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Ohara Y, Ozeki Y, Tateishi Y, Mashima T, Arisaka F, Tsunaka Y, Fujiwara Y, Nishiyama A, Yoshida Y, Kitadokoro K, Kobayashi H, Kaneko Y, Nakagawa I, Maekura R, Yamamoto S, Katahira M, Matsumoto S. Correction: Significance of a histone-like protein with its native structure for the diagnosis of asymptomatic tuberculosis. PLoS One 2021; 16:e0256946. [PMID: 34449816 PMCID: PMC8396761 DOI: 10.1371/journal.pone.0256946] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0204160.].
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Kitadokoro K, Tanaka M, Hikima T, Okuno Y, Yamamoto M, Kamitani S. Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat. Sci Rep 2020; 10:5469. [PMID: 32214208 PMCID: PMC7096528 DOI: 10.1038/s41598-020-62427-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/25/2019] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor and may be a therapeutic target for infectious diseases. Herein, we determined the 3D structure of native SAL, the mutated S116A inactive form, and the inhibitor complex using the anti-obesity drug orlistat to aid in drug development. The determined crystal structures showed a typical α/β hydrolase motif with a dimeric form. Fatty acids bound near the active site in native SAL and inactive S116A mutant structures. We found that orlistat potently inhibits SAL activity, and it covalently bound to the catalytic Ser116 residue. This is the first report detailing orlistat–lipase binding. It provides structure-based information on the production of potent anti-SAL drugs and lipase inhibitors. These results also indicated that orlistat can be repositioned to treat bacterial diseases.
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Affiliation(s)
- Kengo Kitadokoro
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Mutsumi Tanaka
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Takaaki Hikima
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masaki Yamamoto
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Shigeki Kamitani
- Graduate School of Comprehensive Rehabilitation, College of Health and Human Sciences, Osaka Prefecture University, 3-7-30 Habikino, Habikino, 583-8555, Osaka, Japan
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Kitadokoro K, Kakara M, Matsui S, Osokoshi R, Thumarat U, Kawai F, Kamitani S. Structural insights into the unique polylactate-degrading mechanism of Thermobifida alba cutinase. FEBS J 2019; 286:2087-2098. [PMID: 30761732 DOI: 10.1111/febs.14781] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 08/24/2018] [Revised: 01/16/2019] [Accepted: 02/12/2019] [Indexed: 11/30/2022]
Abstract
Cutinases are enzymes known to degrade polyester-type plastics. Est119, a plastic-degrading type of cutinase from Thermobifida alba AHK119 (herein called Ta_cut), shows a broad substrate specificity toward polyesters, and can degrade substrates including polylactic acid (PLA). However, the PLA-degrading mechanism of cutinases is still poorly understood. Here, we report the structure complexes of cutinase with ethyl lactate (EL), the constitutional unit. From this complex structure, the electron density maps clearly showed one lactate (LAC) and one EL occupying different positions in the active site cleft. The binding mode of EL is assumed to show a figure prior to reaction and LAC is an after-reaction product. These complex structures demonstrate the role of active site residues in the esterase reaction and substrate recognition. The complex structures were compared with other documented complex structures of cutinases and with the structure of PETase from Ideonella sakaiensis. The amino acid residues involved in substrate interaction are highly conserved among these enzymes. Thus, mapping the precise interactions in the Ta_cut and EL complex will pave the way for understanding the plastic-degrading mechanism of cutinases and suggest ways of creating more potent enzymes by structural protein engineering.
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Affiliation(s)
- Kengo Kitadokoro
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Mizuki Kakara
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Shingo Matsui
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Ryouhei Osokoshi
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Uschara Thumarat
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Thailand
| | - Fusako Kawai
- Center for Fiber and Textile Science, Kyoto Institute of Technology, Japan
| | - Shigeki Kamitani
- Graduate School of Comprehensive Rehabilitation, College of Health and Human Sciences, Osaka Prefecture University, Habikino, Japan
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Ohara Y, Ozeki Y, Tateishi Y, Mashima T, Arisaka F, Tsunaka Y, Fujiwara Y, Nishiyama A, Yoshida Y, Kitadokoro K, Kobayashi H, Kaneko Y, Nakagawa I, Maekura R, Yamamoto S, Katahira M, Matsumoto S. Significance of a histone-like protein with its native structure for the diagnosis of asymptomatic tuberculosis. PLoS One 2018; 13:e0204160. [PMID: 30359374 PMCID: PMC6201868 DOI: 10.1371/journal.pone.0204160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis causes the highest mortality among all single infections. Asymptomatic tuberculosis, afflicting one third of the global human population, is the major source as 5–10% of asymptomatic cases develop active tuberculosis during their lifetime. Thus it is one of important issues to develop diagnostic tools for accurately detecting asymptomatic infection. Mycobacterial DNA-binding protein 1 (MDP1) is a major protein in persistent Mycobacterium tuberculosis and has potential for diagnostic use in detecting asymptomatic infection. However, a previous ELISA-based study revealed a specificity problem; IgGs against MDP1 were detected in both M. tuberculosis-infected and uninfected individuals. Although the tertiary structures of an antigen are known to influence antibody recognition, the MDP1 structural details have not yet been investigated. The N-terminal half of MDP1, homologous to bacterial histone-like protein HU, is predicted to be responsible for DNA-binding, while the C-terminal half is assumed as totally intrinsically disordered regions. To clarify the relationship between the MDP1 tertiary structure and IgG recognition, we refined the purification method, which allow us to obtain a recombinant protein with the predicted structure. Furthermore, we showed that an IgG-ELISA using MDP1 purified by our refined method is indeed useful in the detection of asymptomatic tuberculosis.
