1
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Abe J, Takeda Y, Kikuma T, Kizuka Y, Kajiura H, Kajihara Y, Ito Y. Squaryl group-modified UDP analogs as inhibitors of the endoplasmic reticulum-resident folding sensor enzyme UGGT. Chem Commun (Camb) 2023; 59:2803-2806. [PMID: 36790024 DOI: 10.1039/d2cc06634c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
UDP-Glc:glycoprotein glucosyltransferase (UGGT) has a central role to retain quality control of correctly folded N-glycoprotein in the endoplasmic reticulum (ER). A selective and potent inhibitor against UGGT could lead to elucidation of UGGT-related events, but such a molecule has not been identified so far. Examples of small molecules with UGGT inhibitory activity are scarce. Here, we report squaryl group-modified UDP analogs as a promising UGGT inhibitor. Among these, the compound possessing a 2'-amino group of the uridine moiety and hydroxyethyl-substituted squaramide exhibited the highest potency, suggesting its relevance as a molecule for further optimization.
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Affiliation(s)
- Junpei Abe
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan
| | - Yoichi Takeda
- College of Life Sciences, Ritsumeikan University, Kusastu, 525-8577, Japan
| | - Takashi Kikuma
- College of Life Sciences, Ritsumeikan University, Kusastu, 525-8577, Japan
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Suita, 565-0871, Japan
| | - Yasuhiro Kajihara
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan
| | - Yukishige Ito
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan.,RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
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2
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Higashi S, Imamura Y, Kikuma T, Matoba T, Orita S, Yamaguchi Y, Ito Y, Takeda Y. Analysis of Selenoprotein F Binding to UDP-Glucose:Glycoprotein Glucosyltransferase (UGGT) by a Photoreactive Crosslinker. Chembiochem 2023; 24:e202200444. [PMID: 36219527 DOI: 10.1002/cbic.202200444] [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: 08/02/2022] [Revised: 10/03/2022] [Indexed: 11/06/2022]
Abstract
In the endoplasmic reticulum glycoprotein quality control system, UDP-glucose : glycoprotein glucosyltransferase (UGGT) functions as a folding sensor. Although it is known to form a heterodimer with selenoprotein F (SelenoF), the details of the complex formation remain obscure. A pulldown assay using co-transfected SelenoF and truncated mutants of human UGGT1 (HUGT1) revealed that SelenoF binds to the TRXL2 domain of HUGT1. Additionally, a newly developed photoaffinity crosslinker was selectively introduced into cysteine residues of recombinant SelenoF to determine the spatial orientation of SelenoF to HUGT1. The crosslinking experiments showed that SelenoF formed a covalent bond with amino acids in the TRXL3 region and the interdomain between βS2 and GT24 of HUGT1 via the synthetic crosslinker. SelenoF might play a role in assessing and refining the disulfide bonds of misfolded glycoproteins in the hydrophobic cavity of HUGT1 as it binds to the highly flexible region of HUGT1 to reach its long hydrophobic cavity. Clarification of the SelenoF-binding domain of UGGT and its relative position will help predict and reveal the function of SelenoF from a structural perspective.
