1
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Hou XN, Tang C. The pros and cons of ubiquitination on the formation of protein condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1084-1098. [PMID: 37294105 PMCID: PMC10423694 DOI: 10.3724/abbs.2023096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Ubiquitination, a post-translational modification that attaches one or more ubiquitin (Ub) molecules to another protein, plays a crucial role in the phase-separation processes. Ubiquitination can modulate the formation of membrane-less organelles in two ways. First, a scaffold protein drives phase separation, and Ub is recruited to the condensates. Second, Ub actively phase-separates through the interactions with other proteins. Thus, the role of ubiquitination and the resulting polyUb chains ranges from bystanders to active participants in phase separation. Moreover, long polyUb chains may be the primary driving force for phase separation. We further discuss that the different roles can be determined by the lengths and linkages of polyUb chains which provide preorganized and multivalent binding platforms for other client proteins. Together, ubiquitination adds a new layer of regulation for the flow of material and information upon cellular compartmentalization of proteins.
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Affiliation(s)
- Xue-Ni Hou
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chun Tang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Center for Quantitate BiologyPKU-Tsinghua Center for Life ScienceAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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2
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Hiranyakorn M, Yagi-Utsumi M, Yanaka S, Ohtsuka N, Momiyama N, Satoh T, Kato K. Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains. Int J Mol Sci 2023; 24:ijms24076075. [PMID: 37047047 PMCID: PMC10094362 DOI: 10.3390/ijms24076075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
In multidomain proteins, individual domains connected by flexible linkers are dynamically rearranged upon ligand binding and sensing changes in environmental factors, such as pH and temperature. Here, we characterize dynamic domain rearrangements of Lys48-linked ubiquitin (Ub) chains as models of multidomain proteins in which molecular surfaces mediating intermolecular interactions are involved in intramolecular domain-domain interactions. Using NMR and other biophysical techniques, we characterized dynamic conformational interconversions of diUb between open and closed states regarding solvent exposure of the hydrophobic surfaces of each Ub unit, which serve as binding sites for various Ub-interacting proteins. We found that the hydrophobic Ub-Ub interaction in diUb was reinforced by cysteine substitution of Lys48 of the distal Ub unit because of interaction between the cysteinyl thiol group and the C-terminal segment of the proximal Ub unit. In contrast, the replacement of the isopeptide linker with an artificial ethylenamine linker minimally affected the conformational distributions. Furthermore, we demonstrated that the mutational modification allosterically impacted the exposure of the most distal Ub unit in triUb. Thus, the conformational interconversion of Ub chains offers a unique design framework in Ub-based protein engineering not only for developing biosensing probes but also for allowing new opportunities for the allosteric regulation of multidomain proteins.
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Affiliation(s)
- Methanee Hiranyakorn
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Maho Yagi-Utsumi
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Saeko Yanaka
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Naoya Ohtsuka
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Norie Momiyama
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Department of Functional Molecular Science, School of Physical Science, The Graduate University for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
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3
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Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell 2021; 81:4176-4190.e6. [PMID: 34529927 PMCID: PMC8550791 DOI: 10.1016/j.molcel.2021.08.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/29/2021] [Accepted: 08/19/2021] [Indexed: 01/10/2023]
Abstract
Of the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains. The activity of MINDY1/2 is inhibited by the Cys-loop, and we find that substrate interaction relieves autoinhibition to activate these DUBs. We also find that MINDY1/2 use a non-canonical catalytic triad composed of Cys-His-Thr. Our findings highlight multiple layers of regulation modulating DUB activity in MINDY1 and MINDY2. The catalytic domain of MINDY1/2 has five distinct Ub binding sites Dynamics of the Cys loop regulate DUB activity Non-canonical catalytic triad composed of Cys-His-Thr MINDY1/2 uses an exo- or endo-cleavage mode that is determined by Ub chain length
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Lee A Armstrong
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sven M Lange
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yosua Adi Kristariyanto
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Tobias W Gräwert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Axel Knebel
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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4
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Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D, Zhang P, Walters KJ. Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome. Structure 2020; 28:1206-1217.e4. [PMID: 32783951 PMCID: PMC7642156 DOI: 10.1016/j.str.2020.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/06/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022]
