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Kimura-Someya T, Katsura K, Kato-Murayama M, Hosaka T, Uchikubo-Kamo T, Ihara K, Hanada K, Sato S, Murayama K, Kataoka M, Shirouzu M, Someya Y. Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography revealing binding sites for human monoclonal antibodies. J Virol 2024:e0019724. [PMID: 38593321 DOI: 10.1128/jvi.00197-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Noroviruses are major causative agents of acute nonbacterial gastroenteritis in humans. There are neither antiviral therapeutic agents nor vaccines for noroviruses at this time. To evaluate the potential usefulness of two previously isolated human monoclonal antibody fragments, CV-1A1 and CV-2F5, we first conducted a single-particle analysis to determine the cryo-electron microscopy structure of virus-like particles (VLPs) from the genogroup I genotype 4 (GI.4) Chiba strain uniformly coated with CV-1A1 fragments. The results revealed that the GI.4-specific CV-1A1 antibody bound to the P2 subdomain, in which amino acids are less conserved and variable. Interestingly, a part of the CV-1A1 intrudes into the histo-blood group antigen-binding site, suggesting that this antibody might exert neutralizing activity. Next, we determined the crystal structure of the protruding (P) domain of the capsid protein in the complex form with the CV-2F5 antibody fragment. Consistent with the cross-reactivity, the CV-2F5 bound to the P1 subdomain, which is rich in amino acids conserved among the GI strains, and moreover induced a disruption of Chiba VLPs. These results suggest that the broadly reactive CV-2F5 antibody can be used as both a universal detection reagent and an antiviral drug for GI noroviruses. IMPORTANCE We conducted the structural analyses of the VP1 protein from the GI.4 Chiba norovirus to identify the binding sites of the previously isolated human monoclonal antibodies CV-1A1 and CV-2F5. The cryo-electron microscopy of the Chiba virus-like particles (VLPs) complexed with the Fv-clasp forms of GI.4-specific CV-1A1 revealed that this antibody binds to the highly variable P2 subdomain, suggesting that this antibody may have neutralizing ability against the GI.4 strains. X-ray crystallography revealed that the CV-2F5 antibody bound to the P1 subdomain, which is rich in conserved amino acids. This result is consistent with the ability of the CV-2F5 antibody to react with a wide variety of GI norovirus strains. It is also found that the CV-2F5 antibody caused a disruption of VLPs. Our findings, together with previous reports on the structures of VP1 proteins and VLPs, are expected to open a path for the structure-based development of antivirals and vaccines against norovirus disease.
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Affiliation(s)
| | - Kazushige Katsura
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | | | - Toshiaki Hosaka
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | | | - Kentaro Ihara
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kazuharu Hanada
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Shin Sato
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kazutaka Murayama
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yuichi Someya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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2
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Murayama K, Kato-Murayama M, Hosaka T, Okitsu N, Tanaka Y, Shirouzu M. Molecular basis of ligand recognition specificity of flavone glucosyltransferases in Nemophila menziesii. Arch Biochem Biophys 2024; 753:109926. [PMID: 38346547 DOI: 10.1016/j.abb.2024.109926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/19/2024]
Abstract
Of the more than 100 families of glycosyltransferases, family 1 glycosyltransferases catalyze glycosylation using uridine diphosphate (UDP)-sugar as a sugar donor and are thus referred to as UDP-sugar:glycosyl transferases. The blue color of the Nemophila menziesii flower is derived from metalloanthocyanin, which consists of anthocyanin, flavone, and metal ions. Flavone 7-O-β-glucoside-4'-O-β-glucoside in the plant is sequentially biosynthesized from flavons by UDP-glucose:flavone 4'-O-glucosyltransferase (NmF4'GT) and UDP-glucose:flavone 4'-O-glucoside 7-O-glucosyltransferase (NmF4'G7GT). To identify the molecular mechanisms of glucosylation of flavone, the crystal structures of NmF4'G7GT in its apo form and in complex with UDP-glucose or luteolin were determined, and molecular structure prediction using AlphaFold2 was conducted for NmF4'GT. The crystal structures revealed that the size of the ligand-binding pocket and interaction environment for the glucose moiety at the pocket entrance plays a critical role in the substrate preference in NmF4'G7GT. The substrate specificity of NmF4'GT was examined by comparing its model structure with that of NmF4'G7GT. The structure of NmF4'GT may have a smaller acceptor pocket, leading to a substrate preference for non-glucosylated flavones (or flavone aglycones).