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Affiliation(s)
- Sayaka Higashi
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Yuki Imamura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Takashi Kikuma
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Takahiro Matoba
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Saya Orita
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, 981-8558, Japan
| | - Yukishige Ito
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan.,RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Yoichi Takeda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
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3
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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4
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Glycan dependent refolding activity of ER glucosyltransferase (UGGT). Biochim Biophys Acta Gen Subj 2020; 1864:129709. [DOI: 10.1016/j.bbagen.2020.129709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 01/21/2023]
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5
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Ito Y, Kajihara Y, Takeda Y. Chemical‐Synthesis‐Based Approach to Glycoprotein Functions in the Endoplasmic Reticulum. Chemistry 2020; 26:15461-15470. [DOI: 10.1002/chem.202004158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Yukishige Ito
- Project Research Center for Fundamental Sciences Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
- RIKEN Cluster for Pioneering Research Wako Saitama 3510198 Japan
| | - Yasuhiro Kajihara
- Project Research Center for Fundamental Sciences Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
- Department of Chemistry Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
| | - Yoichi Takeda
- Department of Biotechnology Ritsumeikan University Kusatsu Shiga 5258577 Japan
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6
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Kozlov G, Gehring K. Calnexin cycle - structural features of the ER chaperone system. FEBS J 2020; 287:4322-4340. [PMID: 32285592 PMCID: PMC7687155 DOI: 10.1111/febs.15330] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
Abstract
The endoplasmic reticulum (ER) is the major folding compartment for secreted and membrane proteins and is the site of a specific chaperone system, the calnexin cycle, for folding N-glycosylated proteins. Recent structures of components of the calnexin cycle have deepened our understanding of quality control mechanisms and protein folding pathways in the ER. In the calnexin cycle, proteins carrying monoglucosylated glycans bind to the lectin chaperones calnexin and calreticulin, which recruit a variety of function-specific chaperones to mediate protein disulfide formation, proline isomerization, and general protein folding. Upon trimming by glucosidase II, the glycan without an inner glucose residue is no longer able to bind to the lectin chaperones. For proteins that have not yet folded properly, the enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a checkpoint by adding a glucose back to the N-glycan. This allows the misfolded proteins to re-associate with calnexin and calreticulin for additional rounds of chaperone-mediated refolding and prevents them from exiting the ERs. Here, we review progress in structural studies of the calnexin cycle, which reveal common features of how lectin chaperones recruit function-specific chaperones and how UGGT recognizes misfolded proteins.
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Affiliation(s)
- Guennadi Kozlov
- From the Department of Biochemistry & Centre for Structural BiologyMcGill UniversityMontréalQCCanada
| | - Kalle Gehring
- From the Department of Biochemistry & Centre for Structural BiologyMcGill UniversityMontréalQCCanada
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7
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Goltyaev MV, Mal'tseva VN, Varlamova EG. Expression of ER-resident selenoproteins and activation of cancer cells apoptosis mechanisms under ER-stress conditions caused by methylseleninic acid. Gene 2020; 755:144884. [PMID: 32562739 DOI: 10.1016/j.gene.2020.144884] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/10/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
The aim of this work was to study changes in gene expression levels of 7 ER-resident selenoproteins under ER-stress caused by the action of a selenium-containing compound of organic nature, methylselenic acid using three human cancer cell lines DU 145 (prostate carcinoma), MCF 7 (breast adenocarcinoma)and HT-1080 (fibrosarcoma). According to the obtained results, we can speak of a synchronous changes in the expression of SELT and SEP15 mRNA depending on the concentration of MSA for 24 h, while the pattern of SELM expression was completely opposite and was radically different from other selenoproteins. It should be noted that in HT-1080 cells, the expression pattern of SELM differed from the expression pattern in two other cancer cells, while the expression patterns of other ER-resident selenoproteins (SELT, SEP15, SELK, SELS, SELN and DIO2) differed slightly depending on the cell line. Also we investigated the molecular mechanisms of UPR caused by MSA-induced ER stress in three cancer cell lines. According to the obtained results, it can be assumed that in DU 145 cells, MSA promotes activation of the PERK signaling pathway of UPR. In fibrosarcoma cells MSA was promoted the activation of ATF-6 UPR signaling pathway. In MCF 7 cells, MSA promoted the activation of two pro-apoptotic UPR signaling pathways at once: IRE1 and ATF-6.The results of this work once again demonstrate that the mechanisms of ER-stress regulation caused by the same agent, in this case, MSA, lead to the activation of different UPR signaling pathways in different cancer cells, and about their relationship.
