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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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2
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Bilić L, Barić D, Sandala GM, Smith DM, Kovačević B. Glycerol as a Substrate and Inactivator of Coenzyme B 12 -Dependent Diol Dehydratase. Chemistry 2021; 27:7930-7941. [PMID: 33792120 DOI: 10.1002/chem.202100416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Diol dehydratase, dependent on coenzyme B12 (B12 -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B12 -independent glycerol dehydratase (B12 -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B12 -dDDH and that of resistance of B12 -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B12 -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B12 -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.
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Affiliation(s)
- Luka Bilić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.,PULS Group, Institute for Theoretical Physics FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany
| | - Danijela Barić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Gregory M Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, New Brunswick, E4L 1G8, Sackville, Canada
| | - David Mathew Smith
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Borislav Kovačević
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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3
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Bilić L, Barić D, Banhatti RD, Smith DM, Kovačević B. Computational Study of Glycerol Binding within the Active Site of Coenzyme B12-Dependent Diol Dehydratase. J Phys Chem B 2019; 123:6178-6187. [DOI: 10.1021/acs.jpcb.9b04071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luka Bilić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Barić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - David M. Smith
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Borislav Kovačević
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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4
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Kovačević B, Barić D, Babić D, Bilić L, Hanževački M, Sandala GM, Radom L, Smith DM. Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12. J Am Chem Soc 2018; 140:8487-8496. [DOI: 10.1021/jacs.8b03109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Borislav Kovačević
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Danijela Barić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Darko Babić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Luka Bilić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marko Hanževački
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Gregory M. Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick E4L 1G8, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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5
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Dai L, Tao F, Tang H, Guo Y, Shen Y, Xu P. Directing enzyme devolution for biosynthesis of alkanols and 1,n-alkanediols from natural polyhydroxy compounds. Metab Eng 2017; 44:70-80. [DOI: 10.1016/j.ymben.2017.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/01/2022]
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6
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Doitomi K, Kamachi T, Toraya T, Yoshizawa K. Computational Mutation Study of the Roles of Catalytic Residues in Coenzyme B12-Dependent Diol Dehydratase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Mori K, Oiwa T, Kawaguchi S, Kondo K, Takahashi Y, Toraya T. Catalytic Roles of Substrate-Binding Residues in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. Biochemistry 2014; 53:2661-71. [DOI: 10.1021/bi500223k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Mori
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Toshihiro Oiwa
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Satoshi Kawaguchi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kyosuke Kondo
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Takahashi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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8
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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Arch Biochem Biophys 2014; 544:40-57. [DOI: 10.1016/j.abb.2013.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 01/12/2023]
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9
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Kothandaraman P, Koh BQ, Limpanuparb T, Hirao H, Chan PWH. 1-(2′-Anilinyl)prop-2-yn-1-ol Rearrangement for Oxindole Synthesis. Chemistry 2012. [DOI: 10.1002/chem.201202606] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Doitomi K, Kamachi T, Yoshizawa K. [Computational mutation analysis of enzymatic reaction]. YAKUGAKU ZASSHI 2012; 132:1297-305. [PMID: 23123722 DOI: 10.1248/yakushi.12-00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Density functional theory (DFT) calculations are established as a useful research tool to investigate the structures and reactivity of biological systems; however, their high computational costs still restrict their applicability to systems of several tens up to a few hundred atoms. Recently, a combined quantum mechanical/molecular mechanical (QM/MM) approach has become an important method to study enzymatic reactions. In the past several years, we have investigated B12-dependent diol dehydratase using QM/MM calculations. The enzyme catalyzes chemically difficult reactions by utilizing the high reactivity of free radicals. In this paper, we explain our QM/MM calculations for the structure and reactivity of diol dehydratase and report key findings with respect to the catalytic roles of the active-site amino acid residues, computational mutational analysis of the active-site amino acid residues, assignment of the central metal ion, and function of the central metal ion. Our QM/MM calculations can correctly describe the structures and activation barriers of intermediate and transition states in the protein environment. Moreover, predicted relative activities of mutants are consistent with experimentally observed reactivity. These results will encourage the application of QM/MM research to the mechanistic study of enzymatic reactions, functional analysis of active-site residues, and rational design of enzymes with new catalytic functions.
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Affiliation(s)
- Kazuki Doitomi
- Institute for Materials Chemistry and Engneering, Kyushu University, Fukuoka, Japan
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11
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Feliks M, Ullmann GM. Glycerol Dehydratation by the B12-Independent Enzyme May Not Involve the Migration of a Hydroxyl Group: A Computational Study. J Phys Chem B 2012; 116:7076-87. [DOI: 10.1021/jp301165b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikolaj Feliks
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
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12
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Toraya T, Honda S, Mori K. Coenzyme B12-Dependent Diol Dehydratase Is a Potassium Ion-Requiring Calcium Metalloenzyme: Evidence That the Substrate-Coordinated Metal Ion Is Calcium. Biochemistry 2010; 49:7210-7. [DOI: 10.1021/bi100561m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
- Department of Industrial Biochemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Susumu Honda
- Department of Industrial Biochemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koichi Mori
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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13
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Sandala GM, Smith DM, Radom L. Modeling the reactions catalyzed by coenzyme B12-dependent enzymes. Acc Chem Res 2010; 43:642-51. [PMID: 20136160 DOI: 10.1021/ar900260c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.
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Affiliation(s)
- Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - David M. Smith
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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14
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Fernández I, Cossío FP, Sierra MA. Dyotropic Reactions: Mechanisms and Synthetic Applications. Chem Rev 2009; 109:6687-711. [DOI: 10.1021/cr900209c] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Fernando P. Cossío
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
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15
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Tureček F, Yao C, Fung YME, Hayakawa S, Hashimoto M, Matsubara H. Histidine-Containing Radicals in the Gas Phase. J Phys Chem B 2009; 113:7347-66. [DOI: 10.1021/jp900719n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Chunxiang Yao
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Y. M. Eva Fung
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Shigeo Hayakawa
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Mami Hashimoto
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Hiroshi Matsubara
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington, 98195, and Department of Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
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Ogura KI, Kunita SI, Mori K, Tobimatsu T, Toraya T. Roles of adenine anchoring and ion pairing at the coenzyme B12-binding site in diol dehydratase catalysis. FEBS J 2008; 275:6204-16. [DOI: 10.1111/j.1742-4658.2008.06745.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Pierik AJ, Graf T, Pemberton L, Golding BT, Rétey J. But-3-ene-1,2-diol: A Mechanism-Based Active Site Inhibitor for Coenzyme B12-Dependent Glycerol Dehydratase. Chembiochem 2008; 9:2268-75. [DOI: 10.1002/cbic.200800213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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