7F1P
| Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form. | Descriptor: | L-methionine gamma-lyase | Authors: | Okawa, A, Handa, H, Yasuda, E, Murota, M, Kudo, D, Tamura, T, Shiba, T, Inagaki, K. | Deposit date: | 2021-06-09 | Release date: | 2022-04-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine. J.Biosci.Bioeng., 133, 2022
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7CIM
| Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with 3-methlythiopropylamine (geminal diamine form). | Descriptor: | L-methionine decarboxylase, [6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate | Authors: | Okawa, A, Shiba, T, Hayashi, M, Onoue, Y, Murota, M, Sato, D, Inagaki, J, Tamura, T, Harada, S, Inagaki, K. | Deposit date: | 2020-07-07 | Release date: | 2021-01-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis for substrate specificity of l-methionine decarboxylase. Protein Sci., 30, 2021
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6AJ6
| Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+ | Descriptor: | Isocitrate dehydrogenase [NADP], NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Wang, X, Inaoka, D.K, Shiba, T, Balogun, E.O, Ziebart, N, Allman, S, Watanabe, Y, Nozaki, T, Boshart, M, Bringaud, F, Harada, S, Kita, K. | Deposit date: | 2018-08-27 | Release date: | 2019-08-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) To Be Published
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6AJC
| Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and ca2+ | Descriptor: | CALCIUM ION, ISOCITRIC ACID, Isocitrate dehydrogenase [NADP], ... | Authors: | Wang, X, Inaoka, D.K, Shiba, T, Balogun, E.O, Ziebart, N, Allman, S, Watanabe, Y, Nozaki, T, Boshart, M, Bringaud, F, Harada, S, Kita, K. | Deposit date: | 2018-08-27 | Release date: | 2019-08-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) To Be Published
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6AJA
| Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADPH, alpha-ketoglutarate and ca2+ | Descriptor: | 2-OXOGLUTARIC ACID, CALCIUM ION, GLYCEROL, ... | Authors: | Wang, X, Inaoka, D.K, Shiba, T, Balogun, E.O, Ziebart, N, Allman, S, Watanabe, Y, Nozaki, T, Boshart, M, Bringaud, F, Harada, S, Kita, K. | Deposit date: | 2018-08-27 | Release date: | 2019-08-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) To Be Published
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6AJB
| Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+ | Descriptor: | 2-OXOGLUTARIC ACID, CALCIUM ION, Isocitrate dehydrogenase [NADP], ... | Authors: | Wang, X, Inaoka, D.K, Shiba, T, Balogun, E.O, Ziebart, N, Allman, S, Watanabe, Y, Nozaki, T, Boshart, M, Bringaud, F, Harada, S, Kita, K. | Deposit date: | 2018-08-27 | Release date: | 2019-08-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) To Be Published
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5ZFB
| Structure of human dihydroorotate dehydrogenase in complex with ascofuranone (open-form) | Descriptor: | 3-chloro-4,6-dihydroxy-5-[(2Z,6Z,8E)-11-hydroxy-3,7,11-trimethyl-10-oxododeca-2,6,8-trien-1-yl]-2-methylbenzaldehyde, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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2E6D
| Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate | Descriptor: | COBALT HEXAMMINE(III), Dihydroorotate dehydrogenase, FLAVIN MONONUCLEOTIDE, ... | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-12-26 | Release date: | 2008-01-15 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction Biochemistry, 47, 2008
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5ZF4
| Structure of human dihydroorotate dehydrogenase in complex with 275-10-COOMe | Descriptor: | ACETATE ION, Dihydroorotate dehydrogenase (quinone), mitochondrial, ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.66 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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5ZFA
| Structure of human dihydroorotate dehydrogenase in complex with 287-12-OCOiPr | Descriptor: | (2E,6E)-8-(3-chloro-5-formyl-2,6-dihydroxy-4-methylphenyl)-3,6-dimethylocta-2,6-dien-1-yl 2-methylpropanoate, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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5ZF8
| Structure of human dihydroorotate dehydrogenase in complex with 277-11-OAc | Descriptor: | (2S,3E,7E)-9-(3-chloro-5-formyl-2,6-dihydroxy-4-methylphenyl)-3,7-dimethylnona-3,7-dien-2-yl acetate, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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5ZF7
| Structure of human dihydroorotate dehydrogenase in complex with 277-9-OH | Descriptor: | 3-chloro-4,6-dihydroxy-5-[(2E,6E,8S)-8-hydroxy-3,7-dimethylnona-2,6-dien-1-yl]-2-methylbenzaldehyde, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.79 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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5AZI
| Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP | Descriptor: | 4-NITROPHENYL PHOSPHATE, GLYCEROL, Glycerol kinase | Authors: | Balogun, E.O, Inaoka, D.K, Shiba, T, Tokuoka, S.M, Tokumasu, F, Sakamoto, K, Michels, P.A.M, Harada, S, Kita, K. | Deposit date: | 2015-10-08 | Release date: | 2016-10-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity. Biochim Biophys Acta Gen Subj, 1861, 2017
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5ZF9