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Affiliation(s)
- M V Goltyaev
- Federal State Institution of Science Institute of Cell Biophysics, Russian Academy of Sciences, Institutskaya st. 3, 142290 Pushchino, Moscow Region, Russia
| | - V N Mal'tseva
- Federal State Institution of Science Institute of Cell Biophysics, Russian Academy of Sciences, Institutskaya st. 3, 142290 Pushchino, Moscow Region, Russia
| | - E G Varlamova
- Federal State Institution of Science Institute of Cell Biophysics, Russian Academy of Sciences, Institutskaya st. 3, 142290 Pushchino, Moscow Region, Russia.
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8
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Protein-protein interactions of ER-resident selenoproteins with their physiological partners. Biochimie 2020; 171-172:197-204. [PMID: 32188576 DOI: 10.1016/j.biochi.2020.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022]
Abstract
ER is a highly specialized complex of branched microtubules enclosed in a membrane and communicating with each other, its functions in the cell are important and very diverse: lipid and phospholipid synthesis, calcium storage, hormone synthesis, protein synthesis and maturation, membrane production, toxin neutralization, etc. The high concentration of calcium ions and the oxidizing properties of the contents of the ER cavities contribute to the proper synthesis and folding of proteins designed for secretion or exposure on the surface of the cell membrane. However, disturbance of redox regulation can lead to the accumulation of improperly folded proteins in the ER, disruption of calcium regulation, which can cause ER-stress. This review is devoted to the role of ER-resident selenoproteins in the processes occurring in this organelle of a cell. The main emphasis is placed on the study of protein-protein interactions of selenoproteins with their physiological partners; this will facilitate understanding of their functional purpose in this organelle. Currently, 7 selenoproteins are known that are localized in the ER, but the functions of most of them are not at all clear, for some, physiological partners have been identified. It is known that selenoproteins are oxidoreductases with antioxidant properties, this is extremely important for the normal functioning of ER. Therefore, this review can be very useful for understanding the full picture of the functions of ER-resident selenoproteins obtained on the basis of recent data.
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9
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Kiuchi T, Izumi M, Mukogawa Y, Shimada A, Okamoto R, Seko A, Sakono M, Takeda Y, Ito Y, Kajihara Y. Monitoring of Glycoprotein Quality Control System with a Series of Chemically Synthesized Homogeneous Native and Misfolded Glycoproteins. J Am Chem Soc 2018; 140:17499-17507. [DOI: 10.1021/jacs.8b08653] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tatsuto Kiuchi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Mukogawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Arisa Shimada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akira Seko
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masafumi Sakono
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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10
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Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018; 86 Suppl 1:27-50. [PMID: 28960539 PMCID: PMC5820184 DOI: 10.1002/prot.25392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022]
Abstract
The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Pedro Bule
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Alessandro T Caputo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Ana Luisa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Johan C Hill
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Andrzej Joachimiak
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Karolina Michalska
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
| | - John Moult
- Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Valentina Nardone
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Thanh-Hong Nguyen
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France
| | - Sandra Postel
- University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Mark J van Raaij
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - Amir Shimon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Eric J Sundberg
- Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
- Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Torsten Schwede
- Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland
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11
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Optimum Substrates for Imaging Biological Molecules with High-Speed Atomic Force Microscopy. Methods Mol Biol 2018; 1814:159-179. [PMID: 29956232 DOI: 10.1007/978-1-4939-8591-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent progresses in high-speed atomic force microscopy (HS-AFM) have enabled us to directly visualize dynamic processes of various proteins in liquid conditions. One of the key factors leading to successful HS-AFM observations is the selection of an appropriate substrate depending on molecules to be observed. For the HS-AFM imaging, a target molecule must be absorbed on a substrate by controlling its orientation without impairing the dynamics or physiological function of the molecule. In this chapter, we describe protocols for preparation of substrates that have been used for HS-AFM and then introduce observation examples on dynamic processes of biological molecules.
