider O, Wang Y, Samara NL, Walters KJ, Beck DB, Werner A. Shared and distinct mechanisms of UBA1 inactivation across different diseases. EMBO J 2024; 43:1919-1946. [PMID: 38360993 PMCID: PMC11099125 DOI: 10.1038/s44318-024-00046-z] [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: 09/22/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Most cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquired UBA1 missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causing UBA1 mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associated UBA1 mutations, but not in spinal muscular atrophy-causing UBA1 mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
Collapse
Affiliation(s)
- Jason C Collins
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA
| | - Samuel J Magaziner
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya English
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Nicholas Balanda
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Meghan Anderson
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Athena Lam
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | | | - Bernice Kwong
- Department of Dermatology, Stanford University Cancer Center, Stanford, CA, USA
| | - Peter L Greenberg
- Division of Hematology, Stanford University Cancer Center, Stanford, CA, USA
| | - Benjamin Terrier
- Department of Internal Medicine, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mary E Likhite
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Olivier Kosmider
- Laboratory of Hematology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Nadine L Samara
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Achim Werner
- Stem Cell Biochemistry Section, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
2
|
Nayak D, Lv D, Yuan Y, Zhang P, Hu W, Nayak A, Ruben EA, Lv Z, Sung P, Hromas R, Zheng G, Zhou D, Olsen SK. Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Nat Commun 2024; 15:2743. [PMID: 38548768 PMCID: PMC10979003 DOI: 10.1038/s41467-024-46922-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.
Collapse
Affiliation(s)
- Digant Nayak
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Dongwen Lv
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Peiyi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
| | - Daohong Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
3
|
Banerjee S, Varga JK, Kumar M, Zoltsman G, Rotem-Bamberger S, Cohen-Kfir E, Isupov MN, Rosenzweig R, Schueler-Furman O, Wiener R. Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation. EMBO Rep 2023; 24:e56920. [PMID: 37988244 DOI: 10.15252/embr.202356920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023] Open
Abstract
Ufmylation plays a crucial role in various cellular processes including DNA damage response, protein translation, and ER homeostasis. To date, little is known about how the enzymes responsible for ufmylation coordinate their action. Here, we study the details of UFL1 (E3) activity, its binding to UFC1 (E2), and its relation to UBA5 (E1), using a combination of structural modeling, X-ray crystallography, NMR, and biochemical assays. Guided by Alphafold2 models, we generate an active UFL1 fusion construct that includes its partner DDRGK1 and solve the crystal structure of this critical interaction. This fusion construct also unveiled the importance of the UFL1 N-terminal helix for binding to UFC1. The binding site suggested by our UFL1-UFC1 model reveals a conserved interface, and competition between UFL1 and UBA5 for binding to UFC1. This competition changes in the favor of UFL1 following UFM1 charging of UFC1. Altogether, our study reveals a novel, terminal helix-mediated regulatory mechanism, which coordinates the cascade of E1-E2-E3-mediated transfer of UFM1 to its substrate and provides new leads to target this modification.
Collapse
Affiliation(s)
- Sayanika Banerjee
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Julia K Varga
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manoj Kumar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
4
|
Collins JC, Magaziner SJ, English M, Hassan B, Chen X, Balanda N, Anderson M, Lam A, Fernandez-Pol S, Kwong B, Greenberg PL, Terrier B, Likhite ME, Kosmider O, Wang Y, Samara NL, Walters KJ, Beck DB, Werner A. Shared and Distinct Mechanisms of UBA1 Inactivation Across Different Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561769. [PMID: 37873213 PMCID: PMC10592724 DOI: 10.1101/2023.10.10.561769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Most cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquired UBA1 missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causing UBA1 mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associated UBA1 mutations, but not in spinal muscular atrophy-causing UBA1 mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
Collapse
Affiliation(s)
- Jason C. Collins
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Samuel J. Magaziner
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Maya English
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Nicholas Balanda
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Meghan Anderson
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Athena Lam
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | | | - Bernice Kwong
- Department of Dermatology, Stanford University Cancer Center, Stanford, CA, USA
| | - Peter L. Greenberg
- Division of Hematology, Stanford University Cancer Center, Stanford, California, USA
| | - Benjamin Terrier
- Department of Internal Medicine, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris
| | - Mary E. Likhite
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Olivier Kosmider
- Laboratory of Hematology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Nadine L. Samara
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| | - Kylie J. Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - David B. Beck
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National institutes of Health, Bethesda, MD
| |
Collapse
|
5
|
Afsar M, Liu G, Jia L, Ruben EA, Nayak D, Sayyad Z, Bury PDS, Cano KE, Nayak A, Zhao XR, Shukla A, Sung P, Wasmuth EV, Gack MU, Olsen SK. Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun 2023; 14:4786. [PMID: 37553340 PMCID: PMC10409785 DOI: 10.1038/s41467-023-39780-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells.
