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Han X, Maita N, Shimada A, Kohda D. Effects of targeting signal mutations in a mitochondrial presequence on the spatial distribution of the conformational ensemble in the binding site of Tom20. Protein Sci 2022; 31:e4433. [PMID: 36173160 PMCID: PMC9490799 DOI: 10.1002/pro.4433] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022]
Abstract
The 20-kDa TOM (translocase of outer mitochondrial membrane) subunit, Tom20, is the first receptor of the protein import pathway into mitochondria. Tom20 recognizes the mitochondrial targeting signal embedded in the presequences attached to mature mitochondrial proteins, as an N-terminal extension. Consequently, ~1,000 different mitochondrial proteins are sorted into the mitochondrial matrix, and distinguished from non-mitochondrial proteins. We previously reported the MPRIDE (multiple partial recognitions in dynamic equilibrium) mechanism to explain the structural basis of the promiscuous recognition of presequences by Tom20. A subset of the targeting signal features is recognized in each pose of the presequence in the binding state, and all of the features are collectively recognized in the dynamic equilibrium between the poses. Here, we changed the volumes of the hydrophobic side chains in the targeting signal, while maintaining the binding affinity. We tethered the mutated presequences to the binding site of Tom20 and placed them in the crystal contact-free space (CCFS) created in the crystal lattice. The spatial distributions of the mutated presequences were visualized as smeared electron densities in the low-pass filtered difference maps obtained by X-ray crystallography. The mutated presequence ensembles shifted their positions in the binding state to accommodate the larger side chains, thus providing positive evidence supporting the use of the MPRIDE mechanism in the promiscuous recognition by Tom20.
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Affiliation(s)
- Xiling Han
- Division of Structural Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Nobuo Maita
- Division of Structural Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
- Institute for Quantum Life Science, National Institutes for Quantum Science and TechnologyChibaJapan
| | - Atsushi Shimada
- Division of Structural Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
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2
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Obita T, Inaka K, Kohda D, Maita N. Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2022; 78:210-216. [PMID: 35506766 PMCID: PMC9067373 DOI: 10.1107/s2053230x22004472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phosphate (PtdIns-P) binding site, suggesting an inability to bind PtdIns-P molecules.
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3
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Ohno A, Maita N, Tabata T, Nagano H, Arita K, Ariyoshi M, Uchida T, Nakao R, Ulla A, Sugiura K, Kishimoto K, Teshima-Kondo S, Okumura Y, Nikawa T. Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza. Life Sci Alliance 2021; 4:4/6/e202000849. [PMID: 33820827 PMCID: PMC8046417 DOI: 10.26508/lsa.202000849] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 11/26/2022] Open
Abstract
The structure of extracellular domain of MSPL and inhibitor complex helps to understand the TTSP functions, including TMPRSS2, and provides the insights of the infection of influenza and SARS-CoV. Infection of certain influenza viruses is triggered when its HA is cleaved by host cell proteases such as proprotein convertases and type II transmembrane serine proteases (TTSP). HA with a monobasic motif is cleaved by trypsin-like proteases, including TMPRSS2 and HAT, whereas the multibasic motif found in high pathogenicity avian influenza HA is cleaved by furin, PC5/6, or MSPL. MSPL belongs to the TMPRSS family and preferentially cleaves [R/K]-K-K-R↓ sequences. Here, we solved the crystal structure of the extracellular region of human MSPL in complex with an irreversible substrate-analog inhibitor. The structure revealed three domains clustered around the C-terminal α-helix of the SPD. The inhibitor structure and its putative model show that the P1-Arg inserts into the S1 pocket, whereas the P2-Lys and P4-Arg interacts with the Asp/Glu-rich 99-loop that is unique to MSPL. Based on the structure of MSPL, we also constructed a homology model of TMPRSS2, which is essential for the activation of the SARS-CoV-2 spike protein and infection. The model may provide the structural insight for the drug development for COVID-19.
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Affiliation(s)
- Ayako Ohno
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan
| | - Nobuo Maita
- Division of Disease Proteomics, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Takanori Tabata
- Laboratory for Pharmacology, Pharmaceutical Research Center, Asahikasei Pharma, Shizuoka, Japan
| | - Hikaru Nagano
- Department of Nutrition, Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan
| | - Mariko Ariyoshi
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Takayuki Uchida
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan
| | - Reiko Nakao
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan
| | - Anayt Ulla
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan
| | - Kosuke Sugiura
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan.,Department of Orthopedics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Koji Kishimoto
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Shigetada Teshima-Kondo
- Department of Nutrition, Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, Japan
| | - Yuushi Okumura
- Department of Nutrition and Health, Faculty of Nutritional Science, Sagami Women's University, Kanagawa, Japan
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan
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Rachadech W, Kato Y, Abou El-Magd RM, Shishido Y, Kim SH, Sogabe H, Maita N, Yorita K, Fukui K. P219L substitution in human D-amino acid oxidase impacts the ligand binding and catalytic efficiency. J Biochem 2021; 168:557-567. [PMID: 32730563 DOI: 10.1093/jb/mvaa083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/29/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Human D-amino acid oxidase (DAO) is a flavoenzyme that is implicated in neurodegenerative diseases. We investigated the impact of replacement of proline with leucine at Position 219 (P219L) in the active site lid of human DAO on the structural and enzymatic properties, because porcine DAO contains leucine at the corresponding position. The turnover numbers (kcat) of P219L were unchanged, but its Km values decreased compared with wild-type, leading to an increase in the catalytic efficiency (kcat/Km). Moreover, benzoate inhibits P219L with lower Ki value (0.7-0.9 µM) compared with wild-type (1.2-2.0 µM). Crystal structure of P219L in complex with flavin adenine dinucleotide (FAD) and benzoate at 2.25 Å resolution displayed conformational changes of the active site and lid. The distances between the H-bond-forming atoms of arginine 283 and benzoate and the relative position between the aromatic rings of tyrosine 224 and benzoate were changed in the P219L complex. Taken together, the P219L substitution leads to an increase in the catalytic efficiency and binding affinity for substrates/inhibitors due to these structural changes. Furthermore, an acetic acid was located near the adenine ring of FAD in the P219L complex. This study provides new insights into the structure-function relationship of human DAO.