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Affiliation(s)
- Yukiko Ohara
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
- Department of Microbiology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
- * E-mail: (YOh); (YOz); (SM)
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
- * E-mail: (YOh); (YOz); (SM)
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
| | - Tsukasa Mashima
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Fumio Arisaka
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
| | - Yutaka Yoshida
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medicine, Niigata University, Niigata, Japan
| | - Kengo Kitadokoro
- Graduate School of Science and Technology, Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasakigosyokaido-cho, Sakyo-ku, Kyoto, Japan
| | - Haruka Kobayashi
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
| | - Yukihiro Kaneko
- Department of Bacteriology and Virology, Osaka-City University Graduate School of Medicine, Osaka, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
| | - Ryoji Maekura
- Department of Respiratory Medicine, National Hospital Organization Toneyama National Hospital, 5-1-1 Toneyama, Toyonaka, Osaka, Japan
- Graduate School of Health Care Sciences, Jikei Institute, Osaka, Japan
| | - Saburo Yamamoto
- Central Laboratory, Japan BCG Laboratory, Kiyose-shi, Tokyo, Japan
| | - Masato Katahira
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
- * E-mail: (YOh); (YOz); (SM)
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Tanaka M, Kamitani S, Kitadokoro K. Staphylococcus aureus lipase: purification, kinetic characterization, crystallization and crystallographic study. Acta Crystallogr F Struct Biol Commun 2018; 74:567-570. [PMID: 30198889 PMCID: PMC6130426 DOI: 10.1107/s2053230x18010506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/21/2018] [Accepted: 07/21/2018] [Indexed: 11/11/2022] Open
Abstract
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor in S. aureus and may be a therapeutic target for infectious diseases caused by S. aureus. For the purposes of anti-SAL drug development using structure-based drug design, X-ray crystallographic analysis of SAL overexpressed in Escherichia coli was performed. The recombinant protein was purified using a three-step protocol involving immobilized metal-affinity chromatography, cation-exchange chromatography and anion-exchange chromatography flowthrough methods, yielding 40 mg of protein per litre of bacterial culture. Crystals were obtained using the sitting-drop vapor-diffusion technique. Diffraction data to 3.0 Å resolution were collected on the BL44XU beamline at SPring-8 at the zinc peak of 1.2842 Å for SAD phasing. The crystals belonged to space group P4122 or P4322, with unit-cell parameters a = 131.0, b = 131.0, c = 250.6 Å, and are likely to contain four SAL molecules (408 residues) per asymmetric unit.
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Affiliation(s)
- Mutsumi Tanaka
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, 5 Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shigeki Kamitani
- Graduate School of Comprehensive Rehabilitation, College of Health and Human Sciences, Osaka Prefecture University, 3-7-30 Habikino, Osaka 583-8555, Japan
| | - Kengo Kitadokoro
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, 5 Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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Amatsu S, Sugawara Y, Matsumura T, Kitadokoro K, Fujinaga Y. Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex. J Biol Chem 2013; 288:35617-25. [PMID: 24165130 DOI: 10.1074/jbc.m113.521179] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.
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Affiliation(s)
- Sho Amatsu
- From the Graduate School of Science and Technology, Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasakigosyokaido-cho, Sakyo-ku, Kyoto 606-8585 and
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Karatani H, Namikawa Y, Mori N, Nishikawa Y, Imai S, Ihara Y, Kinoshita A, Kitadokoro K, Oyama H. Visualization of mitochondria in living cells with a genetically encoded yellow fluorescent protein originating from a yellow-emitting luminous bacterium. Photochem Photobiol Sci 2013; 12:944-56. [PMID: 23493994 DOI: 10.1039/c3pp25360k] [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] [Indexed: 11/21/2022]
Abstract
We have visualized redox and structural changes in the mitochondria of yeast Saccharomyces cerevisiae as a eukaryotic cell model using a genetically encoded yellow fluorescent protein (Y1-Yellow) and conventional fluorescence microscopy. Y1-Yellow originating from a yellow emitting luminous bacterium Aliivibrio sifiae Y1 was fused with a mitochondria-targeted sequence (mt-sequence). Y1-Yellow fluorescence arising only from the mitochondrial site and the color of yellow fluorescence could be easily differentiated from cellular autofluorescence and from that of conventional probes. Y1-Yellow expressing S. cerevisiae made the yellow fluorescence conspicuous at the mitochondrial site in response to reactive oxygen species (ROS) transiently derived in the wake of pretreatment with hydrogen peroxide. Based on our observation with Y1-Yellow fluorescence, we also showed that mitochondria rearrange to form a cluster structure surrounding chromosomal DNA via respiratory inhibition by cyanide, followed by the generation of ROS. In contrast, uptake of an uncoupler of oxidative phosphorylation is not responsible for mitochondrial rearrangement. These results indicate the utility of Y1-Yellow for visualization of mitochondrial vitality and morphology in living cells.