Abstract
The 26S proteasome is specialized for regulated protein degradation and formed by a dynamic regulatory particle (RP) that caps a hollow cylindrical core particle (CP) where substrates are proteolyzed. Its diverse substrates unify as proteasome targets by ubiquitination. We used cryogenic electron microscopy (cryo-EM) to study how human 26S proteasome interacts with M1-linked hexaubiquitin (M1-Ub6) unanchored to a substrate and E3 ubiquitin ligase E6AP/UBE3A. Proteasome structures are available with model substrates extending through the RP ATPase ring and substrate-conjugated K63-linked ubiquitin chains present at inhibited deubiquitinating enzyme hRpn11 and the nearby ATPase hRpt4/hRpt5 coiled coil. In this study, we find M1-Ub6 at the hRpn11 site despite the absence of conjugated substrate, indicating that ubiquitin binding at this location does not require substrate interaction with the RP. Moreover, unanchored M1-Ub6 binds to this hRpn11 site of the proteasome with the CP gating residues in both the closed and opened conformational states.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zachary Dorris
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Frederick High School, Frederick, MD 21702, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Rick K Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Htet Khant
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe, AZ 85287, USA
| | - Ping Zhang
- Kinase Complexes Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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5
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Shine A, Shenoy J, Jayan P, Jiji AC, Vijayan V. Residual Dipolar‐Coupling‐Based Conformational Comparison of Noncovalent Ubiquitin Homodimer with Covalently Linked Diubiquitin. Chemphyschem 2020; 21:888-894. [DOI: 10.1002/cphc.201901100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- A. Shine
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - J. Shenoy
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Parvathy Jayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - A. C. Jiji
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Vinesh Vijayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
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6
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Lu X, Ebelle DL, Matsuo H, Walters KJ. An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Structure 2020; 28:495-506.e3. [PMID: 32160516 DOI: 10.1016/j.str.2020.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 12/24/2022]
Abstract
Rpn13/Adrm1 is recruited to the proteasome by PSMD1/Rpn2, where it serves as a substrate receptor that binds preferentially to K48-linked ubiquitin chains, an established signal for protein proteolysis. Here, we use NMR to solve the structure of hRpn13 Pru:hRpn2 (940-953):K48-diubiquitin. Surprisingly, hRpn2-bound hRpn13 selects a dynamic, extended conformation of K48-diubiquitin that is unique from previously determined structures. NMR experiments on free K48-diubiquitin demonstrate the presence of the reported "closed" conformation observed by crystallography, but also this more extended state, in which the hRpn13-binding surface is exposed. This extended K48-diubiquitin conformation is defined by interactions between L73 from G76-linked (distal) ubiquitin and a Y59-centered surface of K48-linked (proximal) ubiquitin. Furthermore, hRpn13 exchanges between the two ubiquitins within 100 ms, although prefers the proximal ubiquitin due to interactions with the K48 linker region. Altogether, these data lead to a revised model of how ubiquitinated substrates interact with the proteasome.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle L Ebelle
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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7
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Mass spectrometry techniques for studying the ubiquitin system. Biochem Soc Trans 2017; 45:1137-1148. [PMID: 28939693 DOI: 10.1042/bst20170091] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022]
Abstract
Post-translational control of proteins through covalent attachment of ubiquitin plays important roles in all eukaryotic cell functions. The ubiquitin system in humans consists of 2 E1, 35 E2 and >600 E3 ubiquitin ligases as well as hundreds of deubiquitylases, which reverse ubiquitin attachment. Moreover, there are hundreds of proteins with ubiquitin-binding domains that bind one of the eight possible polyubiquitin chains. Dysfunction of the ubiquitin system is associated with many diseases such as cancer, autoimmunity and neurodegeneration, demonstrating the importance of ubiquitylation. Therefore, enzymes of the ubiquitin system are considered highly attractive drug targets. In recent years, mass spectrometry (MS)-based techniques have become increasingly important in the deciphering of the ubiquitin system. This short review addresses the state-of-the-art MS techniques for the identification of ubiquitylated proteins and their ubiquitylation sites. We also discuss the identification and quantitation of ubiquitin chain topologies and highlight how the activity of enzymes in the ubiquitin pathway can be measured. Finally, we present current MS tools that can be used for drug discovery in the ubiquitin space.
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8
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Gao S, Pan M, Zheng Y, Huang Y, Zheng Q, Sun D, Lu L, Tan X, Tan X, Lan H, Wang J, Wang T, Wang J, Liu L. Monomer/Oligomer Quasi-Racemic Protein Crystallography. J Am Chem Soc 2016; 138:14497-14502. [PMID: 27768314 DOI: 10.1021/jacs.6b09545] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.