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Affiliation(s)
- Wanitcha Rachadech
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan.,Division of Chemistry, Faculty of Science, Udon Thani Rajabhat University, 64 Thahan Road, Muang, Udon Thani 41000, Thailand
| | - Yusuke Kato
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Rabab M Abou El-Magd
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Yuji Shishido
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Soo Hyeon Kim
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Hirofumi Sogabe
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Nobuo Maita
- Division of Disease Proteomics, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kazuko Yorita
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kiyoshi Fukui
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
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5
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Kato Y, Hin N, Maita N, Thomas AG, Kurosawa S, Rojas C, Yorita K, Slusher BS, Fukui K, Tsukamoto T. Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids. Eur J Med Chem 2018; 159:23-34. [PMID: 30265959 PMCID: PMC6193832 DOI: 10.1016/j.ejmech.2018.09.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022]
Abstract
A series of thiophene-2-carboxylic acids and thiophene-3-carboxylic acids were identified as a new class of DAO inhibitors. Structure-activity relationship (SAR) studies revealed that small substituents are well-tolerated on the thiophene ring of both the 2-carboxylic acid and 3-carboxylic acid scaffolds. Crystal structures of human DAO in complex with potent thiophene carboxylic acids revealed that Tyr224 was tightly stacked with the thiophene ring of the inhibitors, resulting in the disappearance of the secondary pocket observed with other DAO inhibitors. Molecular dynamics simulations of the complex revealed that Tyr224 preferred the stacked conformation irrespective of whether Tyr224 was stacked or not in the initial state of the simulations. MM/GBSA indicated a substantial hydrophobic interaction between Tyr244 and the thiophene-based inhibitor. In addition, the active site was tightly closed with an extensive network of hydrogen bonds including those from Tyr224 in the stacked conformation. The introduction of a large branched side chain to the thiophene ring markedly decreased potency. These results are in marked contrast to other DAO inhibitors that can gain potency with a branched side chain extending to the secondary pocket due to Tyr224 repositioning. These insights should be of particular importance in future efforts to optimize DAO inhibitors with novel scaffolds.
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Affiliation(s)
- Yusuke Kato
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Niyada Hin
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Nobuo Maita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Ajit G Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Sumire Kurosawa
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Camilo Rojas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kazuko Yorita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kiyoshi Fukui
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan.
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
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6
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Affiliation(s)
- Nobuo Maita
- Division of Disease Proteomics, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
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7
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Itoh K, Nishioka SI, Hidaka T, Tsuji D, Maita N. Development of Enzyme Drugs Derived from Transgenic Silkworms to Treat Lysosomal Diseases. YAKUGAKU ZASSHI 2018; 138:885-893. [DOI: 10.1248/yakushi.17-00202-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kohji Itoh
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University
| | - So-ichiro Nishioka
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Tomo Hidaka
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University
| | - Daisuke Tsuji
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University
| | - Nobuo Maita
- Division of Disease Proteomics, Institute for Advanced Medical Sciences, Tokushima University
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Kitakaze K, Mizutani Y, Sugiyama E, Tasaki C, Tsuji D, Maita N, Hirokawa T, Asanuma D, Kamiya M, Sato K, Setou M, Urano Y, Togawa T, Otaka A, Sakuraba H, Itoh K. Protease-resistant modified human β-hexosaminidase B ameliorates symptoms in GM2 gangliosidosis model. J Clin Invest 2016; 126:1691-703. [PMID: 27018595 DOI: 10.1172/jci85300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/09/2016] [Indexed: 01/24/2023] Open
Abstract
GM2 gangliosidoses, including Tay-Sachs and Sandhoff diseases, are neurodegenerative lysosomal storage diseases that are caused by deficiency of β-hexosaminidase A, which comprises an αβ heterodimer. There are no effective treatments for these diseases; however, various strategies aimed at restoring β-hexosaminidase A have been explored. Here, we produced a modified human hexosaminidase subunit β (HexB), which we have termed mod2B, composed of homodimeric β subunits that contain amino acid sequences from the α subunit that confer GM2 ganglioside-degrading activity and protease resistance. We also developed fluorescent probes that allow visualization of endocytosis of mod2B via mannose 6-phosphate receptors and delivery of mod2B to lysosomes in GM2 gangliosidosis models. In addition, we applied imaging mass spectrometry to monitor efficacy of this approach in Sandhoff disease model mice. Following i.c.v. administration, mod2B was widely distributed and reduced accumulation of GM2, asialo-GM2, and bis(monoacylglycero)phosphate in brain regions including the hypothalamus, hippocampus, and cerebellum. Moreover, mod2B administration markedly improved motor dysfunction and a prolonged lifespan in Sandhoff disease mice. Together, the results of our study indicate that mod2B has potential for intracerebrospinal fluid enzyme replacement therapy and should be further explored as a gene therapy for GM2 gangliosidoses.