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Affiliation(s)
- Hajime Karatani
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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Kawai F, Thumarat U, Kitadokoro K, Waku T, Tada T, Tanaka N, Kawabata T. Comparison of Polyester-Degrading Cutinases from Genus Thermobifida. Green Polymer Chemistry: Biocatalysis and Materials II 2013. [DOI: 10.1021/bk-2013-1144.ch009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fusako Kawai
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Uschara Thumarat
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Kengo Kitadokoro
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Tomonori Waku
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Tomoko Tada
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Naoki Tanaka
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Takeshi Kawabata
- Center for Nanomaterials and Devices, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Division of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Current address: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
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Kitadokoro K, Thumarat U, Nakamura R, Nishimura K, Karatani H, Suzuki H, Kawai F. Crystal structure of cutinase Est119 from Thermobifida alba AHK119 that can degrade modified polyethylene terephthalate at 1.76Å resolution. Polym Degrad Stab 2012. [DOI: 10.1016/j.polymdegradstab.2012.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Nishimura K, Kitadokoro K, Takegahara Y, Sugawara Y, Matsumura T, Karatani H, Fujinaga Y. Crystallization and preliminary crystallographic studies of the HA3 subcomponent of the type B botulinum neurotoxin complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1244-6. [PMID: 22102038 DOI: 10.1107/s1744309111027412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 07/08/2011] [Indexed: 11/10/2022]
Abstract
The haemagglutinin subcomponent HA3 of the type B botulinum neurotoxin complex, which is important in toxin absorption from the gastrointestinal tract, has been expressed, purified and subsequently crystallized in two crystal forms at different pH values. Form I belonged to space group R32, with unit-cell parameters a = b = 357.4, c = 249.5 Å, α = β = 90, γ = 120°. Form II belonged to space group I4(1)32, with unit-cell parameters a = b = c = 259.0 Å, α = β = γ = 90°. Diffraction data were collected from these crystals to a resolution of 3.0 Å for both form I and form II.
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Affiliation(s)
- Kohsuke Nishimura
- Graduate School of Science and Technology, Department of Biomolecular Engineering, Kyoto Institute of Technology, Kyoto 606-8585, Japan
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Kamitani S, Ao S, Toshima H, Tachibana T, Hashimoto M, Kitadokoro K, Fukui-Miyazaki A, Abe H, Horiguchi Y. Enzymatic actions of Pasteurella multocida toxin detected by monoclonal antibodies recognizing the deamidated α subunit of the heterotrimeric GTPase Gq. FEBS J 2011; 278:2702-12. [PMID: 21624053 DOI: 10.1111/j.1742-4658.2011.08197.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pasteurella multocida toxin (PMT) is a virulence factor responsible for the pathogenesis of some Pasteurellosis. PMT exerts its toxic effects through the activation of heterotrimeric GTPase (G(q), G(12/13) and G(i))-dependent pathways, by deamidating a glutamine residue in the α subunit of these GTPases. However, the enzymatic characteristics of PMT are yet to be analyzed in detail because the deamidation has only been observed in cell-based assays. In the present study, we developed rat monoclonal antibodies, specifically recognizing the deamidated Gα(q), to detect the actions of PMT by immunological techniques such as western blotting. Using the monoclonal antibodies, we found that the toxin deamidated Gα(q) only under reducing conditions. The C-terminal region of PMT, C-PMT, was more active than the full-length PMT. The C3 domain possessing the enzyme core catalyzed the deamidation in vitro without any other domains. These results not only support previous observations on toxicity, but also provide insights into the enzymatic nature of PMT. In addition, we present several lines of evidence that Gα(11), as well as Gα(q), could be a substrate for PMT.
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Affiliation(s)
- Shigeki Kamitani
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita-shi, Osaka, Japan.
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Kitadokoro K, Nishimura K, Kamitani S, Fukui-Miyazaki A, Toshima H, Abe H, Kamata Y, Sugita-Konishi Y, Yamamoto S, Karatani H, Horiguchi Y. Crystal structure of Clostridium perfringens enterotoxin displays features of beta-pore-forming toxins. J Biol Chem 2011; 286:19549-55. [PMID: 21489981 DOI: 10.1074/jbc.m111.228478] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridium perfringens enterotoxin (CPE) is a cause of food poisoning and is considered a pore-forming toxin, which damages target cells by disrupting the selective permeability of the plasma membrane. However, the pore-forming mechanism and the structural characteristics of the pores are not well documented. Here, we present the structure of CPE determined by x-ray crystallography at 2.0 Å. The overall structure of CPE displays an elongated shape, composed of three distinct domains, I, II, and III. Domain I corresponds to the region that was formerly referred to as C-CPE, which is responsible for binding to the specific receptor claudin. Domains II and III comprise a characteristic module, which resembles those of β-pore-forming toxins such as aerolysin, C. perfringens ε-toxin, and Laetiporus sulfureus hemolytic pore-forming lectin. The module is mainly made up of β-strands, two of which span its entire length. Domain II and domain III have three short β-strands each, by which they are distinguished. In addition, domain II has an α-helix lying on the β-strands. The sequence of amino acids composing the α-helix and preceding β-strand demonstrates an alternating pattern of hydrophobic residues that is characteristic of transmembrane domains forming β-barrel-made pores. These structural features imply that CPE is a β-pore-forming toxin. We also hypothesize that the transmembrane domain is inserted into the membrane upon the buckling of the two long β-strands spanning the module, a mechanism analogous to that of the cholesterol-dependent cytolysins.