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Affiliation(s)
- Shuai Gao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yong Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yichao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Demeng Sun
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lining Lu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xiaodan Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xianglong Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Huan Lan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiaxing Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiawei Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
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9
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Trempe JF, Šašková KG, Sivá M, Ratcliffe CDH, Veverka V, Hoegl A, Ménade M, Feng X, Shenker S, Svoboda M, Kožíšek M, Konvalinka J, Gehring K. Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family. Sci Rep 2016; 6:33671. [PMID: 27646017 PMCID: PMC5028754 DOI: 10.1038/srep33671] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.
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Affiliation(s)
- Jean-François Trempe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Klára Grantz Šašková
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Monika Sivá
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Katerinska 32, 121 08, Prague 2, Czech Republic
| | - Colin D H Ratcliffe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Václav Veverka
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Annabelle Hoegl
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Marie Ménade
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Xin Feng
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Solomon Shenker
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Michal Svoboda
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Milan Kožíšek
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jan Konvalinka
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Kalle Gehring
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
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10
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A Cell Cycle-Regulated Toxoplasma Deubiquitinase, TgOTUD3A, Targets Polyubiquitins with Specific Lysine Linkages. mSphere 2016; 1:mSphere00085-16. [PMID: 27340699 PMCID: PMC4917281 DOI: 10.1128/msphere.00085-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/28/2016] [Indexed: 11/20/2022] Open
Abstract
The role of ubiquitin-mediated processes in the regulation of the apicomplexan cell cycle is beginning to be elucidated. The recent analysis of the Toxoplasma “ubiquitome” highlights the importance of ubiquitination in the parasite cell cycle. The machinery regulating the ubiquitin dynamics in T. gondii has remained understudied. Here, we provide a biochemical characterization of an OTU (ovarian tumor) family deubiquitinase, TgOTUD3A, defining its localization and dynamic expression pattern at various stages of the cell cycle. We further establish that TgOTUD3A has activity preference for polyubiquitin chains with certain lysine linkages—such unique activity has not been previously reported in any apicomplexan. This is particularly important given the finding in this study that Toxoplasma gondii proteins are modified by diverse lysine-linked polyubiquitin chains and that these modifications are very dynamic across the cell cycle, pointing toward the sophistication of the “ubiquitin code” as a potential mechanism to regulate parasite biology. The contribution of ubiquitin-mediated mechanisms in the regulation of the Toxoplasma gondii cell cycle has remained largely unexplored. Here, we describe the functional characterization of a T. gondii deubiquitinase (TGGT1_258780) of the ovarian-tumor domain-containing (OTU) family, which, based on its structural homology to the human OTUD3 clade, has been designated TgOTUD3A. The TgOTUD3A protein is expressed in a cell cycle-dependent manner mimicking its mRNA expression, indicating that it is regulated primarily at the transcriptional level. TgOTUD3A, which was found in the cytoplasm at low levels in G1 parasites, increased in abundance with the progression of the cell cycle and exhibited partial localization to the developing daughter scaffolds during cytokinesis. Recombinant TgOTUD3A but not a catalytic-site mutant TgOTUD3A (C229A) exhibited activity against poly- but not monoubiquitinated targets. This activity was selective for polyubiquitin chains with preference for specific lysine linkages (K48 > K11 > K63). All three of these polyubiquitin linkage modifications were found to be present in Toxoplasma, where they exhibited differential levels and localization patterns in a cell cycle-dependent manner. TgOTUD3A removed ubiquitin from the K48- but not the K63-linked ubiquitinated T. gondii proteins independently of the modified target protein, thereby exhibiting the characteristics of an exodeubiquitinase. In addition to cell cycle association, the demonstration of multiple ubiquitin linkages together with the selective deubiquitinase activity of TgOTUD3A reveals an unappreciated level of complexity in the T. gondii “ubiquitin code.” IMPORTANCE The role of ubiquitin-mediated processes in the regulation of the apicomplexan cell cycle is beginning to be elucidated. The recent analysis of the Toxoplasma “ubiquitome” highlights the importance of ubiquitination in the parasite cell cycle. The machinery regulating the ubiquitin dynamics in T. gondii has remained understudied. Here, we provide a biochemical characterization of an OTU (ovarian tumor) family deubiquitinase, TgOTUD3A, defining its localization and dynamic expression pattern at various stages of the cell cycle. We further establish that TgOTUD3A has activity preference for polyubiquitin chains with certain lysine linkages—such unique activity has not been previously reported in any apicomplexan. This is particularly important given the finding in this study that Toxoplasma gondii proteins are modified by diverse lysine-linked polyubiquitin chains and that these modifications are very dynamic across the cell cycle, pointing toward the sophistication of the “ubiquitin code” as a potential mechanism to regulate parasite biology.