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Sugawara A, Maita N, Gouda H, Yamamoto T, Hirose T, Kimura S, Saito Y, Nakano H, Kasai T, Nakano H, Shiomi K, Hirono S, Watanabe T, Taniguchi H, O̅mura S, Sunazuka T. Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase. J Med Chem 2015; 58:4984-97. [DOI: 10.1021/acs.jmedchem.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Akihiro Sugawara
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuo Maita
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Hiroaki Gouda
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tsuyoshi Yamamoto
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Saori Kimura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoshifumi Saito
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hayato Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takako Kasai
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hirofumi Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuro Shiomi
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuichi Hirono
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takeshi Watanabe
- Department
of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hisaaki Taniguchi
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Satoshi O̅mura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Saito S, Ohno K, Maita N, Sakuraba H. Structural and clinical implications of amino acid substitutions in α-L-iduronidase: insight into the basis of mucopolysaccharidosis type I. Mol Genet Metab 2014; 111:107-12. [PMID: 24480078 DOI: 10.1016/j.ymgme.2013.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/06/2013] [Accepted: 10/07/2013] [Indexed: 11/26/2022]
Abstract
Allelic mutations, predominantly missense ones, of the α-l-iduronidase (IDUA) gene cause mucopolysaccharidosis type I (MPS I), which exhibits heterogeneous phenotypes. These phenotypes are basically classified into severe, intermediate, and attenuated types. We previously examined the structural changes in IDUA due to MPS I by homology modeling, but the reliability was limited because of the low sequence identity. In this study, we built new structural models of mutant IDUAs due to 57 amino acid substitutions that had been identified in 27 severe, 1 severe-intermediate, 13 intermediate, 1 attenuated-intermediate and 15 attenuated type MPS I patients based on the crystal structure of human IDUA, which was recently determined by us. The structural changes were examined by calculating the root-mean-square distances (RMSD) and the number of atoms influenced by the amino acid replacements. The results revealed that the structural changes of the enzyme protein tended to be correlated with the severity of the disease. Then we focused on the structural changes resulting from amino acid replacements in the immunoglobulin-like domain and adjacent region, of which the structure had been missing in the IDUA model previously built. Coloring of atoms influenced by an amino acid substitution was performed in each case and the results revealed that the structural changes occurred in a region far from the active site of IDUA, suggesting that they affected protein folding. Structural analysis is thus useful for elucidation of the basis of MPS I.
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Affiliation(s)
- Seiji Saito
- Department of Medical Management and Informatics, Hokkaido Information University, Hokkaido, Japan
| | - Kazuki Ohno
- NPO for the Promotion of Research on Intellectual Property Tokyo, Tokyo, Japan
| | - Nobuo Maita
- Laboratory of X-ray Crystallography, Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
| | - Hitoshi Sakuraba
- Department of Clinical Genetics, Meiji Pharmaceutical University, Tokyo, Japan.
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Nyirenda J, Matsumoto S, Saitoh T, Maita N, Noda NN, Inagaki F, Kohda D. Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance. Structure 2012. [PMID: 23177926 DOI: 10.1016/j.str.2012.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Oligosaccharyltransferase (OST) is a membrane-bound enzyme that catalyzes the transfer of an oligosaccharide to an asparagine residue in glycoproteins. It possesses a binding pocket that recognizes Ser and Thr residues at the +2 position in the N-glycosylation consensus, Asn-X-Ser/Thr. We determined the crystal structures of the C-terminal globular domains of the catalytic subunits of two archaeal OSTs. A comparison with previously determined structures identified a segment with remarkable conformational plasticity, induced by crystal contact effects. We characterized its dynamic properties in solution by (15)N NMR relaxation analyses. Intriguingly, the mobile region contains the +2 Ser/Thr-binding pocket. In agreement, the flexibility restriction forced by an engineered disulfide crosslink abolished the enzymatic activity, and its cleavage fully restored activity. These results suggest the necessity of multiple conformational states in the reaction. The dynamic nature of the Ser/Thr pocket could facilitate the efficient scanning of N-glycosylation sequons along nascent polypeptide chains.
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Affiliation(s)
- James Nyirenda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shunsuke Matsumoto
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Saitoh
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute of Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Nobuo N Noda
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Fuyuhiko Inagaki
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Research Center for Advanced Immunology, Kyushu University, Fukuoka 812-8582, Japan.
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Maita N, Taniguchi H, Sakuraba H. Crystallization, X-ray diffraction analysis and SIRAS phasing of human α-L-iduronidase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1363-6. [PMID: 23143250 DOI: 10.1107/s1744309112040432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/24/2012] [Indexed: 11/10/2022]
Abstract
Human lysosomal α-L-iduronidase, whose deficiency causes mucopolysaccharidosis type I, was crystallized using sodium/potassium tartrate and polyethylene glycol 3350 as a precipitant. Using synchrotron radiation, a native data set was collected from a single crystal at 100 K to 2.3 Å resolution. The crystal belonged to space group R3 with unit-cell dimensions of a=b=259.22, c=71.83 Å. To obtain the phase information, mercury-derivative crystals were prepared and a single-wavelength anomalous dispersion (SAD) data set was collected at the Hg peak wavelength. Phase calculation with the single isomorphous replacement with anomalous scattering (SIRAS) method successfully yielded an interpretable electron-density map.
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Affiliation(s)
- Nobuo Maita
- Laboratory of X-ray Crystallography, Institute for Enzyme Research, University of Tokushima, 3-18-15, Kuramotocho, Tokushima 770-8503, Japan.