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Affiliation(s)
- Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, 980-8575, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Naoko Okitsu
- Research Institute, Suntory Global Innovation Center Ltd, Kyoto, 619-0284, Japan
| | - Yoshikazu Tanaka
- Research Institute, Suntory Global Innovation Center Ltd, Kyoto, 619-0284, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan.
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3
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Qin XY, Furutani Y, Yonezawa K, Shimizu N, Kato-Murayama M, Shirouzu M, Xu Y, Yamano Y, Wada A, Gailhouste L, Shrestha R, Takahashi M, Keillor JW, Su T, Yu W, Fujii S, Kagechika H, Dohmae N, Shirakami Y, Shimizu M, Masaki T, Matsuura T, Suzuki H, Kojima S. Targeting transglutaminase 2 mediated exostosin glycosyltransferase 1 signaling in liver cancer stem cells with acyclic retinoid. Cell Death Dis 2023; 14:358. [PMID: 37308486 DOI: 10.1038/s41419-023-05847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 06/14/2023]
Abstract
Transglutaminase 2 (TG2) is a multifunctional protein that promotes or suppresses tumorigenesis, depending on intracellular location and conformational structure. Acyclic retinoid (ACR) is an orally administered vitamin A derivative that prevents hepatocellular carcinoma (HCC) recurrence by targeting liver cancer stem cells (CSCs). In this study, we examined the subcellular location-dependent effects of ACR on TG2 activity at a structural level and characterized the functional role of TG2 and its downstream molecular mechanism in the selective depletion of liver CSCs. A binding assay with high-performance magnetic nanobeads and structural dynamic analysis with native gel electrophoresis and size-exclusion chromatography-coupled multi-angle light scattering or small-angle X-ray scattering showed that ACR binds directly to TG2, induces oligomer formation of TG2, and inhibits the transamidase activity of cytoplasmic TG2 in HCC cells. The loss-of-function of TG2 suppressed the expression of stemness-related genes, spheroid proliferation and selectively induced cell death in an EpCAM+ liver CSC subpopulation in HCC cells. Proteome analysis revealed that TG2 inhibition suppressed the gene and protein expression of exostosin glycosyltransferase 1 (EXT1) and heparan sulfate biosynthesis in HCC cells. In contrast, high levels of ACR increased intracellular Ca2+ concentrations along with an increase in apoptotic cells, which probably contributed to the enhanced transamidase activity of nuclear TG2. This study demonstrates that ACR could act as a novel TG2 inhibitor; TG2-mediated EXT1 signaling is a promising therapeutic target in the prevention of HCC by disrupting liver CSCs.
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Affiliation(s)
- Xian-Yang Qin
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Yutaka Furutani
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yali Xu
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yumiko Yamano
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo, Japan
| | - Luc Gailhouste
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Brain Development and Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Rajan Shrestha
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Pharmacy, Kathmandu University, Dhulikhel, Kavre, Nepal
| | - Masataka Takahashi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jeffrey W Keillor
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Ting Su
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Wenkui Yu
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Shinya Fujii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yohei Shirakami
- Department of Gastroenterology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Masahito Shimizu
- Department of Gastroenterology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takahiro Masaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Tomokazu Matsuura
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Soichi Kojima
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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4
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Hamana H, Yasutake Y, Kato-Murayama M, Hosaka T, Shirouzu M, Sakasegawa SI, Sugimori D, Murayama K. Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668. Biosci Biotechnol Biochem 2022; 87:74-81. [PMID: 36307380 DOI: 10.1093/bbb/zbac169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Lysoplasmalogen-specific phospholipase D (LyPls-PLD) hydrolyzes choline lysoplasmalogen to choline and 1-(1-alkenyl)-sn-glycero-3-phosphate. Mutation of F211 to leucine altered its substrate specificity from lysoplasmalogen to 1-O-hexadecyl-2-hydroxy-sn-glycero-3-phosphocholine (lysoPAF). Enzymes specific to lysoPAF have good potential for clinical application, and understanding the mechanism of their activity is important. The crystal structure of LyPls-PLD exhibited a TIM barrel fold assigned to glycerophosphocholine phosphodiesterase, a member of glycerophosphodiester phosphodiesterase. LyPls-PLD possesses a hydrophobic cleft for the binding of the aliphatic chain of the substrate. In the structure of the F211L mutant, Met232 and Tyr258 form a "small lid" structure that stabilizes the binding of the aliphatic chain of the substrate. In contrast, F211 may inhibit small lid formation in the wild-type structure. LysoPAF possesses a flexible aliphatic chain; therefore, a small lid is effective for stabilizing the substrate during catalytic reactions.
