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Chung IYW, Li L, Cygler M. Legionella effector LegA15/AnkH contains an unrecognized cysteine protease-like domain and displays structural similarity to LegA3/AnkD, but differs in host cell localization. Acta Crystallogr D Struct Biol 2021; 77:1535-1542. [PMID: 34866609 DOI: 10.1107/s2059798321010469] [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: 08/23/2021] [Accepted: 10/08/2021] [Indexed: 11/11/2022] Open
Abstract
Legionella pneumophila is a human pathogen that causes Legionnaires' disease, a severe form of pneumonia. It can be found in various aquatic environments ranging from cooling towers to ponds. In addition to causing disease in humans, it can also infect free-living amoebae commonly found in various aquatic environments. Once inside a human lung macrophage, it creates a niche called the Legionella-containing vacuole where it can evade phagolysosomal degradation and replicate. During infection, normal cellular functions are hijacked by proteins that are secreted by the pathogen, called bacterial effectors. Here, the structural characterization of the effector LegA15/AnkD is reported. The protein contains an ankyrin-repeat domain followed by a cysteine protease-like (CPL) domain with a putative catalytic triad consisting of His268-Asn290-Cys361. The CPL domain shows similarity to the CE clan in the MEROPS database, which contains ubiquitin-like hydrolases. The C-terminal segment of LegA15, including the CPL domain, shows structural similarity to another effector, LegA3/AnkH, while they share only 12% sequence identity. When expressed in mammalian cells, LegA15 is localized within the cytoplasm, in contrast to LegA3, which localizes to the nucleus.
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Affiliation(s)
- Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lei Li
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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2
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Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernadó P. Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets. Structure 2021; 29:1074-1090.e4. [PMID: 33862013 DOI: 10.1016/j.str.2021.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Transient biomolecular interactions play crucial roles in many cellular signaling and regulation processes. However, deciphering the structure of these assemblies is challenging owing to the difficulties in isolating complexes from the individual partners. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the species present in these mixtures, but decomposition into structural and thermodynamic information is difficult. We present a chemometric approach enabling the decomposition of titration SAXS data into species-specific information. Using extensive synthetic SAXS data, we demonstrate that robust decomposition can be achieved for titrations with a maximum fraction of complex of 0.5 that can be extended to 0.3 when two orthogonal titrations are simultaneously analyzed. The effect of the structural features, titration points, relative concentrations, and noise are thoroughly analyzed. The validation of the strategy with experimental data highlights the power of the approach to provide unique insights into this family of biomolecular assemblies.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
| | - Fátima Herranz-Trillo
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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3
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Giovannone AJ, Reales E, Bhattaram P, Nackeeran S, Monahan AB, Syed R, Weimbs T. The H abc domain of syntaxin 3 is a ubiquitin binding domain. Sci Rep 2020; 10:21350. [PMID: 33288783 PMCID: PMC7721868 DOI: 10.1038/s41598-020-78412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/24/2020] [Indexed: 11/08/2022] Open
Abstract
Syntaxins are a family of membrane-anchored SNARE proteins that are essential components required for membrane fusion in eukaryotic intracellular membrane trafficking pathways. Syntaxins contain an N-terminal regulatory domain, termed the Habc domain that is not highly conserved at the primary sequence level but folds into a three-helix bundle that is structurally conserved among family members. The syntaxin Habc domain has previously been found to be structurally very similar to the GAT domain present in GGA family members and related proteins that are otherwise completely unrelated to syntaxins. Because the GAT domain has been found to be a ubiquitin binding domain we hypothesized that the Habc domain of syntaxins may also bind to ubiquitin. Here, we report that the Habc domain of syntaxin 3 (Stx3) indeed binds to monomeric ubiquitin with low affinity. This domain binds efficiently to K63-linked poly-ubiquitin chains within a narrow range of chain lengths but not to K48-linked poly-ubiquitin chains. Other syntaxin family members also bind to K63-linked poly-ubiquitin chains but with different chain length specificities. Molecular modeling suggests that residues of the GGA3-GAT domain known to be important for ionic and hydrophobic interactions with ubiquitin may have equivalent, conserved residues within the Habc domain of Stx3. We conclude that the syntaxin Habc domain and the GAT domain are both structurally and functionally related, and likely share a common ancestry despite sequence divergence. Binding of Ubiquitin to the Habc domain may regulate the function of syntaxins in membrane fusion or may suggest additional functions of this protein family.
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Affiliation(s)
- Adrian J Giovannone
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Elena Reales
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Organic Chemistry, School of Sciences, University of Cadiz, Cádiz, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cádiz, Spain
| | - Pallavi Bhattaram
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Orthopaedics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Sirpi Nackeeran
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Adam B Monahan
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Rashid Syed
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA
| | - Thomas Weimbs
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA.