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12
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Satoh T, Kato K. Structural Aspects of ER Glycoprotein Quality-Control System Mediated by Glucose Tagging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:149-169. [PMID: 30484248 DOI: 10.1007/978-981-13-2158-0_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N-linked oligosaccharides attached to proteins act as tags for glycoprotein quality control, ensuring their appropriate folding and trafficking in cells. Interactions with a variety of intracellular lectins determine glycoprotein fates. Monoglucosylated glycoforms are the hallmarks of incompletely folded glycoproteins in the protein quality-control system, in which glucosidase II and UDP-glucose/glycoprotein glucosyltransferase are, respectively, responsible for glucose trimming and attachment. In this review, we summarize a recently emerging view of the structural basis of the functional mechanisms of these key enzymes as well as substrate N-linked oligosaccharides exhibiting flexible structures, as revealed by applying a series of biophysical techniques including small-angle X-ray scattering, X-ray crystallography, high-speed atomic force microscopy , electron microscopy , and computational simulation in conjunction with NMR spectroscopy.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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13
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Satoh T, Song C, Zhu T, Toshimori T, Murata K, Hayashi Y, Kamikubo H, Uchihashi T, Kato K. Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT. Sci Rep 2017; 7:12142. [PMID: 28939828 PMCID: PMC5610325 DOI: 10.1038/s41598-017-12283-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/06/2017] [Indexed: 01/11/2023] Open
Abstract
In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
| | - Chihong Song
- National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Tong Zhu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
- Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takayasu Toshimori
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Yugo Hayashi
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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14
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Izumi M, Kuruma R, Okamoto R, Seko A, Ito Y, Kajihara Y. Substrate Recognition of Glycoprotein Folding Sensor UGGT Analyzed by Site-Specifically 15N-Labeled Glycopeptide and Small Glycopeptide Library Prepared by Parallel Native Chemical Ligation. J Am Chem Soc 2017; 139:11421-11426. [DOI: 10.1021/jacs.7b03277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Masayuki Izumi
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rie Kuruma
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akira Seko
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Synthetic
Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasuhiro Kajihara
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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15
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Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint. Proc Natl Acad Sci U S A 2017; 114:8544-8549. [PMID: 28739903 DOI: 10.1073/pnas.1703682114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glycoproteins traversing the eukaryotic secretory pathway begin life in the endoplasmic reticulum (ER), where their folding is surveyed by the 170-kDa UDP-glucose:glycoprotein glucosyltransferase (UGGT). The enzyme acts as the single glycoprotein folding quality control checkpoint: it selectively reglucosylates misfolded glycoproteins, promotes their association with ER lectins and associated chaperones, and prevents premature secretion from the ER. UGGT has long resisted structural determination and sequence-based domain boundary prediction. Questions remain on how this single enzyme can flag misfolded glycoproteins of different sizes and shapes for ER retention and how it can span variable distances between the site of misfold and a glucose-accepting N-linked glycan on the same glycoprotein. Here, crystal structures of a full-length eukaryotic UGGT reveal four thioredoxin-like (TRXL) domains arranged in a long arc that terminates in two β-sandwiches tightly clasping the glucosyltransferase domain. The fold of the molecule is topologically complex, with the first β-sandwich and the fourth TRXL domain being encoded by nonconsecutive stretches of sequence. In addition to the crystal structures, a 15-Å cryo-EM reconstruction reveals interdomain flexibility of the TRXL domains. Double cysteine point mutants that engineer extra interdomain disulfide bridges rigidify the UGGT structure and exhibit impaired activity. The intrinsic flexibility of the TRXL domains of UGGT may therefore endow the enzyme with the promiscuity needed to recognize and reglucosylate its many different substrates and/or enable reglucosylation of N-linked glycans situated at variable distances from the site of misfold.