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Affiliation(s)
- Hiroaki Hamana
- Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba, Sendai, Japan
| | - Yoshiaki Yasutake
- Applied Molecular Microbiology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 3-4-1 Okubo, Shinjuku, Tokyo, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan
| | | | - Daisuke Sugimori
- Materials Science Course, Faculty of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, Japan
| | - Kazutaka Murayama
- Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba, Sendai, Japan.,Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan
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5
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Kimura-Someya T, Kato-Murayama M, Katsura K, Sakai N, Murayama K, Hanada K, Shirouzu M, Someya Y. Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis. FEBS Open Bio 2022; 12:560-570. [PMID: 35038379 PMCID: PMC8886331 DOI: 10.1002/2211-5463.13370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 11/12/2022] Open
Abstract
Noroviruses have been identified as major causative agents of acute nonbacterial gastroenteritis in humans. Histo‐blood group antigens (HBGAs) are thought to play a major role among the host cellular factors influencing norovirus infection. Genogroup I, genotype 9 (GI.9) is the most recently identified genotype within genogroup I, whose representative strain is the Vancouver 730 norovirus. However, the molecular interactions between host antigens and the GI.9 capsid protein have not been investigated in detail. In this study, we demonstrate that the GI.9 norovirus preferentially binds Lewis antigens over blood group A, B, and H antigens, as revealed by an HBGA binding assay using virus‐like particles. We determined the crystal structures of the protruding domain of the GI.9 capsid protein in the presence or absence of Lewis antigens. Our analysis demonstrated that Lewis fucose (α1–3/4 fucose) represents a key moiety for the GI.9 protein–HBGA interaction, thus suggesting that Lewis antigens might play a critical role during norovirus infection. In addition to previously reported findings, our observations may support the future design of antiviral agents and vaccines against noroviruses.
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Affiliation(s)
- Tomomi Kimura-Someya
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Miyuki Kato-Murayama
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazushige Katsura
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoki Sakai
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazutaka Murayama
- Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Kazuharu Hanada
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuichi Someya
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, 4-7-1 Gakuen, Tokyo, 208-0011, Japan
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Shimizu K, Iyoda T, Sanpei A, Nakazato H, Okada M, Ueda S, Kato-Murayama M, Murayama K, Shirouzu M, Harada N, Hidaka M, Fujii SI. Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2. Commun Biol 2021; 4:1365. [PMID: 34857854 PMCID: PMC8640030 DOI: 10.1038/s42003-021-02885-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/12/2021] [Indexed: 12/30/2022] Open
Abstract
SARS-CoV-2-specific CD8+ T cells are scarce but detectable in unexposed healthy donors (UHDs). It remains unclear whether pre-existing human coronavirus (HCoV)-specific CD8+ T cells are converted to functionally competent T cells cross-reactive to SARS-CoV-2. Here, we identified the HLA-A24-high binding, immunodominant epitopes in SARS-CoV-2 spike region that can be recognized by seasonal coronavirus-specific CD8+ T cells from HLA-A24+ UHDs. Cross-reactive CD8+ T cells were clearly reduced in patients with hematological malignancy, who are usually immunosuppressed, compared to those in UHDs. Furthermore, we showed that CD8+ T cells in response to a selected dominant epitope display multifunctionality and cross-functionality across HCoVs in HLA-A24+ donors. Cross-reactivity of T-cell receptors isolated from them exhibited selective diversity at the single-cell level. Taken together, when stimulated well by immunodominant epitopes, selective pre-existing CD8+ T cells with high functional avidity may be cross-reactive against SARS-CoV-2.