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4
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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5
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Yeates EFA, Tesco G. The Endosome-associated Deubiquitinating Enzyme USP8 Regulates BACE1 Enzyme Ubiquitination and Degradation. J Biol Chem 2016; 291:15753-66. [PMID: 27302062 DOI: 10.1074/jbc.m116.718023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 01/04/2023] Open
Abstract
The β-site amyloid precursor protein-cleaving enzyme (BACE1) is the rate-limiting enzyme in the production of amyloid-β, the toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. Our previous studies have shown that BACE1 is degraded via the lysosomal pathway and that that depletion of the trafficking molecule Golgi-localized γ-ear-containing ARF-binding protein 3 (GGA3) results in increased BACE1 levels and activity because of impaired lysosomal degradation. We also determined that GGA3 regulation of BACE1 levels requires its ability to bind ubiquitin. Accordingly, we reported that BACE1 is ubiquitinated at lysine 501 and that lack of ubiquitination at lysine 501 produces BACE1 stabilization. Ubiquitin conjugation is a reversible process mediated by deubiquitinating enzymes. The ubiquitin-specific peptidase 8 (USP8), an endosome-associated deubiquitinating enzyme, regulates the ubiquitination, trafficking, and lysosomal degradation of several plasma membrane proteins. Here, we report that RNAi-mediated depletion of USP8 reduced levels of both ectopically expressed and endogenous BACE1 in H4 human neuroglioma cells. Moreover, USP8 depletion increased BACE1 ubiquitination, promoted BACE1 accumulation in the early endosomes and late endosomes/lysosomes, and decreased levels of BACE1 in the recycling endosomes. We also found that decreased BACE1 protein levels were accompanied by a decrease in BACE1-mediated amyloid precursor protein cleavage and amyloid-β levels. Our findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. These studies suggest that therapies able to accelerate BACE1 degradation (e.g. by increasing BACE1 ubiquitination) may represent a potential treatment for Alzheimer disease.
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Affiliation(s)
| | - Giuseppina Tesco
- From the Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111
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6
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Paczkowski JE, Richardson BC, Fromme JC. Cargo adaptors: structures illuminate mechanisms regulating vesicle biogenesis. Trends Cell Biol 2015; 25:408-16. [PMID: 25795254 DOI: 10.1016/j.tcb.2015.02.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/11/2015] [Accepted: 02/19/2015] [Indexed: 12/29/2022]
Abstract
Cargo adaptors sort transmembrane protein cargos into nascent vesicles by binding directly to their cytosolic domains. Recent studies have revealed previously unappreciated roles for cargo adaptors and regulatory mechanisms governing their function. The adaptor protein (AP)-1 and AP-2 clathrin adaptors switch between open and closed conformations that ensure they function at the right place at the right time. The exomer cargo adaptor has a direct role in remodeling the membrane for vesicle fission. Several different cargo adaptors functioning in distinct trafficking pathways at the Golgi are similarly regulated through bivalent binding to the ADP-ribosylation factor 1 (Arf1) GTPase, potentially enabling regulation by a threshold concentration of Arf1. Taken together, these studies highlight that cargo adaptors do more than just adapt cargos.
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Affiliation(s)
- Jon E Paczkowski
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian C Richardson
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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7
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Cui D, Ou S, Patel S. Protein-spanning water networks and implications for prediction of protein-protein interactions mediated through hydrophobic effects. Proteins 2014; 82:3312-26. [DOI: 10.1002/prot.24683] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/30/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Di Cui
- Department of Chemistry and Biochemistry; University of Delaware; Newark Delaware 19716
| | - Shuching Ou
- Department of Chemistry and Biochemistry; University of Delaware; Newark Delaware 19716
| | - Sandeep Patel
- Department of Chemistry and Biochemistry; University of Delaware; Newark Delaware 19716
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8
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PtdIns(4)P signalling and recognition systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:59-83. [PMID: 23775691 DOI: 10.1007/978-94-007-6331-9_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Golgi apparatus is a sorting platform that exchanges extensively with the endoplasmic reticulum (ER), endosomes (Es) and plasma membrane (PM) compartments. The last compartment of the Golgi, the trans-Golgi Network (TGN) is a large complex of highly deformed membranes from which vesicles depart to their targeted organelles but also are harbored from retrograde pathways. The phosphoinositide (PI) composition of the TGN is marked by an important contingent of phosphatidylinositol-4-phosphate (PtdIns(4)P). Although this PI is present throughout the Golgi, its proportion grows along the successive cisternae and peaks at the TGN. The levels of this phospholipid are controlled by a set of kinases and phosphatases that regulate its concentrations in the Golgi and maintain a dynamic gradient that determines the cellular localization of several interacting proteins. Though not exclusive to the Golgi, the synthesis of PtdIns(4)P in other membranes is relatively marginal and has unclear consequences. The significance of PtdIns(4)P within the TGN has been demonstrated for numerous cellular events such as vesicle formation, lipid metabolism, and membrane trafficking.