Collapse
Affiliation(s)
- Mohammad Afsar
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Zuberwasim Sayyad
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Xiang Ru Zhao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Ankita Shukla
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
6
|
Abstract
Background Identifying CO2-binding proteins is vital for our knowledge of CO2-regulated molecular processes. The carbamate post-translational modification is a reversible CO2-mediated adduct that can form on neutral N-terminal α-amino or lysine ε-amino groups. Methods We have developed triethyloxonium ion (TEO) as a chemical proteomics tool to trap the carbamate post-translational modification on protein covalently. We use 13C-NMR and TEO and identify ubiquitin as a plant CO2-binding protein. Results We observe the carbamate post-translational modification on the Arabidopsis thaliana ubiquitin ε-amino groups of lysines 6, 33, and 48. We show that biologically relevant near atmospheric PCO2 levels increase ubiquitin conjugation dependent on lysine 6. We further demonstrate that CO2 increases the ubiquitin E2 ligase (AtUBC5) charging step via the transthioesterification reaction in which Ub is transferred from the E1 ligase active site to the E2 active site. Conclusions and general significance Therefore, plant ubiquitin is a CO2-binding protein, and the carbamate post-translational modification represents a potential mechanism through which plant cells can respond to fluctuating PCO2.
Collapse
Affiliation(s)
- Harry G Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
| |
Collapse
|
7
|
Zhou L, Jeong IH, Xue S, Xue M, Wang L, Li S, Liu R, Jeong GH, Wang X, Cai J, Yin J, Huang B. Inhibition of the Ubiquitin Transfer Cascade by a Peptidomimetic Foldamer Mimicking the E2 N-Terminal Helix. J Med Chem 2023; 66:491-502. [PMID: 36571278 DOI: 10.1021/acs.jmedchem.2c01459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The enzymatic cascades for ubiquitin transfer regulate key cellular processes and are the intense focus of drug development for treating cancer and neurodegenerative diseases. E1 is at the apex of the UB transfer cascade, and molecules inhibiting E1 have shown promising activities against cancer cell proliferation. Compared to small molecules, peptidomimetics have emerged as powerful tools to disrupt the protein-protein interactions (PPI) with less drug resistance and high stability in the cell. Herein, we harnessed the D-sulfono-γ-AA peptide to mimic the N-terminal helix of E2 and thereby inhibit E1-E2 interaction. Two stapled peptidomimetics, M1-S1 and M1-S2, were identified as effective inhibitors to block UB transfer from E1 to E2, as shown by in vitro and cellular assays. Our work suggested that PPIs with the N-terminal helix of E2 at the E1-E2 and E2-E3 interfaces could be a promising target for designing inhibitors against protein ubiquitination pathways in the cell.
Collapse
Affiliation(s)
- Li Zhou
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - In Ho Jeong
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - Songyi Xue
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Menglin Xue
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Lei Wang
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Sihao Li
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Ruochuan Liu
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - Geon Ho Jeong
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - Xiaoyu Wang
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Jun Yin
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia30303, United States
| | - Bo Huang
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| |
Collapse
|
8
|
Yuan L, Gao F, Lv Z, Nayak D, Nayak A, Santos Bury PD, Cano KE, Jia L, Oleinik N, Atilgan FC, Ogretmen B, Williams KM, Davies C, El Oualid F, Wasmuth EV, Olsen SK. Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Nat Commun 2022; 13:4880. [PMID: 35986001 PMCID: PMC9391358 DOI: 10.1038/s41467-022-32613-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.
Collapse
Affiliation(s)
- Lingmin Yuan
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Fei Gao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Research & Development, Beijing IPE Center for Clinical Laboratory CO, Beijing, 100176, China
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Natalia Oleinik
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Firdevs Cansu Atilgan
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Katelyn M Williams
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Christopher Davies
- Department of Biochemistry & Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Farid El Oualid
- UbiQ Bio B.V., Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
9
|
Interactions of Environmental Variables and Water Use Efficiency in the Matopiba Region via Multivariate Analysis. SUSTAINABILITY 2022. [DOI: 10.3390/su14148758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This study aimed to evaluate the interaction of environmental variables and Water Use Efficiency (WUE) via multivariate analysis to understand the importance of each variable in the carbon–water balance in MATOPIBA. Principal Component Analysis (PCA) was applied to reduce spatial dimensionality and to identify patterns by using the following data: (i) LST (MOD11A2) and WUE (ratio between GPP-MOD17A2 and ET-MOD16A2), based on MODIS orbital products; (ii) Rainfall based on CHIRPS precipitation product; (iii) slope, roughness, and elevation from the GMTED and SRTM version 4.1 products; and (iv) geographic data, Latitude, and Longitude. All calculations were performed in R version 3.6.3 and Quantum GIS (QGIS) version 3.4.6. Eight variables were initially used. After applying the PCA, only four were suitable: Elevation, LST, Rainfall, and WUE, with values greater than 0.7. A positive correlation (≥0.78) between the variables (Elevation, LST, and Rainfall) and vegetation was identified. According to the KMO test, a series-considered medium was obtained (0.7 < KMO < 0.8), and it was explained by one PC (PC1). PC1 was explained by four variables (Elevation, LST, Rainfall, and WUE), among which WUE (0.8 < KMO < 0.9) was responsible for detailing 65.77% of the total explained variance. Positive scores were found in the states of Maranhão and Tocantins and negative scores in Piauí and Bahia. The positive scores show areas with greater Rainfall, GPP, and ET availability, while the negative scores show areas with greater water demand and LST. It was concluded that variations in variables such as Rainfall, LST, GPP, and ET can influence the local behavior of the carbon–water cycle of the vegetation, impacting the WUE in MATOPIBA.