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Affiliation(s)
- Kanako Shimizu
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Tomonori Iyoda
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - An Sanpei
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Hiroshi Nakazato
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Masahiro Okada
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Shogo Ueda
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Miyuki Kato-Murayama
- grid.508743.dLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Kazutaka Murayama
- grid.508743.dLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan ,grid.69566.3a0000 0001 2248 6943Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Mikako Shirouzu
- grid.508743.dLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Naoko Harada
- grid.415538.eDepartment of Hematology, National Hospital Organization Kumamoto Medical Center, Kumamoto, Japan
| | - Michihiro Hidaka
- grid.415538.eDepartment of Hematology, National Hospital Organization Kumamoto Medical Center, Kumamoto, Japan
| | - Shin-ichiro Fujii
- grid.509459.40000 0004 0472 0267Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan ,grid.7597.c0000000094465255Program for Drug Discovery and Medical Technology Platforms (DMP), RIKEN, Yokohama, Japan
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7
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Murayama K, Kato-Murayama M, Sato T, Hosaka T, Ishiguro K, Mizuno T, Kitao K, Honma T, Yokoyama S, Tanaka Y, Shirouzu M. Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin. Phytochemistry 2021; 186:112727. [PMID: 33743393 DOI: 10.1016/j.phytochem.2021.112727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/03/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
The acylation of anthocyanins contributes to their structural diversity. Aromatic acylation is responsible for the blue color of anthocyanins and certain flowers. Aromatic acyltransferase from Gentiana triflora Pall. (Gentianaceae) (Gt5,3'AT) catalyzes the acylation of glucosyl moieties at the 5 and 3' positions of anthocyanins. Anthocyanin acyltransferase transfers an acyl group to a single position, such that Gt5,3'AT possesses a unique enzymatic activity. Structural investigation of this aromatic acyl group transfer is fundamental to understand the molecular mechanism of the acylation of double positions. In this study, structural analyses of Gt5,3'AT were conducted to identify the underlying mechanism. The crystal structure indicated that Gt5,3'AT shares structural similarities with other BAHD family enzymes, consisting of N and C terminal lobes. Structural comparison revealed that acyl group preference (aromatic or aliphatic) for the enzymes was determined by four amino acid positions, which are well conserved in aromatic and aliphatic CoA-binding acyltransferases. Although a complex structure with anthocyanins was not obtained, the binding of delphinidin 3,5,3'-triglucoside to Gt5,3'AT was investigated by evaluating the molecular dynamics. The simulation indicated that acyl transfer by Gt5,3'AT preferentially occurs at the 5-position rather than at the 3'-position, with interacting amino acids that are mainly located in the C-terminal lobe. Subsequent assays of chimeric enzymes (exchange of the N-terminal lobe and the C-terminal lobe between Gt5,3'AT and lisianthus anthocyanin 5AT) demonstrated that acyl transfer selectivity may be caused by the C-terminal lobe.
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Affiliation(s)
- Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, 980-8575, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Tomohiro Sato
- Laboratory for Structure-Based Molecular Design, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Kanako Ishiguro
- Research Institute, Suntory Global Innovation Center Ltd, Kyoto, 619-0284, Japan
| | - Takayuki Mizuno
- Department of Botany, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
| | - Kazunori Kitao
- Research Institute, Suntory Global Innovation Center Ltd, Kyoto, 619-0284, Japan
| | - Teruki Honma
- Laboratory for Structure-Based Molecular Design, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, 230-0045, Japan
| | - Yoshikazu Tanaka
- Research Institute, Suntory Global Innovation Center Ltd, Kyoto, 619-0284, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan.
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8
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Dileep KV, Sakai N, Ihara K, Kato-Murayama M, Nakata A, Ito A, Sivaraman DM, Shin JW, Yoshida M, Shirouzu M, Zhang KYJ. Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors. Int J Biol Macromol 2020; 170:415-423. [PMID: 33373636 DOI: 10.1016/j.ijbiomac.2020.12.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022]
Abstract
Alzheimer's disease (AD), a common chronic neurodegenerative disease, has become a major public health concern. Despite years of research, therapeutics for AD are limited. Overexpression of secretory glutaminyl cyclase (sQC) in AD brain leads to the formation of a highly neurotoxic pyroglutamate variant of amyloid beta, pGlu-Aβ, which acts as a potential seed for the aggregation of full length Aβ. Preventing the formation of pGlu-Aβ through inhibition of sQC has become an attractive disease-modifying therapy in AD. In this current study, through a pharmacophore assisted high throughput virtual screening, we report a novel sQC inhibitor (Cpd-41) with a piperidine-4-carboxamide moiety (IC50 = 34 μM). Systematic molecular docking, MD simulations and X-ray crystallographic analysis provided atomistic details of the binding of Cpd-41 in the active site of sQC. The unique mode of binding and moderate toxicity of Cpd-41 make this molecule an attractive candidate for designing high affinity sQC inhibitors.