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16
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Calles-Garcia D, Yang M, Soya N, Melero R, Ménade M, Ito Y, Vargas J, Lukacs GL, Kollman JM, Kozlov G, Gehring K. Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins. J Biol Chem 2017; 292:11499-11507. [PMID: 28490633 DOI: 10.1074/jbc.m117.789495] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/07/2017] [Indexed: 11/06/2022] Open
Abstract
The enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) mediates quality control of glycoproteins in the endoplasmic reticulum by attaching glucose to N-linked glycan of misfolded proteins. As a sensor, UGGT ensures that misfolded proteins are recognized by the lectin chaperones and do not leave the secretory pathway. The structure of UGGT and the mechanism of its selectivity for misfolded proteins have been unknown for 25 years. Here, we used negative-stain electron microscopy and small-angle X-ray scattering to determine the structure of UGGT from Drosophila melanogaster at 18-Å resolution. Three-dimensional reconstructions revealed a cage-like structure with a large central cavity. Particle classification revealed flexibility that precluded determination of a high-resolution structure. Introduction of biotinylation sites into a fungal UGGT expressed in Escherichia coli allowed identification of the catalytic and first thioredoxin-like domains. We also used hydrogen-deuterium exchange mass spectrometry to map the binding site of an accessory protein, Sep15, to the first thioredoxin-like domain. The UGGT structural features identified suggest that the central cavity contains the catalytic site and is lined with hydrophobic surfaces. This enhances the binding of misfolded substrates with exposed hydrophobic residues and excludes folded proteins with hydrophilic surfaces. In conclusion, we have determined the UGGT structure, which enabled us to develop a plausible functional model of the mechanism for UGGT's selectivity for misfolded glycoproteins.
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Affiliation(s)
- Daniel Calles-Garcia
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Meng Yang
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Naoto Soya
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain
| | - Marie Ménade
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain.,Bioengineering Lab, Escuela Politécnica Superior, Universidad San Pablo CEU, 28668 Madrid, Spain, and
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Guennadi Kozlov
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Kalle Gehring
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada,
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17
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Totani K, Yamaya K, Hirano M, Ito Y. Influence of aglycone structures on N -glycan processing reactions in the endoplasmic reticulum. Carbohydr Res 2017; 439:16-22. [DOI: 10.1016/j.carres.2016.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
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18
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Suzuki T, Kajino M, Yanaka S, Zhu T, Yagi H, Satoh T, Yamaguchi T, Kato K. Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation. Chembiochem 2017; 18:396-401. [PMID: 27995699 DOI: 10.1002/cbic.201600595] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 12/11/2022]
Abstract
Exploration of the conformational spaces of flexible oligosaccharides is essential to gain deeper insights into their functional mechanisms. Here we characterised dynamic conformation of a high-mannose-type dodecasaccharide with a terminal glucose residue, a critical determinant recognised by molecular chaperones. The dodecasaccharide was prepared by our developed chemoenzymatic technique, which uses 13 C labelling and lanthanide tagging to detect conformation-dependent paramagnetic effects by NMR spectroscopy. The NMR-validated molecular dynamics simulation produced the dynamic conformational ensemble of the dodecasaccharide. This determined its spatial distribution as well as the glycosidic linkage conformation of the terminal glucose determinant. Moreover, comparison of our results with previously reported crystallographic data indicates that the chaperone binding to its target oligosaccharides involves an induced-fit mechanism.