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9
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Haglund K, Dikic I. The role of ubiquitylation in receptor endocytosis and endosomal sorting. J Cell Sci 2013; 125:265-75. [PMID: 22357968 DOI: 10.1242/jcs.091280] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ligand-induced activation of transmembrane receptors activates intracellular signaling cascades that control vital cellular processes, such as cell proliferation, differentiation, migration and survival. Receptor signaling is modulated by several mechanisms to ensure that the correct biological outcome is achieved. One such mechanism, which negatively regulates receptor signaling, involves the modification of receptors with ubiquitin. This post-translational modification can promote receptor endocytosis and targets receptors for lysosomal degradation, thereby ensuring termination of receptor signaling. In this Commentary, we review the roles of ubiquitylation in receptor endocytosis and degradative endosomal sorting by drawing on the epidermal growth factor receptor (EGFR) as a well-studied example. Furthermore, we elaborate on the molecular basis of ubiquitin recognition along the endocytic pathway through compartment-specific ubiquitin-binding proteins and highlight how endocytic sorting machineries control these processes. In addition, we discuss the importance of ubiquitin-dependent receptor endocytosis for the maintenance of cellular homeostasis and in the prevention of diseases such as cancer.
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Affiliation(s)
- Kaisa Haglund
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, N-0310 Oslo, Norway.
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10
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Kang EL, Biscaro B, Piazza F, Tesco G. BACE1 protein endocytosis and trafficking are differentially regulated by ubiquitination at lysine 501 and the Di-leucine motif in the carboxyl terminus. J Biol Chem 2012; 287:42867-80. [PMID: 23109336 DOI: 10.1074/jbc.m112.407072] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
β-Site amyloid precursor protein-cleaving enzyme (BACE1) is a membrane-tethered member of the aspartyl proteases that has been identified as β-secretase. BACE1 is targeted through the secretory pathway to the plasma membrane and then is internalized to endosomes. Sorting of membrane proteins to the endosomes and lysosomes is regulated by the interaction of signals present in their carboxyl-terminal fragment with specific trafficking molecules. The BACE1 carboxyl-terminal fragment contains a di-leucine sorting signal ((495)DDISLL(500)) and a ubiquitination site at Lys-501. Here, we report that lack of ubiquitination at Lys-501 (BACE1K501R) does not affect the rate of endocytosis but produces BACE1 stabilization and accumulation of BACE1 in early and late endosomes/lysosomes as well as at the cell membrane. In contrast, the disruption of the di-leucine motif (BACE1LLAA) greatly impairs BACE1 endocytosis and produces a delayed retrograde transport of BACE1 to the trans-Golgi network (TGN) and a delayed delivery of BACE1 to the lysosomes, thus decreasing its degradation. Moreover, the combination of the lack of ubiquitination at Lys-501 and the disruption of the di-leucine motif (BACE1LLAA/KR) produces additive effects on BACE1 stabilization and defective internalization. Finally, BACE1LLAA/KR accumulates in the TGN, while its levels are decreased in EEA1-positive compartments indicating that both ubiquitination at Lys-501 and the di-leucine motif are necessary for the trafficking of BACE1 from the TGN to early endosomes. Our studies have elucidated a differential role for the di-leucine motif and ubiquitination at Lys-501 in BACE1 endocytosis, trafficking, and degradation and suggest the involvement of multiple adaptor molecules.
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Affiliation(s)
- Eugene L Kang
- Alzheimer's Disease Research Laboratory, Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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11
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Clague M, Liu H, Urbé S. Governance of Endocytic Trafficking and Signaling by Reversible Ubiquitylation. Dev Cell 2012; 23:457-67. [DOI: 10.1016/j.devcel.2012.08.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/27/2012] [Accepted: 08/21/2012] [Indexed: 12/17/2022]
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12
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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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13
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Kümmel D, Reinisch KM. Structure of Golgi transport proteins. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a007609. [PMID: 21813399 DOI: 10.1101/cshperspect.a007609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The function of the Golgi has long been recognized to critically depend on vesicular transport from, to, and within its cisternae, involving constant membrane fission and fusion. These processes are mediated by Arf GTPases and coat proteins, and Rabs, tethers and SNARE proteins, respectively. In this article, we describe structural studies of Golgi coats and tethers and their interactions with SNAREs and GTPases as well as insights regarding membrane traffic processes that these have provided.