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Hashiguchi T, Ose T, Kubota M, Maita N, Kamishikiryo J, Maenaka K, Yanagi Y. Crystallization strategy for the glycoprotein-receptor complex between measles virus hemagglutinin and its cellular receptor SLAM. Protein Pept Lett 2011; 19:468-73. [PMID: 21933116 DOI: 10.2174/092986612799789314] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/18/2011] [Accepted: 08/20/2011] [Indexed: 11/22/2022]
Abstract
Measles virus (MV), one of the most contagious agents, infects immune cells using the signaling lymphocyte activation molecule (SLAM) on the cell surface. A complex of SLAM and the attachment protein, hemagglutinin (MVH), has remained elusive due to the intrinsic handling difficulty including glycosylation. Furthermore, crystals obtained of this complex are either nondiffracting or poorly-diffracting. To solve this problem, we designed a systematic approach using a combination of the following techniques; (1) a transient expression system in HEK293SGnTI(-) cells, (2) lysine methylation, (3) structure-guided mutagenesis directed at better crystal packing, (4) Endo H treatment, (5) single-chain formation for stable complex, and (6) floating-drop vapor diffusion. Using our approach, the receptor-binding head domain of MV-H covalently fused with SLAM was successfully crystallized and diffraction was improved from 4.5 Å to a final resolution of 3.15 Å . These combinational methods would be useful as crystallization strategies for complexes of glycoproteins and their receptors.
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Affiliation(s)
- Takao Hashiguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060- 0812, Japan
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Maita N, Taniguchi H, Sakuraba H. Crystal structure of human alpha- L-iduronidase. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311092506] [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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15
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Ueji T, Shirakata A, Kondoh S, Nagano K, Maita A, Maita N, Okumura Y, Nikawa T. Crystal structure of Cbl-b TKB domain in complex with Cblin (Cbl-b inhibitor). Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311092373] [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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16
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Okamura-Ikeda K, Hosaka H, Maita N, Fujiwara K, Yoshizawa AC, Nakagawa A, Taniguchi H. Crystal structure of T-H protein complex of the glycine cleavage system. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311089082] [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: 11/11/2022] Open
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17
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Saitoh T, Igura M, Miyazaki Y, Ose T, Maita N, Kohda D. Crystallographic Snapshots of Tom20–Mitochondrial Presequence Interactions with Disulfide-Stabilized Peptides. Biochemistry 2011; 50:5487-96. [DOI: 10.1021/bi200470x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Saitoh
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Miyazaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Toyoyuki Ose
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute for Enzyme Research, Tokushima University, 2-24, Shinkura-cho, Tokushima 770-8501, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Research Center for Advanced Immunology, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
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18
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Okamura-Ikeda K, Hosaka H, Maita N, Fujiwara K, Yoshizawa AC, Nakagawa A, Taniguchi H. Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism. J Biol Chem 2010; 285:18684-92. [PMID: 20375021 DOI: 10.1074/jbc.m110.110718] [Citation(s) in RCA: 29] [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] [Indexed: 11/06/2022] Open
Abstract
Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10-methylenetetrahydrofolate, and dihydrolipoate-bearing H-protein in the presence of tetrahydrofolate. Several mutations in the human T-protein gene are known to cause nonketotic hyperglycinemia. Here, we report the crystal structure of Escherichia coli T-protein in complex with dihydrolipoate-bearing H-protein and 5-methyltetrahydrofolate, a complex mimicking the ternary complex in the reverse reaction. The structure of the complex shows a highly interacting intermolecular interface limited to a small area and the protein-bound dihydrolipoyllysine arm inserted into the active site cavity of the T-protein. Invariant Arg(292) of the T-protein is essential for complex assembly. The structure also provides novel insights in understanding the disease-causing mutations, in addition to the disease-related impairment in the cofactor-enzyme interactions reported previously. Furthermore, structural and mutational analyses suggest that the reversible transfer of the methylene group between the lipoate and tetrahydrofolate should proceed through the electron relay-assisted iminium intermediate formation.
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Affiliation(s)
- Kazuko Okamura-Ikeda
- Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan.
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19
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Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H. Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. J Biol Chem 2010; 285:9971-9980. [PMID: 20089862 PMCID: PMC2843243 DOI: 10.1074/jbc.m109.078717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [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: 10/23/2009] [Revised: 12/28/2009] [Indexed: 11/06/2022] Open
Abstract
Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645-33651). Here, we report two new LplA structures, LplA.lipoyl-5'-AMP and LplA.octyl-5'-AMP.apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5'-AMP reaction intermediate and rotation of the C-terminal domain by about 180 degrees . These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys(133) residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.
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Affiliation(s)
- Kazuko Fujiwara
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503.
| | - Nobuo Maita
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Harumi Hosaka
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Kazuko Okamura-Ikeda
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Hisaaki Taniguchi
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
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20
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Maita N, Nyirenda J, Igura M, Kamishikiryo J, Kohda D. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases. J Biol Chem 2010; 285:4941-50. [PMID: 20007322 PMCID: PMC2836098 DOI: 10.1074/jbc.m109.081752] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [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: 11/03/2009] [Revised: 11/18/2009] [Indexed: 11/06/2022] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. In the bacterium Campylobacter jejuni, a single-subunit membrane protein, PglB, catalyzes N-glycosylation. We report the 2.8 A resolution crystal structure of the C-terminal globular domain of PglB and its comparison with the previously determined structure from the archaeon Pyrococcus AglB. The two distantly related oligosaccharyltransferases share unexpected structural similarity beyond that expected from the sequence comparison. The common architecture of the putative catalytic sites revealed a new catalytic motif in PglB. Site-directed mutagenesis analyses confirmed the contribution of this motif to the catalytic function. Bacterial PglB and archaeal AglB constitute a protein family of the catalytic subunit of OST along with STT3 from eukaryotes. A structure-aided multiple sequence alignment of the STT3/PglB/AglB protein family revealed three types of OST catalytic centers. This novel classification will provide a useful framework for understanding the enzymatic properties of the OST enzymes from Eukarya, Archaea, and Bacteria.