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Affiliation(s)
- Tatsuya Suzuki
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Megumi Kajino
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Saeko Yanaka
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Tong Zhu
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Hirokazu Yagi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Takumi Yamaguchi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Koichi Kato
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
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19
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Satoh T, Toshimori T, Noda M, Uchiyama S, Kato K. Interaction mode between catalytic and regulatory subunits in glucosidase II involved in ER glycoprotein quality control. Protein Sci 2016; 25:2095-2101. [PMID: 27576940 DOI: 10.1002/pro.3031] [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: 07/29/2016] [Revised: 08/28/2016] [Accepted: 08/29/2016] [Indexed: 12/18/2022]
Abstract
The glycoside hydrolase family 31 (GH31) α-glucosidases play vital roles in catabolic and regulated degradation, including the α-subunit of glucosidase II (GIIα), which catalyzes trimming of the terminal glucose residues of N-glycan in glycoprotein processing coupled with quality control in the endoplasmic reticulum (ER). Among the known GH31 enzymes, only GIIα functions with its binding partner, regulatory β-subunit (GIIβ), which harbors a lectin domain for substrate recognition. Although the structural data have been reported for GIIα and the GIIβ lectin domain, the interaction mode between GIIα and GIIβ remains unknown. Here, we determined the structure of a complex formed between GIIα and the GIIα-binding domain of GIIβ, thereby providing a structural basis underlying the functional extension of this unique GH31 enzyme.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan. .,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
| | - Takayasu Toshimori
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan. .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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20
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Takeda Y, Seko A, Fujikawa K, Izumi M, Kajihara Y, Ito Y. Effects of domain composition on catalytic activity of human UDP-glucose:glycoprotein glucosyltransferases. Glycobiology 2016; 26:999-1006. [DOI: 10.1093/glycob/cww069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
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21
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Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci U S A 2016; 113:E4015-24. [PMID: 27357682 DOI: 10.1073/pnas.1608795113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our understanding of how the endoplasmic reticulum (ER)-associated protein degradation (ERAD) machinery efficiently targets terminally misfolded proteins while avoiding the misidentification of nascent polypeptides and correctly folded proteins is limited. For luminal N-glycoproteins, demannosylation of their N-glycan to expose a terminal α1,6-linked mannose is necessary for their degradation via ERAD, but whether this modification is specific to misfolded proteins is unknown. Here we report that the complex of the mannosidase Htm1p and the protein disulfide isomerase Pdi1p (Htm1p-Pdi1p) acts as a folding-sensitive mannosidase for catalyzing this first committed step in Saccharomyces cerevisiae We reconstitute this step in vitro with Htm1p-Pdi1p and model glycoprotein substrates whose structural states we can manipulate. We find that Htm1p-Pdi1p is a glycoprotein-specific mannosidase that preferentially targets nonnative glycoproteins trapped in partially structured states. As such, Htm1p-Pdi1p is suited to act as a licensing factor that monitors folding in the ER lumen and preferentially commits glycoproteins trapped in partially structured states for degradation.
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22
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Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control. Sci Rep 2016; 6:20575. [PMID: 26847925 PMCID: PMC4742823 DOI: 10.1038/srep20575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/06/2016] [Indexed: 01/10/2023] Open
Abstract
The endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by series of intracellular lectins. Glucosidase II catalyzes two-step hydrolysis at α1,3-linked glucose–glucose and glucose–mannose residues of high-mannose-type glycans to generate a quality control protein tag that is transiently expressed on glycoproteins and recognized by ER chaperones. Here we determined the crystal structures of the catalytic α subunit of glucosidase II (GIIα) complexed with two different glucosyl ligands containing the scissile bonds of first- and second-step reactions. Our structural data revealed that the nonreducing terminal disaccharide moieties of the two kinds of substrates can be accommodated in a gourd-shaped bilocular pocket, thereby providing a structural basis for substrate-binding specificity in the two-step deglucosylation catalyzed by this enzyme.
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23
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Hachisu M, Seko A, Daikoku S, Takeda Y, Sakono M, Ito Y. Hydrophobic Tagged Dihydrofolate Reductase for Creating Misfolded Glycoprotein Mimetics. Chembiochem 2016; 17:300-3. [PMID: 26670196 DOI: 10.1002/cbic.201500595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Indexed: 12/18/2022]
Abstract
In the endoplasmic reticulum (ER), nascent glycoproteins that have not acquired the native conformation are either repaired or sorted for degradation by specific quality-control systems composed by various proteins. Among them, UDP-glucose:glycoprotein glucosyltransferase (UGGT) serves as a folding sensor in the ER. However, the molecular mechanism of its recognition remains obscure. This study used pseudo-misfolded glycoproteins, comprising a modified dihydrofolate reductase with artificial pyrene-cysteine moiety on the protein surface (pDHFR) and Man9 GlcNAc2 -methotrexate (M9-MTX). All five M9-MTX/pDHFR complexes, with a pyrene group at different positions, were found to be good substrates of UGGT, irrespective of the site of pyrene modification. These results suggest UGGT's mode of substrate recognition is fuzzy, thus allowing various glycoproteins to be accommodated in the folding cycle.