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Affiliation(s)
- Daniel Kümmel
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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14
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Wang T, Liu NS, Seet LF, Hong W. The Emerging Role of VHS Domain-Containing Tom1, Tom1L1 and Tom1L2 in Membrane Trafficking. Traffic 2010; 11:1119-28. [DOI: 10.1111/j.1600-0854.2010.01098.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Kang EL, Cameron AN, Piazza F, Walker KR, Tesco G. Ubiquitin regulates GGA3-mediated degradation of BACE1. J Biol Chem 2010; 285:24108-19. [PMID: 20484053 DOI: 10.1074/jbc.m109.092742] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACE1 (beta-site amyloid precursor protein-cleaving enzyme 1) is a membrane-tethered member of the aspartyl proteases, essential for the production of beta-amyloid, a toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. The BACE1 C-terminal fragment contains a DXXLL motif that has been shown to bind the VHS (VPS27, Hrs, and STAM) domain of GGA1-3 (Golgi-localized gamma-ear-containing ARF-binding proteins). GGAs are trafficking molecules involved in the transport of proteins containing the DXXLL signal from the Golgi complex to endosomes. Moreover, GGAs bind ubiquitin and traffic synthetic and endosomal ubiquitinated cargoes to lysosomes. We have previously shown that depletion of GGA3 results in increased BACE1 levels and activity because of impaired lysosomal degradation. Here, we report that the accumulation of BACE1 is rescued by the ectopic expression of GGA3 in H4 neuroglioma cells depleted of GGA3. Accordingly, the overexpression of GGA3 reduces the levels of BACE1 and beta-amyloid. We then established that mutations in the GGA3 VPS27, Hrs, and STAM domain (N91A) or in BACE1 di-leucine motif (L499A/L500A), able to abrogate their binding, did not affect the ability of ectopically expressed GGA3 to rescue BACE1 accumulation in cells depleted of GGA3. Instead, we found that BACE1 is ubiquitinated at lysine 501 and is mainly monoubiquitinated and Lys-63-linked polyubiquitinated. Finally, a GGA3 mutant with reduced ability to bind ubiquitin (GGA3L276A) was unable to regulate BACE1 levels both in rescue and overexpression experiments. These findings indicate that levels of GGA3 tightly and inversely regulate BACE1 levels via interaction with ubiquitin sorting machinery.
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Affiliation(s)
- Eugene L Kang
- Alzheimer's Disease Research Laboratory, Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
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16
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Pasikowski P, Cydzik M, Kluczyk A, Stefanowicz P, Szewczuk Z. Ubiquitin fragments: their known biological activities and putative roles. Biomol Concepts 2010; 1:67-83. [PMID: 25961987 DOI: 10.1515/bmc.2010.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ubiquitin (Ub) is involved in many key processes of cell biology. Identification of compounds that could interfere in the ubiquitination process is of importance. It could be expected that peptides derived from the Ub-binding regions might be able to interact with Ub receptors themselves and modify an ability of the Ub receptors interactions. This review summarizes current knowledge about known Ub-derived peptides and discusses putative activity of unexplored Ub fragments. Among identified biologically active Ub-derived peptides, its decapeptide fragment of the LEDGRTLSDY sequence was found to exhibit strong immunosuppressive effects on the cellular and humoral immune responses, comparable to that of cyclosporine. Some of the Ub fragments possess strong antibacterial and antifungal potency. In the search for new peptides that could interfere in the interaction of Ub with other proteins, we investigated the pentapeptide Ub sequences present in non-ubiquitin proteins. Based on examination of the Swiss-Prot database, we postulated that sequences of some Ub fragments often exist in other protein molecules. However, some of those motives are represented more frequently than others and could be involved in regulation of cellular processes related to Ub.
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17
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Kinjo AR, Nakamura H. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J Mol Biol 2010; 399:526-40. [PMID: 20417638 DOI: 10.1016/j.jmb.2010.04.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 02/05/2023]
Abstract
To elucidate the structural basis of the diversity and universality in protein-protein interactions, an exhaustive all-against-all structural comparison of all known protein interfaces in the Protein Data Bank was performed at atomic resolution. After similar interfaces were clustered, approximately 20,000 structural motifs with at least two members were identified, out of which 3678 motifs consisted of at least 10 interfaces. Except for some trivial interfaces involving single alpha helices, almost all motifs were found to be confined within single protein families. Furthermore, the interaction partners of each motif were found to be very limited, and, accordingly, the interaction networks of the motifs tend to be small and are much more restricted than the binding sites for small ligand molecules. These findings suggest that, at the level of atomic structures, protein-protein interactions are precisely designed; hence, protein interfaces with multiple interacting partners should involve incompletely overlapping multiple interfaces and/or accommodate structural changes upon binding to their targets.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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18
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Perica T, Chothia C. Ubiquitin--molecular mechanisms for recognition of different structures. Curr Opin Struct Biol 2010; 20:367-76. [PMID: 20456943 DOI: 10.1016/j.sbi.2010.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 11/15/2022]
Abstract
The role of ubiquitin in many of the known cellular processes, not just protein degradation, is based on its unique ability to bind a range of proteins that are structurally and functionally different. To understand how ubiquitin can bind to proteins with different structures, we review the extent of the conservation and variation that occur in the structures of two free ubiquitins and ubiquitins in 16 complexes that have been determined at high resolution (1.2-2A). Around 80% of the atomic groups in these structures have positions that differ less than 1A. This conserved core provides a rigid platform for flexible loop regions, 39 residues with side chains that can take up different conformations, and a flexible six-residue region at the C-terminus. In most cases the ability of ubiquitin to bind different structures is limited in part by a central set of residues that largely conserve their conformations. The accommodation of differences in binding proteins is enabled by changes in the flexible surface side chains, loop movements, different specific interactions, water molecules in the interface and the flexible C-terminus.
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Affiliation(s)
- Tina Perica
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 OQH, UK.