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Affiliation(s)
- Kengo Kitadokoro
- Graduate School of Science and Technology, Department of Biomolecular Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
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Kamitani S, Kitadokoro K, Miyazawa M, Toshima H, Fukui A, Abe H, Miyake M, Horiguchi Y. Characterization of the membrane-targeting C1 domain in Pasteurella multocida toxin. J Biol Chem 2010; 285:25467-75. [PMID: 20534589 DOI: 10.1074/jbc.m110.102285] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pasteurella multocida toxin (PMT) is a virulence factor responsible for the pathogenesis of some forms of pasteurellosis. The toxin activates G(q)- and G(12/13)-dependent pathways through the deamidation of a glutamine residue in the alpha-subunit of heterotrimeric GTPases. We recently reported the crystal structure of the C terminus (residues 575-1285) of PMT (C-PMT), which is composed of three domains (C1, C2, and C3), and that the C1 domain is involved in the localization of C-PMT to the plasma membrane, and the C3 domain possesses a cysteine protease-like catalytic triad. In this study, we analyzed the membrane-targeting function of the C1 domain in detail. The C1 domain consists of seven helices of which the first four (residues 590-670), showing structural similarity to the N terminus of Clostridium difficile toxin B, were found to be involved in the recruitment of C-PMT to the plasma membrane. C-PMT lacking these helices (C-PMT DeltaC1(4H)) neither localized to the plasma membrane nor stimulated the G(q/12/13)-dependent signaling pathways. When the membrane-targeting property was complemented by a peptide tag with an N-myristoylation motif, C-PMT DeltaC1(4H) recovered the PMT activity. Direct binding between the C1 domain and liposomes containing phospholipids was evidenced by surface plasmon resonance analyses. These results indicate that the C1 domain of C-PMT functions as a targeting signal for the plasma membrane.
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Affiliation(s)
- Shigeki Kamitani
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita-shi, Osaka 565-0871, Japan.
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Kitadokoro K, Kamitani S, Fukui A, Toshima H, Miyake M, Horiguchi Y. Structure and function of C-terminal catalytic region of Pasteurella multocida toxin. BMC Proc 2008. [DOI: 10.1186/1753-6561-2-s1-p32] [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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Kitadokoro K, Kamitani S, Fukui A, Toshima H, Miyake M, Horiguchi Y. Structure and function of C-terminal catalytic region of Pasteurella multocidatoxin. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308088636] [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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Takao M, Oohata Y, Kitadokoro K, Kobayashi K, Iwai S, Yasui A, Yonei S, Zhang QM. Human Nei-like protein NEIL3 has AP lyase activity specific for single-stranded DNA and confers oxidative stress resistance in Escherichia coli mutant. Genes Cells 2008; 14:261-70. [PMID: 19170771 DOI: 10.1111/j.1365-2443.2008.01271.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Oxidative base damage leads to alteration of genomic information and is implicated as a cause of aging and carcinogenesis. To combat oxidative damage to DNA, cells contain several DNA glycosylases including OGG1, NTH1 and the Nei-like proteins, NEIL1 and NEIL2. A third Nei-like protein, NEIL3, is composed of an amino-terminal Nei-like domain and an unknown carboxy-terminal domain. In contrast to the other well-described DNA glycosylases, the DNA glycosylase activity and in vivo repair function of NEIL3 remains unclear. We show here that the structural modeling of the putative NEIL3 glycosylase domain (1-290) fits well to the known Escherichia coli Fpg crystal structure. In spite of the structural similarity, the recombinant NEIL3 and NEIL3(1-290) proteins do not cleave any of several test oligonucleotides containing a single modified base. Within the substrates, we detected AP lyase activity for single-stranded (ss) DNA but double-stranded (ds) DNA. The activity is abrogated completely in mutants with an amino-terminal deletion and at the zinc-finger motif. Surprisingly, NEIL3 partially rescues an E. coli nth nei mutant from hydrogen peroxide sensitivity. Taken together, repair of certain base damage including base loss in ssDNA may be mediated by NEIL3.
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Affiliation(s)
- Masashi Takao
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.
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Kitadokoro K, Kamitani S, Miyazawa M, Hanajima-Ozawa M, Fukui A, Miyake M, Horiguchi Y. Crystal structures reveal a thiol protease-like catalytic triad in the C-terminal region of Pasteurella multocida toxin. Proc Natl Acad Sci U S A 2007; 104:5139-44. [PMID: 17360394 PMCID: PMC1829276 DOI: 10.1073/pnas.0608197104] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [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: 11/18/2022] Open
Abstract
Pasteurella multocida toxin (PMT), one of the virulence factors produced by the bacteria, exerts its toxicity by up-regulating various signaling cascades downstream of the heterotrimeric GTPases Gq and G12/13 in an unknown fashion. Here, we present the crystal structure of the C-terminal region (residues 575-1,285) of PMT, which carries an intracellularly active moiety. The overall structure of C-terminal region of PMT displays a Trojan horse-like shape, composed of three domains with a "feet"-,"body"-, and "head"-type arrangement, which were designated C1, C2, and C3 from the N to the C terminus, respectively. The C1 domain, showing marked similarity in steric structure to the N-terminal domain of Clostridium difficile toxin B, was found to lead the toxin molecule to the plasma membrane. The C3 domain possesses the Cys-His-Asp catalytic triad that is organized only when the Cys is released from a disulfide bond. The steric alignment of the triad corresponded well to that of papain or other enzymes carrying Cys-His-Asp. PMT toxicities on target cells were completely abrogated when one of the amino acids constituting the triad was mutated. Our results indicate that PMT is an enzyme toxin carrying the cysteine protease-like catalytic triad dependent on the redox state and functions on the cytoplasmic face of the plasma membrane of target cells.
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Affiliation(s)
- Kengo Kitadokoro
- *Research Center for Low Temperature and Materials Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; and
| | - Shigeki Kamitani
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
| | - Masayuki Miyazawa
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
| | - Miyuki Hanajima-Ozawa
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
| | - Aya Fukui
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
| | - Masami Miyake
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
| | - Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Yamada-oka 3-1, Suita, Osaka 565-0871, Japan
- To whom correspondence should be sent. E-mail:
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Miyazawa M, Kitadokoro K, Kamitani S, Shime H, Horiguchi Y. Crystallization and preliminary crystallographic studies of the Pasteurella multocida toxin catalytic domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:906-8. [PMID: 16946476 PMCID: PMC2242868 DOI: 10.1107/s1744309106030375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 06/21/2006] [Accepted: 08/03/2006] [Indexed: 11/10/2022]
Abstract
The C-terminal catalytic domain of Pasteurella multocida toxin, which is the virulence factor of the organism in P. multocida, has been expressed, purified and subsequently crystallized using the sitting-drop vapour-diffusion technique. Native diffraction data to 1.9 A resolution were obtained at the BL44XU beamline of SPring-8 from a flash-frozen crystal at 100 K. The crystals belong to space group C2, with unit-cell parameters a = 111.0, b = 150.4, c = 77.1 A, beta = 105.5 degrees, and are likely to contain one C-PMT (726 residues) per asymmetric unit.