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Affiliation(s)
- Masakazu Hachisu
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Akira Seko
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shusaku Daikoku
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Department of Biotechnology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Masafumi Sakono
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Applied Chemistry, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-855, Japan
| | - Yukishige Ito
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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24
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Lamriben L, Graham JB, Adams BM, Hebert DN. N-Glycan-based ER Molecular Chaperone and Protein Quality Control System: The Calnexin Binding Cycle. Traffic 2016; 17:308-26. [PMID: 26676362 DOI: 10.1111/tra.12358] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/14/2015] [Accepted: 12/14/2015] [Indexed: 12/17/2022]
Abstract
Helenius and colleagues proposed over 20-years ago a paradigm-shifting model for how chaperone binding in the endoplasmic reticulum was mediated and controlled for a new type of molecular chaperone- the carbohydrate-binding chaperones, calnexin and calreticulin. While the originally established basics for this lectin chaperone binding cycle holds true today, there has been a number of important advances that have expanded our understanding of its mechanisms of action, role in protein homeostasis, and its connection to disease states that are highlighted in this review.
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Affiliation(s)
- Lydia Lamriben
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jill B Graham
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Benjamin M Adams
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
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25
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Zhu T, Yamaguchi T, Satoh T, Kato K. A Hybrid Strategy for the Preparation of 13C-labeled High-mannose-type Oligosaccharides with Terminal Glucosylation for NMR Study. CHEM LETT 2015. [DOI: 10.1246/cl.150898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tong Zhu
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- JST, PRESTO
| | - Koichi Kato
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- Medical and Biological Laboratories Co., Ltd
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26
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Ohara K, Takeda Y, Daikoku S, Hachisu M, Seko A, Ito Y. Profiling Aglycon-Recognizing Sites of UDP-glucose:glycoprotein Glucosyltransferase by Means of Squarate-Mediated Labeling. Biochemistry 2015. [PMID: 26196150 DOI: 10.1021/acs.biochem.5b00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of its ability to selectively glucosylate misfolded glycoproteins, UDP-glucose:glycoprotein glucosyltransferase (UGGT) functions as a folding sensor in the glycoprotein quality control system in the endoplasmic reticulum (ER). The unique property of UGGT derives from its ability to transfer a glucose residue to N-glycan moieties of incompletely folded glycoproteins. We have previously discovered nonproteinic synthetic substrates of this enzyme, allowing us to conduct its high-sensitivity assay in a quantitative manner. In this study, we aimed to conduct site-selective affinity labeling of UGGT using a functionalized oligosaccharide probe to identify domain(s) responsible for recognition of the aglycon moiety of substrates. To this end, a probe 1 was designed to selectively label nucleophilic amino acid residues in the proximity of the canonical aglycon-recognizing site of human UGGT1 (HUGT1) via squaramide formation. As expected, probe 1 was able to label HUGT1 in the presence of UDP. Analysis by nano-LC-ESI/MS(n) identified a unique lysine residue (K1424) that was modified by 1. Kyte-Doolittle analysis as well as homology modeling revealed a cluster of hydrophobic amino acids that may be functional in the folding sensing mechanism of HUGT1.
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Affiliation(s)
- Keiichiro Ohara
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Takeda
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shusaku Daikoku
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masakazu Hachisu
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akira Seko
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,‡RIKEN, Synthetic Cellular Chemistry Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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27
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Abstract
The endoplasmic reticulum (ER) supports many cellular processes and performs diverse functions, including protein synthesis, translocation across the membrane, integration into the membrane, folding, and posttranslational modifications including N-linked glycosylation; and regulation of Ca2+ homeostasis. In mammalian systems, the majority of proteins synthesized by the rough ER have N-linked glycans critical for protein maturation. The N-linked glycan is used as a quality control signal in the secretory protein pathway. A series of chaperones, folding enzymes, glucosidases, and carbohydrate transferases support glycoprotein synthesis and processing. Perturbation of ER-associated functions such as disturbed ER glycoprotein quality control, protein glycosylation and protein folding results in activation of an ER stress coping response. Collectively this ER stress coping response is termed the unfolded protein response (UPR), and occurs through the activation of complex cytoplasmic and nuclear signaling pathways. Cellular and ER homeostasis depends on balanced activity of the ER protein folding, quality control, and degradation pathways; as well as management of the ER stress coping response.