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11
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Alfano C, Faggiano S, Pastore A. The Ball and Chain of Polyubiquitin Structures. Trends Biochem Sci 2016; 41:371-385. [PMID: 26899455 DOI: 10.1016/j.tibs.2016.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
Ubiquitylation is a post-translational modification implicated in several different cellular pathways. The possibility of forming chains through covalent crosslinking between any of the seven lysines, or the initial methionine, and the C terminus of another moiety provides ubiquitin (Ub) with special flexibility in its function in signalling. Here, we review the knowledge accumulated over the past several years about the functions and structural features of polyUb chains. This analysis reveals the need to understand further the functional role of some of the linkages and the structural code that determines recognition of polyUbs by protein partners.
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Affiliation(s)
- Caterina Alfano
- Department of Clinical and Basic Neuroscience, King's College London, London, UK
| | | | - Annalisa Pastore
- Department of Clinical and Basic Neuroscience, King's College London, London, UK.
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12
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Pham GH, Rana ASJB, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Sci 2016; 25:456-71. [PMID: 26506216 DOI: 10.1002/pro.2834] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
Abstract
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
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Affiliation(s)
- Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Ambar S J B Rana
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - E Nihal Korkmaz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Vivian H Trang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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13
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Baiady N, Padala P, Mashahreh B, Cohen-Kfir E, Todd EA, Du Pont KE, Berndsen CE, Wiener R. The Vps27/Hrs/STAM (VHS) Domain of the Signal-transducing Adaptor Molecule (STAM) Directs Associated Molecule with the SH3 Domain of STAM (AMSH) Specificity to Longer Ubiquitin Chains and Dictates the Position of Cleavage. J Biol Chem 2015; 291:2033-2042. [PMID: 26601948 DOI: 10.1074/jbc.m115.689869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/06/2022] Open
Abstract
The deubiquitinating enzyme associated molecule with the SH3 domain of STAM (AMSH) is crucial for the removal of ubiquitin molecules during receptor-mediated endocytosis and lysosomal receptor sorting. AMSH interacts with signal transducing adapter molecule (STAM) 1 or 2, which enhances the activity of AMSH through an unknown mechanism. This stimulation is dependent on the ubiquitin-interacting motif of STAM. Here we investigate the specific mechanism of AMSH stimulation by STAM proteins and the role of the STAM Vps27/Hrs/STAM domain. We show that, in the presence of STAM, the length of the ubiquitin chains affects the apparent cleavage rate. Through measurement of the chain cleavage kinetics, we found that, although the kcat of Lys(63)-linked ubiquitin chain cleavage was comparable for di- and tri-ubiquitin, the Km value was lower for tri-ubiquitin. This increased affinity for longer chains was dependent on the Vps27/Hrs/STAM domain of STAM and required that the substrate ubiquitin chain contain homogenous Lys(63)-linkages. In addition, STAM directed AMSH cleavage toward the distal isopeptide bond in tri-ubiquitin chains. Finally, we generated a structural model of AMSH-STAM to show how the complex binds Lys(63)-linked ubiquitin chains and cleaves at the distal end. These data show how a deubiquitinating enzyme-interacting protein dictates the efficiency and specificity of substrate cleavage.
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Affiliation(s)
- Nardeen Baiady
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel and
| | - Prasanth Padala
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel and
| | - Bayan Mashahreh
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel and
| | - Einav Cohen-Kfir
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel and
| | - Emily A Todd
- the Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807
| | - Kelly E Du Pont
- the Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807
| | - Christopher E Berndsen
- the Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807
| | - Reuven Wiener
- From the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel and.
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14
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Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding. Sci Rep 2015; 5:10549. [PMID: 26023027 PMCID: PMC4448524 DOI: 10.1038/srep10549] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/17/2015] [Indexed: 01/09/2023] Open
Abstract
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.