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Dikic I, Wakatsuki S, Walters KJ. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol 2009; 10:659-71. [PMID: 19773779 DOI: 10.1038/nrm2767] [Citation(s) in RCA: 635] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin-binding domains (UBDs) are modular elements that bind non-covalently to the protein modifier ubiquitin. Recent atomic-level resolution structures of ubiquitin-UBD complexes have revealed some of the mechanisms that underlie the versatile functions of ubiquitin in vivo. The preferences of UBDs for ubiquitin chains of specific length and linkage are central to these functions. These preferences originate from multimeric interactions, whereby UBDs synergistically bind multiple ubiquitin molecules, and from contacts with regions that link ubiquitin molecules into a polymer. The sequence context of UBDs and the conformational changes that follow their binding to ubiquitin also contribute to ubiquitin signalling. These new structure-based insights provide strategies for controlling cellular processes by targeting ubiquitin-UBD interfaces.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II and Cluster of Excellence "Macromolecular Complexes", Goethe University Frankfurt, Germany.
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20
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Joshi A, Nagashima K, Freed EO. Defects in cellular sorting and retroviral assembly induced by GGA overexpression. BMC Cell Biol 2009; 10:72. [PMID: 19788741 PMCID: PMC2760529 DOI: 10.1186/1471-2121-10-72] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/29/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND We previously demonstrated that overexpression of Golgi-localized, gamma-ear containing, Arf-binding (GGA) proteins inhibits retrovirus assembly and release by disrupting the function of endogenous ADP ribosylation factors (Arfs). GGA overexpression led to the formation of large, swollen vacuolar compartments, which in the case of GGA1 sequestered HIV-1 Gag. RESULTS In the current study, we extend our previous findings to characterize in depth the GGA-induced compartments and the determinants for retroviral Gag sequestration in these structures. We find that GGA-induced structures are derived from the Golgi and contain aggresome markers. GGA overexpression leads to defects in trafficking of transferrin receptor and recycling of cation-dependent mannose 6-phosphate receptor. Additionally, we find that compartments induced by GGA overexpression sequester Tsg101, poly-ubiquitin, and, in the case of GGA3, Hrs. Interestingly, brefeldin A treatment, which leads to the dissociation of endogenous GGAs from membranes, does not dissociate the GGA-induced compartments. GGA mutants that are defective in Arf binding and hence association with membranes also induce the formation of GGA-induced structures. Overexpression of ubiquitin reverses the formation of GGA-induced structures and partially rescues HIV-1 particle production. We found that in addition to HIV-1 Gag, equine infectious anemia virus Gag is also sequestered in GGA1-induced structures. The determinants in Gag responsible for sequestration map to the matrix domain, and recruitment to these structures is dependent on Gag membrane binding. CONCLUSION These data provide insights into the composition of structures induced by GGA overexpression and their ability to disrupt endosomal sorting and retroviral particle production.
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Affiliation(s)
- Anjali Joshi
- Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland, USA
- Department of Biomedical Sciences, Center of Excellence for Infectious Diseases, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79905, USA
| | - Kunio Nagashima
- Image Analysis Laboratory, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland, USA
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21
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Deng Y, Guo Y, Watson H, Au WC, Shakoury-Elizeh M, Basrai MA, Bonifacino JS, Philpott CC. Gga2 mediates sequential ubiquitin-independent and ubiquitin-dependent steps in the trafficking of ARN1 from the trans-Golgi network to the vacuole. J Biol Chem 2009; 284:23830-41. [PMID: 19574226 DOI: 10.1074/jbc.m109.030015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, ARN1 encodes a transporter for the uptake of ferrichrome, an important nutritional source of iron. In the absence of ferrichrome, Arn1p is sorted directly from the trans-Golgi network (TGN) to the vacuolar lumen via the vacuolar protein-sorting pathway. Arn1p is mis-sorted to the plasma membrane in cells lacking Gga2p, a monomeric clathrin-adaptor protein involved in vesicular transport from the TGN. Although Ggas have been characterized as ubiquitin receptors, we show here that ubiquitin binding by Gga2 was not required for the TGN-to-endosome trafficking of Arn1, but it was required for subsequent sorting of Arn1 into the multivesicular body. In a ubiquitin-binding mutant of Gga2, Arn1p accumulated on the vacuolar membrane in a ubiquitinated form. The yeast epsins Ent3p and Ent4p were also involved in TGN-to-vacuole sorting of Arn1p. Amino-terminal sequences of Arn1p were required for vacuolar protein sorting, as mutation of ubiquitinatable lysine residues resulted in accumulation on the vacuolar membrane, and mutation of either a THN or YGL sequence resulted in mis-sorting to the plasma membrane. These studies suggest that Gga2 is involved in sorting at both the TGN and multivesicular body and that the first step can occur without ubiquitin binding.
