1
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Mori K, Golding BT, Toraya T. The action of coenzyme B12-dependent diol dehydratase on 3,3,3-trifluoro-1,2-propanediol results in elimination of all the fluorides with formation of acetaldehyde. J Biochem 2024; 176:245-254. [PMID: 38987935 DOI: 10.1093/jb/mvae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
3,3,3-Trifluoro-1,2-propanediol undergoes complete defluorination in two distinct steps: first, the conversion into 3,3,3-trifluoropropionaldehyde catalyzed by adenosylcobalamin (coenzyme B12)-dependent diol dehydratase; second, non-enzymatic elimination of all three fluorides from this aldehyde to afford malonic semialdehyde (3-oxopropanoic acid), which is decarboxylated to acetaldehyde. Diol dehydratase accepts 3,3,3-trifluoro-1,2-propanediol as a relatively poor substrate, albeit without significant mechanism-based inactivation of the enzyme during catalysis. Optical and electron paramagnetic resonance (EPR) spectra revealed the steady-state formation of cob(II)alamin and a substrate-derived intermediate organic radical (3,3,3-trifluoro-1,2-dihydroxyprop-1-yl). The coenzyme undergoes Co-C bond homolysis initiating a sequence of reaction by the generally accepted pathway via intermediate radicals. However, the greater steric size of trifluoromethyl and especially its negative impact on the stability of an adjacent radical centre compared to a methyl group has implications for the mechanism of the diol dehydratase reaction. Nevertheless, 3,3,3-trifluoropropionaldehyde is formed by the normal diol dehydratase pathway, but then undergoes non-enzymatic conversion into acetaldehyde, probably via 3,3-difluoropropenal and malonic semialdehyde.
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Affiliation(s)
- Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Bernard T Golding
- School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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2
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Lin Z, Xiao Y, Zhang L, Li L, Dong C, Ma J, Liu GQ. Biochemical and molecular characterization of a novel glycerol dehydratase from Klebsiella pneumoniae 2e with high tolerance against crude glycerol impurities. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:175. [PMID: 37974275 PMCID: PMC10655381 DOI: 10.1186/s13068-023-02427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The direct bioconversion of crude glycerol, a byproduct of biodiesel production, into 1,3-propanediol by microbial fermentation constitutes a remarkably promising value-added applications. However, the low activity of glycerol dehydratase, which is the key and rate-limiting enzyme in the 1,3-propanediol synthetic pathway, caused by crude glycerol impurities is one of the main factors affecting the 1,3-propanediol yield. Hence, the exploration of glycerol dehydratase resources suitable for crude glycerol bioconversion is required for the development of 1,3-propanediol-producing engineered strains. RESULTS In this study, the novel glycerol dehydratase 2eGDHt, which has a tolerance against crude glycerol impurities from Klebsiella pneumoniae 2e, was characterized. The 2eGDHt exhibited the highest activity toward glycerol, with Km and Vm values of 3.42 mM and 58.15 nkat mg-1, respectively. The optimum pH and temperature for 2eGDHt were 7.0 and 37 °C, respectively. 2eGDHt displayed broader pH stability than other reported glycerol dehydratases. Its enzymatic activity was increased by Fe2+ and Tween-20, with 294% and 290% relative activities, respectively. The presence of various concentrations of the crude glycerol impurities, including NaCl, methanol, oleic acid, and linoleic acid, showed limited impact on the 2eGDHt activity. In addition, the enzyme activity was almost unaffected by the presence of an impurity mixture that mimicked the crude glycerol environment. Structural analyses revealed that 2eGDHt possesses more coil structures than reported glycerol dehydratases. Moreover, molecular dynamics simulations and site-directed mutagenesis analyses implied that the existence of unique Val744 from one of the increased coil regions played a key role in the tolerance characteristic by increasing the protein flexibility. CONCLUSIONS This study provides insight into the mechanism for enzymatic action and the tolerance against crude glycerol impurities, of a novel glycerol dehydratase 2eGDHt, which is a promising glycerol dehydratase candidate for biotechnological conversion of crude glycerol into 1,3-PDO.
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Affiliation(s)
- Zifeng Lin
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China
| | - Yuting Xiao
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China
| | - Lu Zhang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China
| | - Le Li
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China
| | - Congying Dong
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China
| | - Jiangshan Ma
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China.
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China.
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China.
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China.
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China.
- Microbial Variety Creation Center, Yuelushan National Laboratory of Seed Industry, Changsha, 410004, China.