| Structure of human dihydroorotate dehydrogenase in complex with 280-12 | Descriptor: | 3-chloro-4,6-dihydroxy-2-methyl-5-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]benzaldehyde, ACETATE ION, Dihydroorotate dehydrogenase (quinone), ... | Authors: | Miyazaki, Y, Inaoka, K.D, Shiba, T, Saimoto, H, Amalia, E, Kido, Y, Sakai, C, Nakamura, M, Moore, L.A, Harada, S, Kita, K. | Deposit date: | 2018-03-02 | Release date: | 2018-09-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.77 Å) | Cite: | Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol, 9, 2018
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5AZJ
| Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge) | Descriptor: | 4-NITROPHENYL PHOSPHATE, GLYCEROL, Glycerol kinase | Authors: | Balogun, E.O, Inaoka, D.K, Shiba, T, Tokuoka, S.M, Tokumasu, F, Sakamoto, K, Michels, P.A.M, Harada, S, Kita, K. | Deposit date: | 2015-10-08 | Release date: | 2016-10-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.61 Å) | Cite: | Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity. Biochim Biophys Acta Gen Subj, 1861, 2017
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2DJL
| Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate | Descriptor: | COBALT HEXAMMINE(III), FLAVIN MONONUCLEOTIDE, GLYCEROL, ... | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-04-04 | Release date: | 2007-06-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.38 Å) | Cite: | Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate To be Published
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2DJX
| Crystal structure of native Trypanosoma cruzi dihydroorotate dehydrogenase | Descriptor: | COBALT HEXAMMINE(III), Dihydroorotate Dehydrogenase, FLAVIN MONONUCLEOTIDE | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-04-05 | Release date: | 2007-06-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | Crystal structure of native Trypanosoma cruzi dihydroorotate dehydrogenase To be Published
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2E6A
| Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with orotate | Descriptor: | COBALT HEXAMMINE(III), Dihydroorotate dehydrogenase, FLAVIN MONONUCLEOTIDE, ... | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-12-26 | Release date: | 2008-01-15 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.64 Å) | Cite: | Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with orotate To be Published
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2E6F
| Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with oxonate | Descriptor: | COBALT HEXAMMINE(III), Dihydroorotate dehydrogenase, FLAVIN MONONUCLEOTIDE, ... | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-12-26 | Release date: | 2008-01-15 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.26 Å) | Cite: | Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with oxonate To be Published
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2E68
| Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate | Descriptor: | (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID, COBALT HEXAMMINE(III), Dihydroorotate dehydrogenase, ... | Authors: | Inaoka, D.K, Shimizu, H, Sakamoto, K, Shiba, T, Kurisu, G, Nara, T, Aoki, T, Harada, S, Kita, K. | Deposit date: | 2006-12-26 | Release date: | 2008-01-15 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.38 Å) | Cite: | Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate To be Published
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2D7I
| Crystal structure of pp-GalNAc-T10 with UDP, GalNAc and Mn2+ | Descriptor: | 2-acetamido-2-deoxy-beta-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Kubota, T, Shiba, T, Sugioka, S, Kato, R, Wakatsuki, S, Narimatsu, H. | Deposit date: | 2005-11-21 | Release date: | 2006-11-07 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10) J.Mol.Biol., 359, 2006
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2D7R
| Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on lectin domain | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Kubota, T, Shiba, T, Sugioka, S, Kato, R, Wakatsuki, S, Narimatsu, H. | Deposit date: | 2005-11-25 | Release date: | 2006-11-07 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10) J.Mol.Biol., 359, 2006
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7E3N
| Crystal structure of Isocitrate dehydrogenase D252N mutant from Trypanosoma brucei in complexed with NADP+, alpha-ketoglutarate, and ca2+ | Descriptor: | CALCIUM ION, ISOCITRIC ACID, Isocitrate dehydrogenase [NADP], ... | Authors: | Arai, N, Shiba, T, Inaoka, D.K, Kita, K, Wang, X, Otani, M, Matsushiro, S, Kojima, C. | Deposit date: | 2021-02-09 | Release date: | 2022-02-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of Isocitrate dehydrogenase from Trypanosoma brucei. To Be Published
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3AGR
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2ZYZ
| Pyrobaculum aerophilum splicing endonuclease | Descriptor: | Putative uncharacterized protein PAE0789, tRNA-splicing endonuclease | Authors: | Yoshinari, S, Inaoka, D.K, Watanabe, Y, Shiba, T, Kurisu, G, Harada, S. | Deposit date: | 2009-01-30 | Release date: | 2009-06-23 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease Nucleic Acids Res., 37, 2009
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