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Affiliation(s)
- Yi Deng
- Liver Diseases Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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22
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Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH. The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Dev Cell 2007; 12:973-86. [PMID: 17543868 PMCID: PMC2292400 DOI: 10.1016/j.devcel.2007.04.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/20/2007] [Accepted: 04/18/2007] [Indexed: 01/29/2023]
Abstract
The yeast Vps27/Hse1 complex and the homologous mammalian Hrs/STAM complex deliver ubiquitinated transmembrane proteins to the ESCRT endosomal-sorting pathway. The Vps27/Hse1 complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. We have solved the crystal structure of the core responsible for the assembly of the Vps27/Hse1 complex at 3.0 A resolution. The structure consists of two intertwined GAT domains, each consisting of two helices from one subunit and one from the other. The two GAT domains are connected by an antiparallel coiled coil, forming a 90 A-long barbell-like structure. This structure places the domains of Vps27 and Hse1 that recruit ubiquitinated cargo and deubiquitinating enzymes close to each other. Coarse-grained Monte Carlo simulations of the Vps27/Hse1 complex on a membrane show how the complex binds cooperatively to lipids and ubiquitinated membrane proteins and acts as a scaffold for ubiquitination reactions.
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Affiliation(s)
- Gali Prag
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
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23
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Wang J, Sun HQ, Macia E, Kirchhausen T, Watson H, Bonifacino JS, Yin HL. PI4P promotes the recruitment of the GGA adaptor proteins to the trans-Golgi network and regulates their recognition of the ubiquitin sorting signal. Mol Biol Cell 2007; 18:2646-55. [PMID: 17494868 PMCID: PMC1924815 DOI: 10.1091/mbc.e06-10-0897] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Phosphatidylinositol 4 phosphate (PI4P) is highly enriched in the trans-Golgi network (TGN). Here we establish that PI4P is a key regulator of the recruitment of the GGA clathrin adaptor proteins to the TGN and that PI4P has a novel role in promoting their recognition of the ubiquitin (Ub) sorting signal. Knockdown of PI4KIIalpha by RNA interference (RNAi), which depletes the TGN's PI4P, impaired the recruitment of the GGAs to the TGN. GGAs bind PI4P primarily through their GAT domain, in a region called C-GAT, which also binds Ub but not Arf1. We identified two basic residues in the GAT domain that are essential for PI4P binding in vitro and for the recruitment of GGAs to the TGN in vivo. Unlike wild-type GGA, GGA with mutated GATs failed to rescue the abnormal TGN phenotype of the GGA RNAi-depleted cells. These residues partially overlap with those that bind Ub, and PI4P increased the affinity of the GAT domain for Ub. Because the recruitment of clathrin adaptors and their cargoes to the TGN is mediated through a web of low-affinity interactions, our results show that the dual roles of PI4P can promote specific GGA targeting and cargo recognition at the TGN.
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Affiliation(s)
- Jing Wang
- *Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Hui-Qiao Sun
- *Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Eric Macia
- Department of Cell Biology and Center for Blood Research Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115; and
| | - Tomas Kirchhausen
- Department of Cell Biology and Center for Blood Research Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115; and
| | - Hadiya Watson
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Juan S. Bonifacino
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Helen L. Yin
- *Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
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Kirkin V, Dikic I. Role of ubiquitin- and Ubl-binding proteins in cell signaling. Curr Opin Cell Biol 2007; 19:199-205. [PMID: 17303403 DOI: 10.1016/j.ceb.2007.02.002] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 02/05/2007] [Indexed: 12/15/2022]
Abstract
Besides tagging proteins for degradation, ubiquitin is now recognized as a signaling module for diverse cellular processes, including progression through the cell cycle, DNA repair, gene transcription, receptor trafficking and endocytosis. Recent advances have indicated the existence of a wide variety of ubiquitin-binding proteins that, upon recognition of conjugated ubiquitin moieties, can control assembly of complex signaling networks. Small ubiquitin-like proteins, like SUMO, emerge to play biological roles distinct from ubiquitin, and require specific recognition by a dedicated set of proteins. Identification and characterization of recognition motifs and domains for ubiquitin-like proteins have just begun, promising new insights into the diversity of functions ubiquitin family proteins have in physiological and pathological settings.
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Affiliation(s)
- Vladimir Kirkin
- Institute of Biochemistry II, Goethe University Hospital, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
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25
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Pak Y, Glowacka WK, Bruce MC, Pham N, Rotin D. Transport of LAPTM5 to lysosomes requires association with the ubiquitin ligase Nedd4, but not LAPTM5 ubiquitination. ACTA ACUST UNITED AC 2007; 175:631-45. [PMID: 17116753 PMCID: PMC2064599 DOI: 10.1083/jcb.200603001] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
LAPTM5 is a lysosomal transmembrane protein expressed in immune cells. We show that LAPTM5 binds the ubiquitin-ligase Nedd4 and GGA3 to promote LAPTM5 sorting from the Golgi to the lysosome, an event that is independent of LAPTM5 ubiquitination. LAPTM5 contains three PY motifs (L/PPxY), which bind Nedd4-WW domains, and a ubiquitin-interacting motif (UIM) motif. The Nedd4-LAPTM5 complex recruits ubiquitinated GGA3, which binds the LAPTM5-UIM; this interaction does not require the GGA3-GAT domain. LAPTM5 mutated in its Nedd4-binding sites (PY motifs) or its UIM is retained in the Golgi, as is LAPTM5 expressed in cells in which Nedd4 or GGA3 is knocked-down with RNAi. However, ubiquitination-impaired LAPTM5 can still traffic to the lysosome, suggesting that Nedd4 binding to LAPTM5, not LAPTM5 ubiquitination, is required for targeting. Interestingly, Nedd4 is also able to ubiquitinate GGA3. These results demonstrate a novel mechanism by which the ubiquitin-ligase Nedd4, via interactions with GGA3 and cargo (LAPTM5), regulates cargo trafficking to the lysosome without requiring cargo ubiquitination.