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Affiliation(s)
- K V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Naoki Sakai
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kentaro Ihara
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Nakata
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - D M Sivaraman
- Laboratory for Advanced Genomics Circuit, Centre for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695 011, Kerala, India
| | - Jay W Shin
- Laboratory for Advanced Genomics Circuit, Centre for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Minoru Yoshida
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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Murayama K, Kato-Murayama M, Itoh Y, Miyazono K, Miyazawa K, Shirouzu M. Structural basis for inhibitory effects of Smad7 on TGF-β family signaling. J Struct Biol 2020; 212:107661. [PMID: 33166654 DOI: 10.1016/j.jsb.2020.107661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/27/2020] [Accepted: 11/03/2020] [Indexed: 01/10/2023]
Abstract
Smad6 and Smad7 are classified as inhibitory Smads (I-Smads). They are crucial in the fine-tuning of signals by cytokines of the transforming growth factor-β (TGF-β) family. They are negative feedback regulators and principally target the activated type I receptors as well as the activated Smad complexes, but with distinct specificities. Smad7 inhibits Smad signaling from all seven type I receptors of the TGF-β family, whereas Smad6 preferentially inhibits Smad signaling from the bone morphogenetic protein (BMP) type I receptors, BMPR1A and BMPR1B. The target specificities are attributed to the C-terminal MH2 domain. Notably, Smad7 utilizes two alternative molecular surfaces for its inhibitory function against type I receptors. One is a basic groove composed of the first α-helix and the L3 loop, a structure that is shared with Smad6 and receptor-regulated Smads (R-Smads). The other is a three-finger-like structure (consisting of residues 331-361, 379-387, and the L3 loop) that is unique to Smad7. The underlying structural basis remains to be elucidated in detail. Here, we report the crystal structure of the MH2 domain of mouse Smad7 at 1.9 Å resolution. The three-finger-like structure is stabilized by a network of hydrogen bonds between residues 331-361 and 379-387, thus forming a molecular surface unique to Smad7. Furthermore, we discuss how Smad7 antagonizes the activated Smad complexes composed of R-Smad and Smad4, a common partner Smad.
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Affiliation(s)
- Kazutaka Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryomachi, Aoba, Sendai 980-8575, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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Sotokawauchi A, Kato-Murayama M, Murayama K, Hosaka T, Maeda I, Onjo M, Ohsawa N, Kato DI, Arima K, Shirouzu M. Structural basis of cucumisin protease activity regulation by its propeptide. J Biochem 2016; 161:45-53. [DOI: 10.1093/jb/mvw053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/27/2016] [Indexed: 01/13/2023] Open
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11
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Murayama K, Kato-Murayama M, Akasaka R, Terada T, Yokoyama S, Shirouzu M. Structure of the Rho-specific guanine nucleotide-exchange factor Xpln. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012. [PMID: 23192023 DOI: 10.1107/s1744309112045265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Xpln is a guanine nucleotide-exchange factor (GEF) for Rho GTPases. A Dbl homology (DH) domain followed by a pleckstrin homology (PH) domain is a widely adopted GEF-domain architecture. The Xpln structure solely comprises these two domains. Xpln activates RhoA and RhoB, but not RhoC, although their GTPase sequences are highly conserved. The molecular mechanism of the selectivity of Xpln for Rho GTPases is still unclear. In this study, the crystal structure of the tandemly arranged DH-PH domains of mouse Xpln, with a single molecule in the asymmetric unit, was determined at 1.79 Å resolution by the multiwavelength anomalous dispersion method. The DH-PH domains of Xpln share high structural similarity with those from neuroepithelial cell-transforming gene 1 protein, PDZ-RhoGEF, leukaemia-associated RhoGEF and intersectins 1 and 2. The crystal structure indicated that the α4-α5 loop in the DH domain is flexible and that the DH and PH domains interact with each other intramolecularly, thus suggesting that PH-domain rearrangement occurs upon RhoA binding.