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15
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Nakashima H, Nguyen T, Goins WF, Chiocca EA. Interferon-stimulated gene 15 (ISG15) and ISG15-linked proteins can associate with members of the selective autophagic process, histone deacetylase 6 (HDAC6) and SQSTM1/p62. J Biol Chem 2014; 290:1485-95. [PMID: 25429107 DOI: 10.1074/jbc.m114.593871] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ubiquitin-like interferon (IFN)-stimulated gene 15 (ISG15) and its specific E1, E2, and E3 enzymes are transcriptionally induced by type I IFNs. ISG15 conjugates newly synthesized proteins. ISG15 linkage to proteins appears to be an important downstream IFN signaling event that discriminates cellular and pathogenic proteins synthesized during IFN stimulation from existing proteins. This eliminates potentially pathogenic proteins as the cell attempts to return to normal homeostasis after IFN "stressed" conditions. However, the molecular events that occur in this process are not well known. Here, we show that the C-terminal LRLRGG of ISG15 interacts with the binder of ubiquitin zinc finger (BUZ) domain of histone deacetylase 6 (HDAC6). Because HDAC6 is involved in the autophagic clearance of ubiquitinated aggregates during which SQSTM1/p62 plays a major role as a cargo adapter, we also were able to confirm that p62 binds to ISG15 protein and its conjugated proteins upon forced expression. Both HDAC6 and p62 co-localized with ISG15 in an insoluble fraction of the cytosol, and this co-localization was magnified by the proteasome inhibitor MG132. In addition, ISG15 was degraded via the lysosome. Overexpression of ISG15, which leads to an increased conjugation level of the cellular proteome, enhanced autophagic degradation independently of IFN signaling transduction. These results thus indicate that ISG15 conjugation marks proteins for interaction with HDAC6 and p62 upon forced stressful conditions likely as a step toward autophagic clearance.
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Affiliation(s)
- Hiroshi Nakashima
- From the Harvey Cushing Neuro-oncology Laboratories, Harvard Institutes of Medicine, Department of Neurosurgery and Institute for the Neurosciences at the Brigham and Women's Hospital, Boston, Massachusetts 02115 and
| | - Tran Nguyen
- From the Harvey Cushing Neuro-oncology Laboratories, Harvard Institutes of Medicine, Department of Neurosurgery and Institute for the Neurosciences at the Brigham and Women's Hospital, Boston, Massachusetts 02115 and
| | - William F Goins
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Ennio Antonio Chiocca
- From the Harvey Cushing Neuro-oncology Laboratories, Harvard Institutes of Medicine, Department of Neurosurgery and Institute for the Neurosciences at the Brigham and Women's Hospital, Boston, Massachusetts 02115 and
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16
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Bouvier B. Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations. Phys Chem Chem Phys 2014; 16:48-60. [DOI: 10.1039/c3cp52436a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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18
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Spasser L, Brik A. Chemistry and Biology of the Ubiquitin Signal. Angew Chem Int Ed Engl 2012; 51:6840-62. [DOI: 10.1002/anie.201200020] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 01/07/2023]
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19
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Abstract
Post-translational modification by ubiquitin (ubiquitination, ubiquitylation, ubiquitinylation) is used as a robust signaling mechanism in a variety of processes that are essential for cell homeostasis. Its signaling specificity is conferred by the inherent dynamics of ubiquitin, the multivalency of ubiquitin chains, and its subcellular context, often defined by ubiquitin receptors and the substrate. Greater than 150 ubiquitin receptors have been found and their ubiquitin-binding domains (UBDs) are structurally diverse and include alpha-helical motifs, zinc fingers (ZnF), pleckstrin-homology (PH) domains, ubiquitin conjugating (Ubc)-related structures and src homology 3 (SH3) domains. New UBD structural motifs continue to be identified expanding the ubiquitin-signaling map to proteins and structural families not previously associated with ubiquitin trafficking. In this manuscript, we highlight several ubiquitin receptors from the multiple UBD folds with a focus on the structural characteristics of their interaction with ubiquitin.
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Affiliation(s)
- Leah Randles
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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20
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Kato K. Structural Biology of Post-translational Modifications of Proteins. YAKUGAKU ZASSHI 2012; 132:563-73. [DOI: 10.1248/yakushi.132.563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- The Glycoscience Institute, Ochanomizu University
- GLYECE Co., Ltd
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21
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Lai MY, Zhang D, Laronde-Leblanc N, Fushman D. Structural and biochemical studies of the open state of Lys48-linked diubiquitin. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:2046-56. [PMID: 22542781 DOI: 10.1016/j.bbamcr.2012.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub-Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub-Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub-Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.