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Affiliation(s)
- Masayuki Miyazawa
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita-shi, Osaka 565-0871, Japan
| | - Kengo Kitadokoro
- Research Center for Low Temperature and Materials Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Kamitani
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita-shi, Osaka 565-0871, Japan
| | - Hiroaki Shime
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita-shi, Osaka 565-0871, Japan
| | - Yasuhiko Horiguchi
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita-shi, Osaka 565-0871, Japan
- Correspondence e-mail:
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Kitadokoro K, Ponassi M, Galli G, Petracca R, Falugi F, Grandi G, Bolognesi M. Structural studies of human CD81 extracellular domain. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090173] [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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20
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Kitadokoro K. [Structural biology of human CD81, a receptor for hepatitis C virus]. Uirusu 2004; 54:39-47. [PMID: 15449903 DOI: 10.2222/jsv.54.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/25/2022]
Abstract
Human CD81, which is belonged to tetraspanin family, has been previously identified as a receptor for the hepatitis C virus envelope E 2 glycoprotein. The crystal structure of the human CD81 long extracellular domain, binding site for E 2 glycoprotein, is presented here at 1.6 A resolution. The tertiary structure of CD81-LEL, which is composed of five alpha-helices, is resemble for a mushroom-shaped molecules (stalk and head subdomains) and forms a dimer in the crystallographic asymmetric unit. The two disulfide bridges, which are conserved all the tetraspanin and are necessary for CD 81-HCV interaction, are stabilizing the conformation of the head domain. This head domain is solvent exposed surface region and is locating the amino acid residues which are essential for the E 2 binding. The hydrophobic cluster in this head domain may suggest that the presence of a docking site for a low complementary surface cavity in the partner E 2 glycoprotein. We proposed that the dimer structure may be important in the interactions of HCV E 2 glycoprotein and also the viral protein may occur in dimeric aggregation on the HCV envelope. This common structural motif of the tetraspanin provides the first insight onto the mechanism of HCV binding to human cell and may be targets for structure-based antiviral drug.
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Affiliation(s)
- Kengo Kitadokoro
- Research Center for Low temperature and Materials Sciences, Kyoto University Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto, Japan.
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Kitadokoro K, Ponassi M, Galli G, Petracca R, Falugi F, Grandi G, Bolognesi M. Subunit association and conformational flexibility in the head subdomain of human CD81 large extracellular loop. Biol Chem 2002; 383:1447-52. [PMID: 12437138 DOI: 10.1515/bc.2002.164] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The large extracellular loop of human CD81, a tetraspanin mediating hepatitis C virus envelope protein E2 binding to human cells, has been crystallized in a hexagonal form. The three-dimensional structure, solved and refined at 2.6 A resolution (R-factor = 22.8%), shows that the protein adopts a dimeric assembly, based on an association interface built up by tetraspanin-conserved residues. Structural comparisons with the tertiary structure of human CD81 large extracellular loop, previously determined in a different crystal form, show marked conformational fluctuations in the molecular regions thought to be involved in binding to the viral protein, suggesting rules for recognition and assembly within the tetraspan web.
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Affiliation(s)
- Kengo Kitadokoro
- Department of Physics-INFM, Center of Excellence for Biomedical Research, University of Genoa, Italy
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Kitadokoro K, Bordo D, Galli G, Petracca R, Falugi F, Abrignani S, Grandi G, Bolognesi M. CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs. EMBO J 2001; 20:12-8. [PMID: 11226150 PMCID: PMC140195 DOI: 10.1093/emboj/20.1.12] [Citation(s) in RCA: 222] [Impact Index Per Article: 9.7] [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] [Indexed: 11/14/2022] Open
Abstract
Human CD81, a known receptor for hepatitis C virus envelope E2 glycoprotein, is a transmembrane protein belonging to the tetraspanin family. The crystal structure of human CD81 large extracellular domain is reported here at 1.6 A resolution. Each subunit within the homodimeric protein displays a mushroom-like structure, composed of five alpha-helices arranged in 'stalk' and 'head' subdomains. Residues known to be involved in virus binding can be mapped onto the head subdomain, providing a basis for the design of antiviral drugs and vaccines. Sequence analysis of 160 tetraspanins indicates that key structural features and the new protein fold observed in the CD81 large extracellular domain are conserved within the family. On these bases, it is proposed that tetraspanins may assemble at the cell surface into homo- and/or hetero-dimers through a conserved hydrophobic interface located in the stalk subdomain, while interacting with other liganding proteins, including hepatitis C virus E2, through the head subdomain. The topology of such interactions provides a rationale for the assembly of the so-called tetraspan-web.