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Affiliation(s)
- Kazutaka Murayama
- Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba, Sendai 980-8575, Japan
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Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M. Crystal Structure of Cucumisin, a Subtilisin-Like Endoprotease from Cucumis melo L. J Mol Biol 2012; 423:386-96. [DOI: 10.1016/j.jmb.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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Morishita EC, Murayama K, Kato-Murayama M, Ishizuka-Katsura Y, Tomabechi Y, Hayashi T, Terada T, Handa N, Shirouzu M, Akiyama T, Yokoyama S. Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of Sam68. Structure 2012; 19:1496-508. [PMID: 22000517 DOI: 10.1016/j.str.2011.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/31/2011] [Accepted: 07/04/2011] [Indexed: 12/14/2022]
Abstract
Adenomatous polyposis coli (APC) is a tumor suppressor protein commonly mutated in colorectal tumors. APC plays important roles in Wnt signaling and other cellular processes. Here, we present the crystal structure of the armadillo repeat (Arm) domain of APC, which facilitates the binding of APC to various proteins. APC-Arm forms a superhelix with a positively charged groove. We also determined the structure of the complex of APC-Arm with the tyrosine-rich (YY) domain of the Src-associated in mitosis, 68 kDa protein (Sam68), which regulates TCF-1 alternative splicing. Sam68-YY forms numerous interactions with the residues on the groove and is thereby fixed in a bent conformation. We assessed the effects of mutations and phosphorylation on complex formation between APC-Arm and Sam68-YY. Structural comparisons revealed different modes of ligand recognition between the Arm domains of APC and other Arm-containing proteins.
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Affiliation(s)
- Ella Czarina Morishita
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Morishita E, Murayama K, Kato-Murayama M, Ishizuka-Katsura Y, Tomabechi Y, Hayashi T, Terada T, Handa N, Shirouzu M, Akiyama T, Yokoyama S. Crystal Structures of the Armadillo Repeat Domain of Adenomatous Polyposis Coli and Its Complex with the Tyrosine-Rich Domain of Sam68. Structure 2011. [DOI: 10.1016/j.str.2011.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Morishita EC, Murayama K, Kato-Murayama M, Hayashi T, Terada T, Handa N, Shirouzu M, Akiyama T, Yokoyama S. Crystal structures of adenomatous polyposis coli and its complex with Sam68. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311091355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Murayama K, Nakayama S, Kato-Murayama M, Akasaka R, Ohbayashi N, Kamewari-Hayami Y, Terada T, Shirouzu M, Tsurumi T, Yokoyama S. Crystal structure of epstein-barr virus DNA polymerase processivity factor BMRF1. J Biol Chem 2009; 284:35896-905. [PMID: 19801550 PMCID: PMC2791018 DOI: 10.1074/jbc.m109.051581] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/02/2009] [Indexed: 11/06/2022] Open
Abstract
The DNA polymerase processivity factor of the Epstein-Barr virus, BMRF1, associates with the polymerase catalytic subunit, BALF5, to enhance the polymerase processivity and exonuclease activities of the holoenzyme. In this study, the crystal structure of C-terminally truncated BMRF1 (BMRF1-DeltaC) was solved in an oligomeric state. The molecular structure of BMRF1-DeltaC shares structural similarity with other processivity factors, such as herpes simplex virus UL42, cytomegalovirus UL44, and human proliferating cell nuclear antigen. However, the oligomerization architectures of these proteins range from a monomer to a trimer. PAGE and mutational analyses indicated that BMRF1-DeltaC, like UL44, forms a C-shaped head-to-head dimer. DNA binding assays suggested that basic amino acid residues on the concave surface of the C-shaped dimer play an important role in interactions with DNA. The C95E mutant, which disrupts dimer formation, lacked DNA binding activity, indicating that dimer formation is required for DNA binding. These characteristics are similar to those of another dimeric viral processivity factor, UL44. Although the R87E and H141F mutants of BMRF1-DeltaC exhibited dramatically reduced polymerase processivity, they were still able to bind DNA and to dimerize. These amino acid residues are located near the dimer interface, suggesting that BMRF1-DeltaC associates with the catalytic subunit BALF5 around the dimer interface. Consequently, the monomeric form of BMRF1-DeltaC probably binds to BALF5, because the steric consequences would prevent the maintenance of the dimeric form. A distinctive feature of BMRF1-DeltaC is that the dimeric and monomeric forms might be utilized for the DNA binding and replication processes, respectively.