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Affiliation(s)
- Nobuo Maita
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - James Nyirenda
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Igura
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jun Kamishikiryo
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Kohda
- From the Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
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21
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Igura M, Maita N, Kamishikiryou J, Nyirenda J, Maenaka K, Kohda D. Successful expression of archaeal STT3/AglB membrane protein in E.colicells. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308091435] [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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22
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Tabata S, Kuroki K, Maita N, Wang J, Shiratori I, Arase H, Kohda D, Maenaka K. Expression, crystallization and preliminary X-ray diffraction analysis of human paired Ig-like type 2 receptor alpha (PILRalpha). Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 64:44-6. [PMID: 18097101 DOI: 10.1107/s1744309107065384] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/04/2007] [Indexed: 11/11/2022]
Abstract
Human paired immunoglobulin-like (Ig-like) type 2 receptor alpha (PILRalpha) is a type I membrane protein that is mainly expressed in immune-related cells such as monocytes, granulocytes and dendritic cells. PILRalpha can suppress the functions of such immune cells because it has the immunoreceptor tyrosine-based inhibitory motif (ITIM) in the intracellular region, which recruits the phosphatase Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP-2) to inhibit phosphorylations induced by activation signals. The extracellular region of human PILRalpha comprises one immunoglobulin superfamily V-set domain and a stalk region. The V-set domain (residues 13-131) of human PILRalpha was overexpressed in Escherichia coli as inclusion bodies, refolded by rapid dilution and purified. The PILRalpha protein was successfully crystallized at 293 K using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.3 A resolution at SPring-8 BL41XU; they belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 40.4, b = 45.0, c = 56.9 A, and contain one molecule per asymmetric unit.
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Affiliation(s)
- Shigekazu Tabata
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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23
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Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D. Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. EMBO J 2007; 27:234-43. [PMID: 18046457 DOI: 10.1038/sj.emboj.7601940] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 11/08/2007] [Indexed: 12/21/2022] Open
Abstract
Asn-glycosylation is widespread not only in eukaryotes but also in archaea and some eubacteria. Oligosaccharyltransferase (OST) catalyzes the co-translational transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. Here, we report that a thermophilic archaeon, Pyrococcus furiosus OST is composed of the STT3 protein alone, and catalyzes the transfer of a heptasaccharide, containing one hexouronate and two pentose residues, onto peptides in an Asn-X-Thr/Ser-motif-dependent manner. We also determined the 2.7-A resolution crystal structure of the C-terminal soluble domain of Pyrococcus STT3. The structure-based multiple sequence alignment revealed a new motif, DxxK, which is adjacent to the well-conserved WWDYG motif in the tertiary structure. The mutagenesis of the DK motif residues in yeast STT3 revealed the essential role of the motif in the catalytic activity. The function of this motif may be related to the binding of the pyrophosphate group of lipid-linked oligosaccharide donors through a transiently bound cation. Our structure provides the first structural insights into the formation of the oligosaccharide-asparagine bond.
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Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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24
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Igura M, Maita N, Obita T, Kamishikiryo J, Maenaka K, Kohda D. Purification, crystallization and preliminary X-ray diffraction studies of the soluble domain of the oligosaccharyltransferase STT3 subunit from the thermophilic archaeon Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:798-801. [PMID: 17768359 PMCID: PMC2376324 DOI: 10.1107/s1744309107040134] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 06/16/2007] [Accepted: 08/13/2007] [Indexed: 11/10/2022]
Abstract
Oligosaccharyltransferase catalyzes the transfer of preassembled oligosaccharides onto asparagine residues in nascent polypeptide chains. The STT3 subunit is thought to bear the catalytic site. The C-terminal domain of the STT3 protein of Pyrococcus furiosus was expressed in Escherichia coli cells. STT3 protein prepared from two different sources, the soluble fraction and the inclusion bodies, produced crystals that diffracted to 2.7 A. During crystallization screening, cocrystals of P. furiosus STT3 with an E. coli 50S ribosomal protein, L7/L12, were accidentally obtained. This cross-species interaction is not biologically relevant, but may be used to design a built-in polypeptide substrate for the STT3 crystals.
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Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Graduate School of Systems Life Sciences, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takayuki Obita
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jun Kamishikiryo
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Katsumi Maenaka
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Correspondence e-mail:
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25
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Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H. Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. Nucleic Acids Res 2007; 35:3918-27. [PMID: 17537809 PMCID: PMC1919474 DOI: 10.1093/nar/gkm397] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 04/25/2007] [Accepted: 05/01/2007] [Indexed: 11/30/2022] Open
Abstract
R1Bm is a long interspersed element (LINE) inserted into a specific sequence within 28S rDNA of the silkworm genome. Of two open reading frames (ORFs) of R1Bm, ORF2 encodes a reverse transcriptase (RT) and an endonuclease (EN) domain which digests specifically both top and bottom strand of the target sequence in 28S rDNA. To elucidate the sequence specificity of EN domain of R1Bm (R1Bm EN), we examined the cleavage tendency for the target sequences, and found that 5'-A(G/C)(A/T)!(A/G)T-3' is the consensus sequence (! = cleavage site). We also determined the crystal structure of R1Bm EN at 2.0 A resolution. Its structure was basically similar to AP endonuclease family, but had a special beta-hairpin at the edge of the DNA binding surface, which is a common feature among EN of LINEs. Point-mutations on the DNA binding surface of R1Bm EN significantly decreased the cleavage activities, but did not affect the sequence recognition in most residues. However, two mutants Y98A and N180A had altered cleavage patterns, suggesting an important role of these residues (Y98 and N180) for the sequence recognition of R1Bm EN. In addition, Y98A mutant showed another cleavage pattern, that implies de novo design of novel sequence-specific EN.