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Affiliation(s)
- Youngshil Pak
- Program in Cell Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
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26
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Abstract
The covalent modification of proteins by ubiquitination is a major regulatory mechanism of protein degradation and quality control, endocytosis, vesicular trafficking, cell-cycle control, stress response, DNA repair, growth-factor signalling, transcription, gene silencing and other areas of biology. A class of specific ubiquitin-binding domains mediates most of the effects of protein ubiquitination. The known membership of this group has expanded rapidly and now includes at least sixteen domains: UBA, UIM, MIU, DUIM, CUE, GAT, NZF, A20 ZnF, UBP ZnF, UBZ, Ubc, UEV, UBM, GLUE, Jab1/MPN and PFU. The structures of many of the complexes with mono-ubiquitin have been determined, revealing interactions with multiple surfaces on ubiquitin. Inroads into understanding polyubiquitin specificity have been made for two UBA domains, whose structures have been characterized in complex with Lys48-linked di-ubiquitin. Several ubiquitin-binding domains, including the UIM, CUE and A20 ZnF (zinc finger) domains, promote auto-ubiquitination, which regulates the activity of proteins that contain them. At least one of these domains, the A20 ZnF, acts as a ubiquitin ligase by recruiting a ubiquitin-ubiquitin-conjugating enzyme thiolester adduct in a process that depends on the ubiquitin-binding activity of the A20 ZnF. The affinities of the mono-ubiquitin-binding interactions of these domains span a wide range, but are most commonly weak, with Kd>100 microM. The weak interactions between individual domains and mono-ubiquitin are leveraged into physiologically relevant high-affinity interactions via several mechanisms: ubiquitin polymerization, modification multiplicity, oligomerization of ubiquitinated proteins and binding domain proteins, tandem-binding domains, binding domains with multiple ubiquitin-binding sites and co-operativity between ubiquitin binding and binding through other domains to phospholipids and small G-proteins.
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Affiliation(s)
- James H Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA.
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27
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Yogosawa S, Kawasaki M, Wakatsuki S, Kominami E, Shiba Y, Nakayama K, Kohsaka S, Akazawa C. Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability. Biochem Biophys Res Commun 2006; 350:82-90. [PMID: 16996030 DOI: 10.1016/j.bbrc.2006.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 09/01/2006] [Indexed: 12/13/2022]
Abstract
GGAs (Golgi-localizing, gamma-adaptin ear domain homology, ADP-ribosylation factor (ARF)-binding proteins), constitute a family of monomeric adaptor proteins and are associated with protein trafficking from the trans-Golgi network to endosomes. Here, we show that GGA3 is monoubiquitylated by a RING-H2 type-ubiquitin ligase hVPS18 (human homologue of vacuolar protein sorting 18). By in vitro ubiquitylation assays, we have identified lysine 258 in the GAT domain as a major ubiquitylation site that resides adjacent to the ubiquitin-binding site. The ubiquitylation is abolished by a mutation in either the GAT domain or ubiquitin that disrupts the GAT-ubiquitin interaction, indicating that the ubiquitin binding is a prerequisite for the ubiquitylation. Furthermore, the GAT domain ubiquitylated by hVPS18 no longer binds to ubiquitin, indicating that ubiquitylation negatively regulates the ubiquitin-binding ability of the GAT domain. These results suggest that the ubiquitin binding and ubiquitylation of GGA3-GAT domain are mutually inseparable through a ubiquitin ligase activity of hVPS18.
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Affiliation(s)
- Satomi Yogosawa
- Department of Neurochemistry, National Institute of Neuroscience, NCNP, Kodaira, Tokyo 187-8502, Japan
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28
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29
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Sasakawa H, Sakata E, Yamaguchi Y, Komatsu M, Tatsumi K, Kominami E, Tanaka K, Kato K. Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1. Biochem Biophys Res Commun 2006; 343:21-6. [PMID: 16527251 DOI: 10.1016/j.bbrc.2006.02.107] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 02/17/2006] [Indexed: 11/17/2022]
Abstract
The ubiquitin-fold modifier 1 (Ufm1) is one of various ubiquitin-like modifiers and conjugates to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting its potential roles in various multicellular organisms. Herein, we analyzed the solution structure and dynamics of human Ufm1 (hsUfm1) by nuclear magnetic resonance spectroscopy. Although the global fold of hsUfm1 is similar to those of ubiquitin (Ub) and NEDD8, the cluster of acidic residues conserved in Ub and NEDD8 does not exist on the Ufm1 surface. 15N spin relaxation data revealed that the amino acid residues of hsUfm1 exhibiting conformational fluctuations form a cluster at the C-terminal segment and its spatial proximity, which correspond to the versatile ligand-binding sites of Ub and other ubiquitin-like proteins (Ubls). We suggest that Ub and other Ubl-modifiers share a common feature of potential conformational multiplicity, which might be associated with the broad ligand specificities of these proteins.