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Affiliation(s)
- Kengo Kitadokoro
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Domenico Bordo
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Giuliano Galli
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Roberto Petracca
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Fabiana Falugi
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Sergio Abrignani
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Guido Grandi
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
| | - Martino Bolognesi
- Department of Physics, INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso, 33, I-16146 Genova, National Institute for Cancer Research c/o Advanced Biotechnology Center, Largo Rosanna Benzi, 10, I-16132 Genova, Chiron Vaccines Research Center, Via Fiorentina, 1, I-53100 Siena, Italy and Research Center for Instrumental Analysis, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Corresponding author e-mail:
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Kitadokoro K, Galli G, Petracca R, Falugi F, Grandi G, Bolognesi M. Crystallization and preliminary crystallographic studies on the large extracellular domain of human CD81, a tetraspanin receptor for hepatitis C virus. Acta Crystallogr D Biol Crystallogr 2001; 57:156-8. [PMID: 11134943 DOI: 10.1107/s0907444900015468] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2000] [Accepted: 10/26/2000] [Indexed: 11/10/2022]
Abstract
The large extracellular domain of CD81, a member of the tetraspanin family and a receptor protein for hepatitis C virus envelope E2 glycoprotein, has been expressed, purified and subsequently crystallized using the sitting-drop vapour-diffusion technique. Native diffraction data to 1.6 A resolution were obtained at the ID14 beamline of the European Synchrotron Radiation Facility from a flash-frozen crystal at 100 K. The crystals belong to space group P2(1), with unit-cell parameters a = 31.5, b = 77.2, c = 38.5 A, beta = 107.4 degrees, and are likely to contain two extracellular domains (2 x 99 residues) per asymmetric unit.
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Affiliation(s)
- K Kitadokoro
- Department of Physics--INFM and Advanced Biotechnology Center, University of Genoa, Via Dodecaneso 33, I-16146 Genova, Italy
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Kitadokoro K, Hagishita S, Sato T, Ohtani M, Miki K. Crystal structure of human secretory phospholipase A2-IIA complex with the potent indolizine inhibitor 120-1032. J Biochem 1998; 123:619-23. [PMID: 9538252 DOI: 10.1093/oxfordjournals.jbchem.a021982] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [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: 02/07/2023] Open
Abstract
Phospholipase A2 is a key enzyme in a number of physiologically important cellular processes including inflammation and transmembrane signaling. Human secretory phospholipase A2-IIA is present at high concentrations in synovial fluid of patients with rheumatoid arthritis and in the plasma of patients with septic shock. Inhibitors of this enzyme have been suggested to be therapeutically useful non-steroidal anti-inflammatory drugs. The crystal structure of human secretory phospholipase A2-IIA bound to a novel potent indolizine inhibitor (120-1032) has been determined. The complex crystallizes in the space group P3121, with cell dimensions of a = b = 75.8 A and c = 51.3 A. The model was refined to an R-factor of 0. 183 for the intensity data collected to a resolution of 2.2 A. It was revealed that the inhibitor is located near the active site and bound to the calcium ion. Although the binding mode of the 120-1032 inhibitor to human secretory phospholipase A2-IIA is similar to that previously determined for an indole inhibitor LY311299, the specific interactions between the enzyme and the inhibitor in the present complex include the oxycarboxylate group which was introduced in this inhibitor. The oxycarboxylate group in 120-1032 is coordinated to the calcium ion and included in the water-mediated hydrogen bonding to the catalytic Asp49. In addition, the ethyl group in 120-1032 gains hydrophobic contacts with the cavity wall of the hydrophobic channel of the enzyme.
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Affiliation(s)
- K Kitadokoro
- Shionogi Research Laboratories, Shionogi and Co., Ltd., Fukushima-ku, Osaka 553-0002.
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Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K. Crystal structure of DNA photolyase from Anacystis nidulans. Nat Struct Biol 1997; 4:887-91. [PMID: 9360600 DOI: 10.1038/nsb1197-887] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The crystal structure at 1.8 A resolution of 8-HDF type photolyase from A. nidulans shows a backbone structure similar to that of MTHF type E. coli photolyase but reveals a completely different binding site for the light-harvesting cofactor.
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Miki K, Tamada T, Kitadokoro K, Higuchi Y, Yasui A, de Ruiter PE, Eker APM. Crystal structure of cyanobacterial photolyase (DNA photoreactivating enzyme) from Anacystis nidulans. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396092495] [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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Kitadokoro K. Crystallization and preliminary X-ray crystallographic studies of glutamic acid-specific proteinase from Bacillus licheniformis complex with Z-Leu-Glu-CH2Cl. Acta Crystallogr D Biol Crystallogr 1995; 51:835-6. [PMID: 15299819 DOI: 10.1107/s0907444995000047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A glutamic acid specific proteinase from Bacillus licheniformis has been crystallized as a complex with the inhibitor Z-Leu-Glu-CH(2)Cl. Crystals were grown by the vapor-diffusion method using sodium formate as a precipitant. The crystals diffracted to about 2.0 A resolution and belonged to the trigonal space group P3(1)21 (P3(2)21) with unit-cell parameters a = b = 134.3, c = 109.7 A. A total of 26 964 independent reflections were obtained up to 2.2 A resolution, the merging R-factor being 0.05 for 42 614 measurements.