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Affiliation(s)
- Nobuo Maita
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwa, Chiba 277-8562, Japan, Graduate School of Engineering Kyoto University, Kyoto 615-8510, Japan and CREST, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
| | - Hideyuki Aoyagi
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwa, Chiba 277-8562, Japan, Graduate School of Engineering Kyoto University, Kyoto 615-8510, Japan and CREST, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
| | - Mizuko Osanai
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwa, Chiba 277-8562, Japan, Graduate School of Engineering Kyoto University, Kyoto 615-8510, Japan and CREST, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Shirakawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwa, Chiba 277-8562, Japan, Graduate School of Engineering Kyoto University, Kyoto 615-8510, Japan and CREST, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
| | - Haruhiko Fujiwara
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan, Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwa, Chiba 277-8562, Japan, Graduate School of Engineering Kyoto University, Kyoto 615-8510, Japan and CREST, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan
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26
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Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M. Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase. J Mol Biol 2006; 359:137-47. [PMID: 16626738 DOI: 10.1016/j.jmb.2006.03.036] [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] [Received: 02/09/2006] [Revised: 03/14/2006] [Accepted: 03/14/2006] [Indexed: 11/15/2022]
Abstract
Modification of cellular proteins by the small ubiquitin-like modifier SUMO is important in regulating various cellular events. Many different nuclear proteins are targeted by SUMO, and the functional consequences of this modification are diverse. For most proteins, however, the functional and structural consequences of modification by specific SUMO isomers are unclear. Conjugation of SUMO to thymine-DNA glycosylase (TDG) induces the dissociation of TDG from its product DNA. Structure determination of the TDG central region conjugated to SUMO-1 previously suggested a mechanism in which the SUMOylation-induced conformational change in the C-terminal region of TDG releases TDG from tight binding to its product DNA. Here, we have determined the crystal structure of the central region of TDG conjugated to SUMO-3. The overall structure of SUMO-3-conjugated TDG is similar to the previously reported structure of TDG conjugated to SUMO-1, despite the relatively low level of amino acid sequence similarity between SUMO-3 and SUMO-1. The two structures revealed that the sequence of TDG that resembles the SUMO-binding motif (SBM) can form an intermolecular beta-sheet with either SUMO-1 or SUMO-3. Structural comparison with the canonical SBM shows that this SBM-like sequence of TDG retains all of the characteristic interactions of the SBM, indicating sequence diversity in the SBM.
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Affiliation(s)
- Daichi Baba
- Graduate School of Integrated Science, Yokohama City University, Japan
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27
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Shirakawa M, Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H. Crystal structure of SUMO1-conjugated thymine DNA glycosylase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090549] [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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28
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Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H. Structure of the N-terminal domain of PEX1 AAA-ATPase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305088574] [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: 11/11/2022] Open
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29
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Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M. Crystal structure of SUMO2-conjugated thymine DNA glycosylase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090525] [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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30
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Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M. Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature 2005; 435:979-82. [PMID: 15959518 DOI: 10.1038/nature03634] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [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: 12/06/2004] [Accepted: 04/14/2005] [Indexed: 11/09/2022]
Abstract
Members of the small ubiquitin-like modifier (SUMO) family can be covalently attached to the lysine residue of a target protein through an enzymatic pathway similar to that used in ubiquitin conjugation, and are involved in various cellular events that do not rely on degradative signalling via the proteasome or lysosome. However, little is known about the molecular mechanisms of SUMO-modification-induced protein functional transfer. During DNA mismatch repair, SUMO conjugation of the uracil/thymine DNA glycosylase TDG promotes the release of TDG from the abasic (AP) site created after base excision, and coordinates its transfer to AP endonuclease 1, which catalyses the next step in the repair pathway. Here we report the crystal structure of the central region of human TDG conjugated to SUMO-1 at 2.1 A resolution. The structure reveals a helix protruding from the protein surface, which presumably interferes with the product DNA and thus promotes the dissociation of TDG from the DNA molecule. This helix is formed by covalent and non-covalent contacts between TDG and SUMO-1. The non-covalent contacts are also essential for release from the product DNA, as verified by mutagenesis.
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Affiliation(s)
- Daichi Baba
- Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan
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Maita N, Hatakeyama K, Okada K, Hakoshima T. Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein. J Biol Chem 2004; 279:51534-40. [PMID: 15448133 DOI: 10.1074/jbc.m409440200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GTP cyclohydrolase I (GTPCHI) is the rate-limiting enzyme involved in the biosynthesis of tetrahydrobiopterin, a key cofactor necessary for nitric oxide synthase and for the hydroxylases that are involved in the production of catecholamines and serotonin. In animals, the GTPCHI feedback regulatory protein (GFRP) binds GTPCHI to mediate feed-forward activation of GTPCHI activity in the presence of phenylalanine, whereas it induces feedback inhibition of enzyme activity in the presence of biopterin. Here, we have reported the crystal structure of the biopterin-induced inhibitory complex of GTPCHI and GFRP and compared it with the previously reported phenylalanine-induced stimulatory complex. The structure reveals five biopterin molecules located at each interface between GTPCHI and GFRP. Induced fitting structural changes by the biopterin binding expand large conformational changes in GTPCHI peptide segments forming the active site, resulting in inhibition of the activity. By locating 3,4-dihydroxy-phenylalanine-responsive dystonia mutations in the complex structure, we found mutations that may possibly disturb the GFRP-mediated regulation of GTPCHI.