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Affiliation(s)
- Hiroaki Sasakawa
- Institute for Molecular Science, Okazaki National Research Institutes, Higashiyama Myodaiji, Okazaki, Aichi 444-8787, Japan
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30
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Penengo L, Mapelli M, Murachelli AG, Confalonieri S, Magri L, Musacchio A, Di Fiore PP, Polo S, Schneider TR. Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell 2006; 124:1183-95. [PMID: 16499958 DOI: 10.1016/j.cell.2006.02.020] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/06/2006] [Accepted: 02/14/2006] [Indexed: 01/25/2023]
Abstract
The interaction between ubiquitinated proteins and intracellular proteins harboring ubiquitin binding domains (UBDs) is critical to a multitude of cellular processes. Here, we report that Rabex-5, a guanine nucleotide exchange factor for Rab5, binds to Ub through two independent UBDs. These UBDs determine a number of properties of Rabex-5, including its coupled monoubiquitination and interaction in vivo with ubiquitinated EGFRs. Structural and biochemical characterization of the UBDs of Rabex-5 revealed that one of them (MIU, motif interacting with ubiquitin) binds to Ub with modes superimposable to those of the UIM (ubiquitin-interacting motif):Ub interaction, although in the opposite orientation. The other UBD, RUZ (Rabex-5 ubiquitin binding zinc finger) binds to a surface of Ub centered on Asp58(Ub) and distinct from the "canonical" Ile44(Ub)-based surface. The two binding surfaces allow Ub to interact simultaneously with different UBDs, thus opening new perspectives in Ub-mediated signaling.
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Affiliation(s)
- Lorenza Penengo
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
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31
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Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, Stenmark H, Wakatsuki S. Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol 2006; 13:272-7. [PMID: 16462748 DOI: 10.1038/nsmb1051] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Accepted: 12/12/2005] [Indexed: 11/08/2022]
Abstract
Hrs has an essential role in sorting of monoubiquitinated receptors to multivesicular bodies for lysosomal degradation, through recognition of ubiquitinated receptors by its ubiquitin-interacting motif (UIM). Here, we present the structure of a complex of Hrs-UIM and ubiquitin at 1.7-A resolution. Hrs-UIM forms a single alpha-helix, which binds two ubiquitin molecules, one on either side. These two ubiquitin molecules are related by pseudo two-fold screw symmetry along the helical axis of the UIM, corresponding to a shift by two residues on the UIM helix. Both ubiquitin molecules interact with the UIM in the same manner, using the Ile44 surface, with equal binding affinities. Mutational experiments show that both binding sites of Hrs-UIM are required for efficient degradative protein sorting. Hrs-UIM belongs to a new subclass of double-sided UIMs, in contrast to its yeast homolog Vps27p, which has two tandem single-sided UIMs.
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Affiliation(s)
- Satoshi Hirano
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
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32
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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33
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Akutsu M, Kawasaki M, Katoh Y, Shiba T, Yamaguchi Y, Kato R, Kato K, Nakayama K, Wakatsuki S. Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. FEBS Lett 2005; 579:5385-91. [PMID: 16199040 DOI: 10.1016/j.febslet.2005.08.076] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 08/15/2005] [Accepted: 08/29/2005] [Indexed: 02/02/2023]
Abstract
Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.
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Affiliation(s)
- Masato Akutsu
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
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34
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Kawasaki M, Nakayama K, Wakatsuki S. Membrane recruitment of effector proteins by Arf and Rab GTPases. Curr Opin Struct Biol 2005; 15:681-9. [PMID: 16289847 DOI: 10.1016/j.sbi.2005.10.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 09/28/2005] [Accepted: 10/21/2005] [Indexed: 01/05/2023]
Abstract
In their GTP-bound form, Arf and Rab family GTPases associate with distinct organelle membranes, to which they recruit specific sets of effector proteins that regulate vesicular transport. The Arf GTPases are involved in the formation of coated carrier vesicles by recruiting coat proteins. On the other hand, the Rab GTPases are involved in the tethering, docking and fusion of transport vesicles with target organelles, acting in concert with the tethering and fusion machineries. Recent structural studies of the Arf1-GGA and Rab5-Rabaptin-5 complexes, as well as other effector structures in complex with the Arf and Rab GTPases, have shed light on the mechanisms underlying the GTP-dependent membrane recruitment of these effector proteins.
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Affiliation(s)
- Masato Kawasaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
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