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Affiliation(s)
- K Kitadokoro
- Shionogi Research Laboratories, Shionogi and Co. Ltd., Osaka, Japan
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Kitadokoro K, Tsuzuki H, Okamoto H, Sato T. Crystal structure analysis of a serine proteinase from Streptomyces fradiae at 0.16-nm resolution and molecular modeling of an acidic-amino-acid-specific proteinase. Eur J Biochem 1994; 224:735-42. [PMID: 7925392 DOI: 10.1111/j.1432-1033.1994.00735.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have determined the three-dimensional structure of a proteinase from Streptomyces fradiae ATCC 14544 (SFase-2) at 0.16-nm resolution. SFase-2, a typical serine proteinase, has broad substrate specificity. The characterization and crystallographic analysis of this enzyme have been reported previously [Kitadokoro, K., Tsuzuki, H., Nakamura, E., Sato, T. & Teraoka, H. (1994) Eur. J. Biochem. 220, 55-61]. In the present study, data were collected to approximately 0.16-nm resolution on a Rigaku R-AXIS IIC imaging plate detector system. Preliminary phases were obtained by molecular replacement methods with a search model derived from the previously determined structure of Streptomyces griseus protease A [Sielecki, A. R., Hendrickson, W. A., Broughton, C. G., Delbaere, L. T., Brayer, G. D. & James, M. N. (1979) J. Mol. Biol. 134, 781-804]. The starting model gave an initial crystallographic R factor of 0.443. Refinement with restrained least-squares converged at a final R factor of 0.182 for 16128 observed reflections. The final model includes 86 water molecules. The crystal structure showed that the enzyme consists of two domains, each of which is comprised of a beta barrel with six-stranded beta sheets and two alpha helices. The overall tertiary structure of SFase-2 is similar to the structures of other chymotrypsin-like proteinases from S. griseus, namely proteinase A and proteinase B. The essential residues of the catalytic triad are located on the cleft between the two domains. These two domains have different sequences, but possess similar three-dimensional structures, indicating that a gene duplication event has occurred to produce these two domains. We predicted the tertiary structure of an acidic-amino-acid-specific proteinase on the basis of the crystal structure of SFase-2, and compared the active-site conformations of these two enzymes. We found a characteristic histidine cluster of three histidine residues in the active site of the acidic-amino-acid-specific proteinase. The substrate recognition mechanism of SFase-2 may be mediated through the hydrophobic amino acid residues. However, in the acidic-amino-acid-specific proteinase, the positive charge of this histidine cluster would attract the negative charges of glutamic acid and aspartic acid.
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Affiliation(s)
- K Kitadokoro
- Shionogi Research Laboratories, Shionogi and Co., Ltd., Osaka, Japan
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Kitadokoro K, Tsuzuki H, Nakamura E, Sato T, Teraoka H. Purification, characterization, primary structure, crystallization and preliminary crystallographic study of a serine proteinase from Streptomyces fradiae ATCC 14544. Eur J Biochem 1994; 220:55-61. [PMID: 8119298 DOI: 10.1111/j.1432-1033.1994.tb18598.x] [Citation(s) in RCA: 30] [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] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A proteinase having wide substrate specificity was isolated from Streptomyces fradiae ATCC 14544. This proteinase, which we propose to call SFase-2, was purified from the culture filtrate by S-Sepharose chromatography. The purified enzyme showed an apparent molecular mass of 19 kDa on SDS/PAGE. When synthetic peptides were used as substrates, SFase-2 showed broad substrate specificity. It also hydrolyzed keratin, elastin and collagen as proteinaceous substrates. It was completely inhibited by diisopropylfluorophosphate and chymostatin, but not by tosylphenylalaninechloromethane, tosyllysinechloromethane or EDTA, indicating that it can be classified as a serine proteinase. The matured protein sequence of SFase-2 was determined by a combination of amino acid sequencing and the DNA sequencing of the gene. SFase-2, consisting of 191 amino acids, is a novel proteinase. It showed 76% similarity in the amino acid sequence with Streptomyces griseus proteinase A [Johnson P. and Smillie L. B. (1974) FEBS Lett. 47, 1-6]. For insight into the three-dimensional structure of SFase-2, we obtained single crystals by the vapor diffusion method using sodium phosphate as a precipitant. These crystals belonged to the orthorhombic, space group P2(1)2(1)2(1) with cell dimensions a = 6.92 nm, b = 7.28 nm, c = 2.99 nm; one molecule was present in the asymmetric unit.
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Yasui K, Kawada K, Kagawa K, Tokura K, Kitadokoro K, Ikenishi Y. Synthesis of manool-related labdane diterpenes as platelet aggregation inhibitors. Chem Pharm Bull (Tokyo) 1993; 41:1698-707. [PMID: 8281569 DOI: 10.1248/cpb.41.1698] [Citation(s) in RCA: 17] [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: 01/29/2023]
Abstract
Enantioselective total synthesis of the labdane diterpene (-)-1, was achieved starting from the R-(-)-enantiomer of the Wieland-Miescher ketone. The enantiomer (+)-1 was obtained by partial synthesis via microbial transformation of sclareol. These results established that the natural compound (+)-1, a platelet aggregation inhibitor, has a normal absolute stereochemistry like that of manool. The B-norlabdane-related compound 44 was also synthesized using a novel ring contraction reaction.