Collapse
|
10
|
Ma Q, Lei H, Cao Y. Intramolecular covalent bonds in Gram-positive bacterial surface proteins. Chembiochem 2022; 23:e202200316. [PMID: 35801833 DOI: 10.1002/cbic.202200316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
Collapse
Affiliation(s)
- Quan Ma
- Nanjing University, Department of Physics, CHINA
| | - Hai Lei
- Nanjing University, Department of Physics, CHINA
| | - Yi Cao
- Nanjing University, Department of Physics, 22 Hankou Road, 210093, Nanjing, CHINA
| |
Collapse
|
11
|
E2 ubiquitin-conjugating enzymes (UBCs): drivers of ubiquitin signalling in plants. Essays Biochem 2022; 66:99-110. [PMID: 35766526 DOI: 10.1042/ebc20210093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/22/2022]
Abstract
Most research in the field of ubiquitination has focused on E3 ubiquitin ligases because they are the specificity determinants of the ubiquitination process. Nevertheless, E2s are responsible for the catalysis during ubiquitin transfer, and are therefore, at the heart of the ubiquitination process. Arabidopsis has 37 ubiquitin E2s with additional ones mediating the attachment of ubiquitin-like proteins (e.g. SUMO, Nedd8 and ATG8). Importantly, E2s largely determine the type of ubiquitin chain built, and therefore, the type of signal that decides over the fate of the modified protein, such as degradation by the proteasome (Lys48-linked ubiquitin chains) or relocalization (Lys63-linked ubiquitin chains). Moreover, new regulatory layers impinging on E2s activity, including post-translational modifications or cofactors, are emerging that highlight the importance of E2s.
Collapse
|
12
|
Nakasone MA, Majorek KA, Gabrielsen M, Sibbet GJ, Smith BO, Huang DT. Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension. Nat Chem Biol 2022; 18:422-431. [PMID: 35027744 PMCID: PMC8964413 DOI: 10.1038/s41589-021-00952-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.
Collapse
Affiliation(s)
| | | | - Mads Gabrielsen
- Cancer Research UK Beatson Institute, Glasgow, UK
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, Glasgow, UK
| | | | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
13
|
Sun H, Bai Y, Lu M, Wang J, Tuo Y, Yan D, Zhang W. Drivers of the water use efficiency changes in China during 1982-2015. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149145. [PMID: 34365270 DOI: 10.1016/j.scitotenv.2021.149145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/01/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
This study investigates the drivers of water use efficiency (WUE), a key metric of water resources management, and its changes over eight regions across China from 1982 to 2015 based on gross primary production (GPP) and actual evapotranspiration (AET) datasets. The order of seasonal change of WUE from large to small is autumn, summer, spring and winter. The drivers include seven variables, air temperature, specific humidity, precipitation, short-wave radiation, Normalized Difference Vegetation Index (NDVI), soil moisture and CO2. Our analysis suggests that the sensitivity of annual average NDVI to WUE changes was high nationwide, but there were some differences in seasonal scales. The annual average contribution of air temperature and CO2 affecting WUE change was relatively high in China's largest area (SW, SE, E, NP). Other influencing factors were only relatively high in the local area. Seasonally, NDVI is the driving factor with the highest contribution rate in summer and autumn for NC and NW region. The seasonal contribution rates of driving factors in other regions are significantly different. For the study period (1982-2015), the shrubland ecosystem had the highest annual WUE followed by forest and cropland. The WUE of the farmland ecosystem was higher than that of the grassland ecosystem in most areas.
Collapse
Affiliation(s)
- Huaiwei Sun
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Yiwen Bai
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Mengge Lu
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China.
| | - Jingfeng Wang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 30318 Atlanta, USA
| | - Ye Tuo
- Chair of Hydrology and River Basin Management, Technical University of Munich, Arcisstrasse 21, 80333 Munich, Germany
| | - Dong Yan
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China.
| | - Wenxin Zhang
- Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 12, 22362 Lund, Sweden
| |
Collapse
|