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Affiliation(s)
- Ming-Yih Lai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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22
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Rohaim A, Kawasaki M, Kato R, Dikic I, Wakatsuki S. Structure of a compact conformation of linear diubiquitin. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:102-8. [DOI: 10.1107/s0907444911051195] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 11/28/2011] [Indexed: 11/11/2022]
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23
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Trempe JF. Reading the ubiquitin postal code. Curr Opin Struct Biol 2011; 21:792-801. [PMID: 22036065 DOI: 10.1016/j.sbi.2011.09.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/16/2011] [Accepted: 09/29/2011] [Indexed: 10/15/2022]
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24
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Hirano T, Serve O, Yagi-Utsumi M, Takemoto E, Hiromoto T, Satoh T, Mizushima T, Kato K. Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution. J Biol Chem 2011; 286:37496-502. [PMID: 21900242 DOI: 10.1074/jbc.m111.256354] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasomal degradation is mediated through modification of target proteins by Lys-48-linked polyubiquitin (polyUb) chain, which interacts with several binding partners in this pathway through hydrophobic surfaces on individual Ub units. However, the previously reported crystal structures of Lys-48-linked diUb exhibit a closed conformation with sequestered hydrophobic surfaces. NMR studies on mutated Lys-48-linked diUb indicated a pH-dependent conformational equilibrium between closed and open states with the predominance of the former under neutral conditions (90% at pH 6.8). To address the question of how Ub-binding proteins can efficiently access the sequestered hydrophobic surfaces of Ub chains, we revisited the conformational dynamics of Lys-48-linked diUb in solution using wild-type diUb and cyclic forms of diUb in which the Ub units are connected through two Lys-48-mediated isopeptide bonds. Our newly determined crystal structure of wild-type diUb showed an open conformation, whereas NMR analyses of cyclic Lys-48-linked diUb in solution revealed that its structure resembled the closed conformation observed in previous crystal structures. Comparison of a chemical shift of wild-type diUb with that of monomeric Ub and cyclic diUb, which mimic the open and closed states, respectively, with regard to the exposure of hydrophobic surfaces to the solvent indicates that wild-type Lys-48-linked diUb in solution predominantly exhibits the open conformation (75% at pH 7.0), which becomes more populated upon lowering pH. The intrinsic properties of Lys-48-linked Ub chains to adopt the open conformation may be advantageous for interacting with Ub-binding proteins.
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Affiliation(s)
- Takashi Hirano
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori Mizuho-ku, Nagoya 467-8603, Japan
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Riedinger C, Boehringer J, Trempe JF, Lowe ED, Brown NR, Gehring K, Noble MEM, Gordon C, Endicott JA. Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12. J Biol Chem 2010; 285:33992-4003. [PMID: 20739285 PMCID: PMC2962499 DOI: 10.1074/jbc.m110.134510] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 08/03/2010] [Indexed: 11/06/2022] Open
Abstract
Schizosaccharomyces pombe Rpn10 (SpRpn10) is a proteasomal ubiquitin (Ub) receptor located within the 19 S regulatory particle where it binds to subunits of both the base and lid subparticles. We have solved the structure of full-length SpRpn10 by determining the crystal structure of the von Willebrand factor type A domain and characterizing the full-length protein by NMR. We demonstrate that the single Ub-interacting motif (UIM) of SpRpn10 forms a 1:1 complex with Lys(48)-linked diUb, which it binds selectively over monoUb and Lys(63)-linked diUb. We further show that the SpRpn10 UIM binds to SpRpn12, a subunit of the lid subparticle, with an affinity comparable with Lys(48)-linked diUb. This is the first observation of a UIM binding other than a Ub fold and suggests that SpRpn12 could modulate the activity of SpRpn10 as a proteasomal Ub receptor.
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Affiliation(s)
- Christiane Riedinger
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonas Boehringer
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jean-Francois Trempe
- the Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, and
| | - Edward D. Lowe
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicholas R. Brown
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Kalle Gehring
- the Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, and
| | - Martin E. M. Noble
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin Gordon
- the Medical Research Council Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, United Kingdom
| | - Jane A. Endicott
- From the Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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