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Affiliation(s)
- Nobuo Maita
- Structural Biology Laboratory, Nara Institute of Science and Technology, CREST, Japan Science and Technology Agency, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H. Crystallographic characterization of the N-terminal domain of PEX1. Acta Crystallogr D Biol Crystallogr 2004; 60:2098-9. [PMID: 15502339 DOI: 10.1107/s090744490402428x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Accepted: 09/28/2004] [Indexed: 11/10/2022]
Abstract
Peroxisomal enzymes are responsible for several primary metabolism pathways, including beta-oxidation and lipid biosynthesis. PEX1 and PEX6 are hexameric AAA-type ATPases and both are necessary for the import of more than 50 peroxisomal resident proteins from the cytosol into peroxisomes. In this study, PEX1 N-terminal domain crystals have been prepared. The crystals belong to space group P3(1) or P3(2), with unit-cell parameters a = b = 63.5 A, c = 33.5 A, and contain one protein molecule per crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.05 A.
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Affiliation(s)
- Kumiko Shiozawa
- Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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33
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Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H. Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. J Biol Chem 2004; 279:50060-8. [PMID: 15328346 DOI: 10.1074/jbc.m407837200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peroxisomes are responsible for several pathways in primary metabolism, including beta-oxidation and lipid biosynthesis. PEX1 and PEX6 are hexameric AAA-type ATPases, both of which are indispensable in targeting over 50 peroxisomal resident proteins from the cytosol to the peroxisomes. Although the tandem AAA-ATPase domains in the central region of PEX1 and PEX6 are highly similar, the N-terminal sequences are unique. To better understand the distinct molecular function of these two proteins, we analyzed the unique N-terminal domain (NTD) of PEX1. Extensive computational analysis revealed weak similarity (<10% identity) of PEX1 NTD to the N-terminal domains of other membrane-related type II AAA-ATPases, such as VCP (p97) and NSF. We have determined the crystal structure of mouse PEX1 NTD at 2.05-A resolution, which clearly demonstrated that the domain belongs to the double-psi-barrel fold family found in the other AAA-ATPases. The N-domains of both VCP and NSF are structural neighbors of PEX1 NTD with a 2.7- and 2.1-A root mean square deviation of backbone atoms, respectively. Our findings suggest that the supradomain architecture, which is composed of a single N-terminal domain followed by tandem AAA domains, is a common feature of organellar membrane-associating AAA-ATPases. We propose that PEX1 functions as a protein unfoldase in peroxisomal biogenesis, using its N-terminal putative adaptor-binding domain.
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Affiliation(s)
- Kumiko Shiozawa
- Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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34
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Maita N, Anzai T, Aoyagi H, Mizuno H, Fujiwara H. Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1. J Biol Chem 2004; 279:41067-76. [PMID: 15247245 DOI: 10.1074/jbc.m406556200] [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] [Indexed: 11/06/2022] Open
Abstract
The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG)n of insects and (TTAGGG)n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-A resolution. TRAS1-EN has a four-layered alpha/beta sandwich structure; its topology is similar to apurinic/apyrimidinic endonucleases, but the beta-hairpin (beta10-beta11) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the beta10-beta11 hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and beta10-beta11 hairpin structure are involved in specific recognition of telomeric repeats.
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Affiliation(s)
- Nobuo Maita
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
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Momma M, Fujimoto Z, Maita N, Haraguchi K, Mizuno H. Expression, crystallization and preliminary X-ray crystallographic studies ofArthrobacter globiformisinulin fructotransferase. Acta Crystallogr D Biol Crystallogr 2003; 59:2286-8. [PMID: 14646096 DOI: 10.1107/s0907444903019140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 09/01/2003] [Indexed: 11/11/2022]
Abstract
A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293 K by the hanging-drop vapour-diffusion technique using 0.1 M Na HEPES pH 7.5 buffer containing 1.5 M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5 A at 100 K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82 A in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the V(M) value for the crystal was 2.15 A(3) Da(-1), indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58 A, beta = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit.
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Affiliation(s)
- Mitsuru Momma
- Department of Biotechnology, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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Maita N, Nishio K, Nishimoto E, Matsui T, Shikamoto Y, Morita T, Sadler JE, Mizuno H. Crystal structure of von Willebrand factor A1 domain complexed with snake venom, bitiscetin: insight into glycoprotein Ibalpha binding mechanism induced by snake venom proteins. J Biol Chem 2003; 278:37777-81. [PMID: 12851390 DOI: 10.1074/jbc.m305566200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [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
Bitiscetin, a platelet adhesion inducer isolated from venom of the snake Bitis arietans, activates the binding of the von Willebrand factor (VWF) A1 domain to glycoprotein Ib (GPIb) in vitro. This activation requires the formation of a bitiscetin-VWF A1 complex, suggesting an allosteric mechanism of action. Here, we report the crystal structure of bitiscetin-VWF A1 domain complex solved at 2.85 A. In the complex structure, helix alpha5 of VWF A1 domain lies on a concave depression on bitiscetin, and binding sites are located at both ends of the depression. The binding sites correspond well with those proposed previously based on alanine-scanning mutagenesis (Matsui, T., Hamako, J., Matsushita, T., Nakayama, T., Fujimura, Y., and Titani, K. (2002) Biochemistry 41, 7939-7946). Against our expectations, the structure of the VWF A1 domain bound to bitiscetin does not differ significantly from the structure of the free A1 domain. These results are similar to the case of botrocetin, another snake-derived inducer of platelet aggregation, although the binding modes of botrocetin and bitiscetin are different. The modeled structure of the ternary bitiscetin-VWF A1-GPIb complex suggests that an electropositive surface of bitiscetin may interact with a favorably positioned anionic region of GPIb. These results suggest that snake venom proteins induce VWF A1-GPIbalpha binding by interacting with both proteins, and not by causing conformational changes in VWF A1.