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Affiliation(s)
- K Yasui
- Shionogi Research Laboratories, Shionogi & Co., Ltd., Osaka, Japan
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Kitadokoro K, Nakamura E, Tamaki M, Horii T, Okamoto H, Shin M, Sato T, Fujiwara T, Tsuzuki H, Yoshida N. Purification, characterization and molecular cloning of an acidic amino acid-specific proteinase from Streptomyces fradiae ATCC 14544. Biochim Biophys Acta 1993; 1163:149-57. [PMID: 8490047 DOI: 10.1016/0167-4838(93)90176-r] [Citation(s) in RCA: 29] [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] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have isolated a novel acidic amino-acid-specific proteinase from Streptomyces fradiae ATCC 14544, using benzyloxycarbonyl-L-Phe-L-Leu-L-Glu-p-nitroanilide (Z-Phe-Leu-Glu-pNA) as a substrate. A proteinase, which we propose to call SFase, was purified from the culture filtrate by salting out, repeated S-Sepharose chromatography, and affinity chromatography (CH-Sepharose-Phe-Leu-D-Glu-OMe). The purified enzyme showed a single band having an apparent molecular weight of 19,000 on sodium dodecyl sulfate polyacrylamide gel electrophoresis. When synthetic peptides were used as substrates, SFase showed high specificity for Z-Phe-Leu-Glu-pNA. Comparison with nitroanilides of glutamic acid and aspartic acid as substrates revealed that the reactivity was about 10-fold higher for a glutamyl bond than an aspartyl bond. SFase selectively hydrolyzed the -Glu-Ala-bond of two glutamyl bonds in the oxidized insulin B-chain within the initial reaction time until the starting material was completely digested. Diisopropylfluorophosphate and benzyloxycarbonyl-Phe-Leu-Glu chloromethylketone completely inhibited SFase, while metalloproteinase inhibitors, such as EDTA and o-phenanthrolin, did not inhibit the enzyme. The findings indicate that SFase can be classified as a serine proteinase, and is highly specific for a glutamyl bond in comparison with an aspartyl bond. To elucidate the complete primary structure and precursor of SFase, its gene was cloned from genomic DNA of the producing strain, and the nucleotide sequence was determined. Consideration of the N- and C-terminal amino-acid sequences of the mature protein of SFase indicates that it consists of 187 amino acids, which follows a prepropeptide of 170 residues. In comparison with the acidic amino-acid-specific proteinase from Streptomyces griseus (Svendsen, I., Jensen, M.R. and Breddam, K. (1991) FEBS Lett. 292, 165-167), SFase had 82% homology in the amino acid sequence. The processing site for maturation of SFase was a unique sequence (-Glu-Val-), so that the propeptide could be released by cleavage of the peptide bond between Glu and Val.
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Affiliation(s)
- K Kitadokoro
- Shionogi Research Laboratories, Shionogi and Co., Ltd., Osaka, Japan
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Kakudo S, Kikuchi N, Kitadokoro K, Fujiwara T, Nakamura E, Okamoto H, Shin M, Tamaki M, Teraoka H, Tsuzuki H. Purification, characterization, cloning, and expression of a glutamic acid-specific protease from Bacillus licheniformis ATCC 14580. J Biol Chem 1992; 267:23782-8. [PMID: 1429718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A glutamic acid-specific protease has been purified to homogeneity from Bacillus licheniformis ATCC 14580 utilizing Phe-Leu-D-Glu-OMe-Sepharose affinity chromatography and crystallized. The molecular weight of the protease was estimated to be approximately 25,000 by SDS-polyacrylamide gel electrophoresis. This protease, which we propose to call BLase (glutamic acid-specific protease from B. licheniformis ATCC 14580), was characterized enzymatically. Using human parathyroid hormone (13-34) and p-nitroanilides of peptidyl glutamic acid and aspartic acid, we found a marked difference between BLase and V8 protease, EC 3.4.21.9, although both proteases showed higher reactivity for glutamyl bonds than for aspartyl bonds. Diisopropyl fluorophosphate and benzyloxycarbonyl Leu-Glu chloromethyl ketone completely inhibited BLase, whereas EDTA reversibly inactivated the enzyme. The findings clearly indicate that BLase can be classified as a serine protease. To elucidate the complete primary structure and precursor of BLase, its gene was cloned from the genomic DNA of B. licheniformis ATCC 14580, and the nucleotide sequence was determined. Taking the amino-terminal amino acid sequence of the purified BLase into consideration, the clones encode a mature peptide of 222 amino acids, which follows a prepropeptide of 94 residues. The recombinant BLase was expressed in Bacillus subtilis and purified to homogeneity. Its key physical and chemical characteristics were the same as those of the wild-type enzyme. BLase was confirmed to be a protease specific for glutamic acid, and the primary structure deduced from the cDNA sequence was found to be identical with that of a glutamic acid-specific endopeptidase isolated from Alcalase (Svendsen, I., and Breddam, K. (1992) Eur. J. Biochem. 204, 165-171), being different from V8 protease and the Glu-specific protease of Streptomyces griseus which consist of 268 and 188 amino acids, respectively.
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Affiliation(s)
- S Kakudo
- Shionogi Research Laboratories, Shionogi and Co., Ltd., Osaka, Japan
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Abstract
A neutral protease, i.e., a zinc-containing metalloendoprotease from Streptomyces caespitosus, has been crystallized using acetone as a precipitating agent. The crystals diffract to better than 1.5 A resolution when a rotating anode X-ray generator is used as an X-ray source. Protein phase angles were calculated by the multiple isomorphous replacement method using two heavy-atom derivatives (HgCl2 and CH3HgCl). A 6 A resolution electron density map clearly showed molecular boundaries. Although its amino acid sequence is not known, the folding pattern of the polypeptide chain could be traced on a 2.5 A resolution electron density map. A large cleft, which is located on the molecular surface, was proved to be the active site of the enzyme by structure analyses of inhibitor-complex crystals. The highest electron density peak, which corresponds to the cleft, was assigned to a catalytically essential zinc atom on difference Fourier synthesis between native and EDTA-soaked crystals.
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Affiliation(s)
- S Harada
- Department of Applied Chemistry, Faculty of Engineering, Osaka University
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Abstract
Lysozyme from Streptomyces globisporus has been crystallized in a form suitable for X-ray structure analysis using ammonium sulfate as a precipitant. The crystals are hexagonal, space group P6(1)22 (P6(5)22) with unit cell dimensions: a = b = 129 A, c = 143 A. There are three or four molecules per asymmetric unit. The crystals diffract X-rays to at least 3.0 A resolution.
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Affiliation(s)
- S Harada
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Japan
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