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Affiliation(s)
- Kazutaka Murayama
- From the Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai 980-8575
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
| | - Sanae Nakayama
- the Division of Virology, Aichi Cancer Center Research Institute, Aichi, Nagoya 464-8681, and
| | | | - Ryogo Akasaka
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
| | - Naomi Ohbayashi
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
| | | | - Takaho Terada
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
| | - Mikako Shirouzu
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
| | - Tatsuya Tsurumi
- the Division of Virology, Aichi Cancer Center Research Institute, Aichi, Nagoya 464-8681, and
| | - Shigeyuki Yokoyama
- the RIKEN Systems Structural Biology Center, Yokohama 230-0045
- the Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
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Hosaka T, Murayama K, Kato-Murayama M, Urushibata A, Akasaka R, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S. Structure of the putative thioesterase protein TTHA1846 from Thermus thermophilus HB8 complexed with coenzyme A and a zinc ion. Acta Crystallogr D Biol Crystallogr 2009; 65:767-76. [PMID: 19622860 DOI: 10.1107/s0907444909015601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 04/27/2009] [Indexed: 11/10/2022]
Abstract
TTHA1846 is a conserved hypothetical protein from Thermus thermophilus HB8 with a molecular mass of 15.1 kDa that belongs to the thioesterase superfamily (Pfam 03061). Here, the 1.9 A resolution crystal structure of TTHA1846 from T. thermophilus is reported. The crystal structure is a dimer of dimers. Each subunit adopts the so-called hot-dog fold composed of five antiparallel beta-strands flanked on one side by a rather long alpha-helix and shares structural similarity to a number of thioesterases. Unexpectedly, TTHA1846 binds one metal ion and one ligand per subunit. The ligand density was modelled as coenzyme A (CoA). Its structure was confirmed by MALDI-TOF mass spectrometry and electron-density mapping. X-ray absorption fine-structure (XAFS) measurement of the crystal unambiguously characterized the metal ion as zinc. The zinc ion is tetrahedrally coordinated by the side chains of Asp18, His22 and Glu50 and the CoA thiol group. This is the first structural report of the interaction of CoA with a zinc ion. From structural and database analyses, it was speculated that the zinc ion may play an inhibitory role in the enzymatic activity.
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Affiliation(s)
- Toshiaki Hosaka
- Protein Research Group, RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan
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Dong X, Kato-Murayama M, Muramatsu T, Mori H, Shirouzu M, Bessho Y, Yokoyama S. The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli. Protein Sci 2007; 16:528-34. [PMID: 17242373 PMCID: PMC2203310 DOI: 10.1110/ps.062616107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is an N-end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl-tRNAs to exposed N-terminal Arg or Lys residues of acceptor proteins. Here, we report the 1.6 A resolution crystal structure of L/F-transferase (JW0868) from Escherichia coli, the first three-dimensional structure of an L/F-transferase. The L/F-transferase adopts a monomeric structure consisting of two domains that form a bilobate molecule. The N-terminal domain forms a small lobe with a novel fold. The large C-terminal domain has a highly conserved fold, which is observed in the GCN5-related N-acetyltransferase (GNAT) family. Most of the conserved residues of L/F-transferase reside in the central cavity, which exists at the interface between the N-terminal and C-terminal domains. A comparison of the structures of L/F-transferase and the bacterial peptidoglycan synthase FemX, indicated a structural homology in the C-terminal domain, and a similar domain interface region. Although the peptidyltransferase function is shared between the two proteins, the enzymatic mechanism would differ. The conserved residues in the central cavity of L/F-transferase suggest that this region is important for the enzyme catalysis.
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Affiliation(s)
- Xuesong Dong
- RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
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Murayama K, Shirouzu M, Kawasaki Y, Kato-Murayama M, Hanawa-Suetsugu K, Sakamoto A, Katsura Y, Suenaga A, Toyama M, Terada T, Taiji M, Akiyama T, Yokoyama S. Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism. J Biol Chem 2006; 282:4238-4242. [PMID: 17190834 DOI: 10.1074/jbc.c600234200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Rac-specific guanine nucleotide exchange factor (GEF) Asef is activated by binding to the tumor suppressor adenomatous polyposis coli mutant, which is found in sporadic and familial colorectal tumors. This activated Asef is involved in the migration of colorectal tumor cells. The GEFs for Rho family GTPases contain the Dbl homology (DH) domain and the pleckstrin homology (PH) domain. When Asef is in the resting state, the GEF activity of the DH-PH module is intramolecularly inhibited by an unidentified mechanism. Asef has a Src homology 3 (SH3) domain in addition to the DH-PH module. In the present study, the three-dimensional structure of Asef was solved in its autoinhibited state. The crystal structure revealed that the SH3 domain binds intramolecularly to the DH domain, thus blocking the Rac-binding site. Furthermore, the RT-loop and the C-terminal region of the SH3 domain interact with the DH domain in a manner completely different from those for the canonical binding to a polyproline-peptide motif. These results demonstrate that the blocking of the Rac-binding site by the SH3 domain is essential for Asef autoinhibition. This may be a common mechanism in other proteins that possess an SH3 domain adjacent to a DH-PH module.