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Affiliation(s)
- Nobuo Maita
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Okada K, Maita N, Hatakeyama K, Hakoshima T. Crystal structures of the stimulatory and inhibitory complexes of rat GTPCHI and GFRP. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302097258] [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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Shimizu T, Seto A, Maita N, Hamada K, Tsukita S, Tsukita S, Hakoshima T. Structural basis for neurofibromatosis type 2. Crystal structure of the merlin FERM domain. J Biol Chem 2002; 277:10332-6. [PMID: 11756419 DOI: 10.1074/jbc.m109979200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [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: 11/06/2022] Open
Abstract
Neurofibromatosis type 2 (NF2) is a dominantly inherited disease associated with the central nervous system. The NF2 gene product merlin is a tumor suppressor, and its mutation or inactivation causes this disease. We report here the crystal structure of the merlin FERM domain containing a 22-residue alpha-helical segment. The structure reveals that the merlin FERM domain consists of three subdomains displaying notable features of the electrostatic surface potentials, although the overall surface potentials similar to those of ezrin/radixin/moesin (ERM) proteins indicate electrostatic membrane association. The structure also is consistent with inactivation mechanisms caused by the pathogenic mutations associated with NF2.
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Affiliation(s)
- Toshiyuki Shimizu
- Structural Biology Laboratory, Nara Institute of Science and Technology and CREST, Japan
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39
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Maita N, Okada K, Hatakeyama K, Hakoshima T. Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP. Proc Natl Acad Sci U S A 2002; 99:1212-7. [PMID: 11818540 PMCID: PMC122169 DOI: 10.1073/pnas.022646999] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the presence of phenylalanine, GTP cyclohydrolase I feedback regulatory protein (GFRP) forms a stimulatory 360-kDa complex with GTP cyclohydrolase I (GTPCHI), which is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin. The crystal structure of the stimulatory complex reveals that the GTPCHI decamer is sandwiched by two GFRP homopentamers. Each GFRP pentamer forms a symmetrical five-membered ring similar to beta-propeller. Five phenylalanine molecules are buried inside each interface between GFRP and GTPCHI, thus enhancing the binding of these proteins. The complex structure suggests that phenylalanine-induced GTPCHI x GFRP complex formation enhances GTPCHI activity by locking the enzyme in the active state.
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Affiliation(s)
- Nobuo Maita
- Department of Molecular Biology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
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40
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Maita N, Okada K, Hirotsu S, Hatakeyama K, Hakoshima T. Preparation and crystallization of the stimulatory and inhibitory complexes of GTP cyclohydrolase I and its feedback regulatory protein GFRP. Acta Crystallogr D Biol Crystallogr 2001; 57:1153-6. [PMID: 11468403 DOI: 10.1107/s0907444901005558] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2000] [Accepted: 05/30/2001] [Indexed: 11/10/2022]
Abstract
Mammalian GTP cyclohydrolase I is a decameric enzyme in the first and rate-limiting step in the biosynthesis of tetrahydrobiopterin, which is an essential cofactor for enzymes producing neurotransmitters such as catecholamines and for nitric oxide synthases. The enzyme is dually regulated by its feedback regulatory protein GFRP in the presence of its stimulatory effector phenylalanine and its inhibitory effector biopterin. Here, both the stimulatory and inhibitory complexes of rat GTP cyclohydrolase I bound to GFRP were crystallized by vapour diffusion. Diffraction data sets at resolutions of 3.0 and 2.64 A were collected for the stimulatory and inhibitory complexes, respectively. Each complex consists of two GTPCHI pentamer rings and two GFRP pentamer rings, with pseudo-52 point-group symmetry.
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Affiliation(s)
- N Maita
- Department of Molecular Biology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
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Yamamoto Y, Maita N, Fujisawa A, Takashima J, Ishii Y, Dunlap WC. A new vitamin E (alpha-tocomonoenol) from eggs of the Pacific salmon Oncorhynchus keta. J Nat Prod 1999; 62:1685-1687. [PMID: 10654418 DOI: 10.1021/np990230v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A novel alpha-tocomonoenol 3,4-dihydro-2,5,7,8-tetramethyl-2-(4,8,12-trimethyl-12-tridecenyl )-2H-1- benzopyran-6-ol[ having an unusual methylene unsaturation at the isoprenoid-chain terminus of alpha-tocopherol was isolated from the lipophilic fraction of chum salmon eggs. The structure of this marine-derived tocopherol (MDT) was established by spectral analyses. The peroxyl radical-trapping activities of MDT and alpha-tocopherol were compared in aqueous phosphatidylcholine liposomal suspension and in methanolic solution at 37 degrees C. The antioxidant activity of MDT was found to be identical to that of alpha-tocopherol under the experimental conditions of measurement.
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Affiliation(s)
- Y Yamamoto
- Research Center for Advanced Science and Technology, University of Tokyo, Japan.
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