1DIO
 
 | | DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA | | Descriptor: | COBALAMIN, POTASSIUM ION, PROTEIN (DIOL DEHYDRATASE), ... | | Authors: | Shibata, N, Masuda, J, Tobimatsu, T, Toraya, T, Suto, K, Morimoto, Y, Yasuoka, N. | | Deposit date: | 1999-01-27 | | Release date: | 2000-01-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Structure Fold.Des., 7, 1999
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1UC5
 | | Structure of diol dehydratase complexed with (R)-1,2-propanediol | | Descriptor: | AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ... | | Authors: | Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T. | | Deposit date: | 2003-04-08 | | Release date: | 2003-07-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.Biol.Chem., 278, 2003
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1EEX
 | | CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA | | Descriptor: | CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Shibata, N, Masuda, J, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-04 | | Release date: | 2001-02-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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1EGV
 | | CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. | | Descriptor: | CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Masuda, J, Shibata, N, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-17 | | Release date: | 2001-02-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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1EGM
 | | CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. | | Descriptor: | CYANOCOBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Masuda, J, Shibata, N, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-15 | | Release date: | 2000-09-20 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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1IWP
 | | Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae | | Descriptor: | COBALAMIN, Glycerol Dehydratase Alpha subunit, Glycerol Dehydratase Beta subunit, ... | | Authors: | Yamanishi, M, Yunoki, M, Tobimatsu, T, Toraya, T. | | Deposit date: | 2002-05-28 | | Release date: | 2002-10-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
Eur.J.Biochem., 269, 2002
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1UC4
 | | Structure of diol dehydratase complexed with (S)-1,2-propanediol | | Descriptor: | AMMONIUM ION, CYANOCOBALAMIN, POTASSIUM ION, ... | | Authors: | Shibata, N, Nakanishi, Y, Fukuoka, M, Yamanishi, M, Yasuoka, N, Toraya, T. | | Deposit date: | 2003-04-08 | | Release date: | 2003-07-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
J.BIOL.CHEM., 278, 2003
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1IWB
 | | Crystal structure of diol dehydratase | | Descriptor: | COBALAMIN, DIOL DEHYDRATASE alpha chain, DIOL DEHYDRATASE beta chain, ... | | Authors: | Shibata, N, Masuda, J, Morimoto, Y, Yasuoka, N, Toraya, T. | | Deposit date: | 2002-05-01 | | Release date: | 2003-05-01 | | Last modified: | 2023-05-31 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Biochemistry, 41, 2002
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2D0O
 | | Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+ | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, SULFATE ION, ... | | Authors: | Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T. | | Deposit date: | 2005-08-05 | | Release date: | 2006-02-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
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2D0P
 | | Structure of diol dehydratase-reactivating factor in nucleotide free form | | Descriptor: | CALCIUM ION, SULFATE ION, diol dehydratase-reactivating factor large subunit, ... | | Authors: | Shibata, N, Mori, K, Hieda, N, Higuchi, Y, Yamanishi, M, Toraya, T. | | Deposit date: | 2005-08-05 | | Release date: | 2006-02-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor
Structure, 13, 2005
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7XRL
 | | Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol | | Descriptor: | (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, CALCIUM ION, ... | | Authors: | Shibata, N, Toraya, T. | | Deposit date: | 2022-05-10 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
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7XRK
 | | Diol dehydratase complexed with AdoMeCbl | | Descriptor: | (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, CALCIUM ION, COBALAMIN, ... | | Authors: | Shibata, N, Toraya, T. | | Deposit date: | 2022-05-10 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
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7XRM
 | | Ethanolamine ammonia-lyase complexed with AdoMeCbl | | Descriptor: | (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ... | | Authors: | Shibata, N, Toraya, T. | | Deposit date: | 2022-05-10 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.13 Å) | | Cite: | Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
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7XRN
 | | Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate | | Descriptor: | (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol, AMMONIUM ION, COBALAMIN, ... | | Authors: | Shibata, N, Toraya, T. | | Deposit date: | 2022-05-10 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Chemistry, 28, 2022
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3AUJ
 | | Structure of diol dehydratase complexed with glycerol | | Descriptor: | CALCIUM ION, COBALAMIN, Diol dehydrase alpha subunit, ... | | Authors: | Yamanishi, M, Kinoshita, K, Fukuoka, M, Shibata, T, Tobimatsu, T, Toraya, T. | | Deposit date: | 2011-02-07 | | Release date: | 2012-02-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols
Febs J., 279, 2012
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5YRV
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5YSR
 | | Ethanolamine ammonia-lyase, AdoCbl/2-amino-1-propanol | | Descriptor: | 5'-DEOXYADENOSINE, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ... | | Authors: | Shibata, N. | | Deposit date: | 2017-11-14 | | Release date: | 2018-09-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
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5YRT
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5YSN
 | | Ethanolamine ammonia-lyase, AdoCbl/substrate-free | | Descriptor: | 5'-DEOXYADENOSINE, COBALAMIN, Ethanolamine ammonia-lyase heavy chain, ... | | Authors: | Shibata, N. | | Deposit date: | 2017-11-14 | | Release date: | 2018-09-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.001 Å) | | Cite: | Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Angew. Chem. Int. Ed. Engl., 57, 2018
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5YSH
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3ABQ
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3ABR
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3ABO
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3ABS
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3ANY
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