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Affiliation(s)
- Kazutaka Murayama
- Tohoku University Biomedical Engineering Research Organization, Sendai 980-8575; RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Mikako Shirouzu
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Yoshihiro Kawasaki
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0033, and the
| | | | | | - Ayako Sakamoto
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Yasuhiro Katsura
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Atsushi Suenaga
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Mitsutoshi Toyama
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Takaho Terada
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Makoto Taiji
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045
| | - Tetsu Akiyama
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0033, and the
| | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences Center, Yokohama Institute, Yokohama 230-0045; Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033 Japan.
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Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S. Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1. J Mol Biol 2005; 348:295-305. [PMID: 15811369 DOI: 10.1016/j.jmb.2005.02.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 02/21/2005] [Indexed: 11/17/2022]
Abstract
In the final step of tRNA splicing, the 2'-phosphotransferase catalyzes the transfer of the extra 2'-phosphate from the precursor-ligated tRNA to NAD. We have determined the crystal structure of the 2'-phosphotransferase protein from Aeropyrum pernix K1 at 2.8 Angstroms resolution. The structure of the 2'-phosphotransferase contains two globular domains (N and C-domains), which form a cleft in the center. The N-domain has the winged helix motif, a subfamily of the helix-turn-helix family, which is shared by many DNA-binding proteins. The C-domain of the 2'-phosphotransferase superimposes well on the NAD-binding fold of bacterial (diphtheria) toxins, which catalyze the transfer of ADP ribose from NAD to target proteins, indicating that the mode of NAD binding by the 2'-phosphotransferase could be similar to that of the bacterial toxins. The conserved basic residues are assembled at the periphery of the cleft and could participate in the enzyme contact with the sugar-phosphate backbones of tRNA. The modes by which the two functional domains recognize the two different substrates are clarified by the present crystal structure of the 2'-phosphotransferase.
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Affiliation(s)
- Miyuki Kato-Murayama
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Murayama K, Kato-Murayama M, Katsura K, Uchikubo-Kamo T, Yamaguchi-Hirafuji M, Kawazoe M, Akasaka R, Hanawa-Suetsugu K, Hori-Takemoto C, Terada T, Shirouzu M, Yokoyama S. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2004; 61:26-9. [PMID: 16508081 PMCID: PMC1952386 DOI: 10.1107/s1744309104032555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Accepted: 12/09/2004] [Indexed: 11/10/2022]
Abstract
The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 A, beta = 106.8 degrees. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 A and refined to an R factor of 16.8% (Rfree = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight beta-strands and seven alpha-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNAPro deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Takaho Terada
- RIKEN Genomic Sciences Center, Yokohama, Japan
- RIKEN Harima Institute at SPring-8, Hyogo, Japan
| | | | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences Center, Yokohama, Japan
- RIKEN Harima Institute at SPring-8, Hyogo, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Correspondence e-mail:
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Kukimoto-Niino M, Murayama K, Kato-Murayama M, Idaka M, Bessho Y, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8. Protein Sci 2004; 13:3038-42. [PMID: 15459330 PMCID: PMC2286578 DOI: 10.1110/ps.041012404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of TT1887 and TT1465 at 1.8 A and 2.2 A resolutions, respectively, as determined by the multiwavelength anomalous dispersion (MAD) method. TT1887 is a homotetramer, while TT1465 is a homohexamer in the crystal and in solution. The structures of the TT1887 and TT1465 monomers contain single domains with the Rossmann fold, comprising six alpha helices and seven beta strands, and are quite similar to each other. The major structural differences exist in the N terminus of TT1465, where there are two additional alpha helices. A comparison of the structures revealed the elements that are responsible for the different oligomerization modes. The distributions of the electrostatic potential on the solvent-accessible surfaces suggested putative active sites.
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