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Caramelo JJ, Parodi AJ. A sweet code for glycoprotein folding. FEBS Lett 2015; 589:3379-87. [PMID: 26226420 DOI: 10.1016/j.febslet.2015.07.021] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 12/11/2022]
Abstract
Glycoprotein synthesis is initiated in the endoplasmic reticulum (ER) lumen upon transfer of a glycan (Glc3Man9GlcNAc2) from a lipid derivative to Asn residues (N-glycosylation). N-Glycan-dependent quality control of glycoprotein folding in the ER prevents exit to Golgi of folding intermediates, irreparably misfolded glycoproteins and incompletely assembled multimeric complexes. It also enhances folding efficiency by preventing aggregation and facilitating formation of proper disulfide bonds. The control mechanism essentially involves four components, resident lectin-chaperones (calnexin and calreticulin) that recognize monoglucosylated polymannose protein-linked glycans, lectin-associated oxidoreductase acting on monoglucosylated glycoproteins (ERp57), a glucosyltransferase that creates monoglucosylated epitopes in protein-linked glycans (UGGT) and a glucosidase (GII) that removes the glucose units added by UGGT. This last enzyme is the only mechanism component sensing glycoprotein conformations as it creates monoglucosylated glycans exclusively in not properly folded glycoproteins or in not completely assembled multimeric glycoprotein complexes. Glycoproteins that fail to properly fold are eventually driven to proteasomal degradation in the cytosol following the ER-associated degradation pathway, in which the extent of N-glycan demannosylation by ER mannosidases play a relevant role in the identification of irreparably misfolded glycoproteins.
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Affiliation(s)
- Julio J Caramelo
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avda. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
| | - Armando J Parodi
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avda. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
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Słomińska-Wojewódzka M, Sandvig K. The Role of Lectin-Carbohydrate Interactions in the Regulation of ER-Associated Protein Degradation. Molecules 2015; 20:9816-46. [PMID: 26023941 PMCID: PMC6272441 DOI: 10.3390/molecules20069816] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 01/08/2023] Open
Abstract
Proteins entering the secretory pathway are translocated across the endoplasmic reticulum (ER) membrane in an unfolded form. In the ER they are restricted to a quality control system that ensures correct folding or eventual degradation of improperly folded polypeptides. Mannose trimming of N-glycans on newly synthesized proteins plays an important role in the recognition and sorting of terminally misfolded glycoproteins for ER-associated protein degradation (ERAD). In this process misfolded proteins are retrotranslocated into the cytosol, polyubiquitinated, and eventually degraded by the proteasome. The mechanism by which misfolded glycoproteins are recognized and recruited to the degradation machinery has been extensively studied during last decade. In this review, we focus on ER degradation-enhancing α-mannosidase-like protein (EDEM) family proteins that seem to play a key role in the discrimination between proteins undergoing a folding process and terminally misfolded proteins directed for degradation. We describe interactions of EDEM proteins with other components of the ERAD machinery, as well as with various protein substrates. Carbohydrate-dependent interactions together with N-glycan-independent interactions seem to regulate the complex process of protein recognition and direction for proteosomal degradation.
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Affiliation(s)
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway.
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway.
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum. Molecules 2015; 20:2475-91. [PMID: 25647580 PMCID: PMC6272264 DOI: 10.3390/molecules20022475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023] Open
Abstract
In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc3Man9GlcNAc2). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing.
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