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3
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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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4
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Cooper CL, Panitz N, Edwards TA, Goyal P. Role of the CarH photoreceptor protein environment in the modulation of cobalamin photochemistry. Biophys J 2021; 120:3688-3696. [PMID: 34310939 DOI: 10.1016/j.bpj.2021.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/17/2021] [Accepted: 07/20/2021] [Indexed: 11/19/2022] Open
Abstract
The photochemistry of cobalamins has recently been found to have biological importance, with the discovery of bacterial photoreceptor proteins, such as CarH and AerR. CarH and AerR, are involved in the light regulation of carotenoid biosynthesis and bacteriochlorophyll biosynthesis, respectively, in bacteria. Experimental transient absorption spectroscopic studies have indicated unusual photochemical behavior of 5'-deoxy-5'-adenosylcobalamin (AdoCbl) in CarH, with excited-state charge separation between cobalt and adenosyl and possible heterolytic cleavage of the Co-adenosyl bond, as opposed to the homolytic cleavage observed in aqueous solution and in many AdoCbl-based enzymes. We employ molecular dynamics and hybrid quantum mechanical/molecular mechanical calculations to obtain a microscopic understanding of the modulation of the excited electronic states of AdoCbl by the CarH protein environment, in contrast to aqueous solution and AdoCbl-based enzymes. Our results indicate a progressive stabilization of the electronic states involving charge transfer (CT) from cobalt/corrin to adenine on changing the environment from gas phase to water to solvated CarH. The solvent exposure of the adenosyl ligand in CarH, the π-stacking interaction between a tryptophan and the adenine moiety, and the hydrogen-bonding interaction between a glutamate and the lower axial ligand of cobalt are found to contribute to the stabilization of the states involving CT to adenine. The combination of these three factors, the latter two of which can be experimentally tested via mutagenesis studies, is absent in an aqueous solvent environment and in AdoCbl-based enzymes. The favored CT from metal and/or corrin to adenine in CarH may promote heterolytic cleavage of the cobalt-adenosyl bond proposed by experimental studies. Overall, this work provides novel, to our knowledge, physical insights into the mechanism of CarH function and directions for future experimental investigations. The fundamental understanding of the mechanism of CarH functioning will serve the development of optogenetic tools based on the new class of B12-dependent photoreceptors.
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Affiliation(s)
- Courtney L Cooper
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York
| | - Naftali Panitz
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York
| | - Travyse A Edwards
- Department of Physics, State University of New York at Binghamton, Binghamton, New York
| | - Puja Goyal
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York.
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5
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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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6
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Buckel W. Enzymatic Reactions Involving Ketyls: From a Chemical Curiosity to a General Biochemical Mechanism. Biochemistry 2019; 58:5221-5233. [PMID: 30995029 DOI: 10.1021/acs.biochem.9b00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ketyls are radical anions with nucleophilic properties. Ketyls obtained by enzymatic one-electron reduction of thioesters were proposed as intermediates for the dehydration of (R)-2-hydroxyacyl-CoA to (E)-2-enoyl-CoA. This concept was extended to the Birch-like reduction of benzoyl-CoA to 1,5-cyclohexadienecarboxyl-CoA. Nature uses two methods to achieve the therefore required low reduction potentials of less than -600 mV, either by an ATP-driven electron transfer similar to that catalyzed by the iron protein of nitrogenase or by electron bifurcation. Ketyls formed by thiyl radical-initiated oxidation of alcohols followed by deprotonation are involved in coenzyme B12-independent diol dehydratases, other glycyl radical enzymes mediating key reactions in the degradations of choline, taurine, and 4-hydroxyproline, and all three classes of ribonucleotide reductases. A special case is the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which most likely proceeds via an oxidation to an allylic ketyl but requires neither a strong reductant nor an external radical generator.
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Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany
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7
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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8
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Asatryan R, Pal Y, Hachmann J, Ruckenstein E. Roaming-like Mechanism for Dehydration of Diol Radicals. J Phys Chem A 2018; 122:9738-9754. [DOI: 10.1021/acs.jpca.8b08690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Yudhajit Pal
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- Computational and Data-Enabled Science and Engineering Graduate Program, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Johannes Hachmann
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- New York State Center of Excellence in Materials Informatics, Buffalo, New York 14203, United States
- Computational and Data-Enabled Science and Engineering Graduate Program, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Eli Ruckenstein
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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9
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Turck D, Bresson JL, Burlingame B, Dean T, Fairweather-Tait S, Heinonen M, Hirsch-Ernst KI, Mangelsdorf I, McArdle H, Neuhäuser-Berthold M, Nowicka G, Pentieva K, Sanz Y, Siani A, Sjödin A, Stern M, Tomé D, Van Loveren H, Vinceti M, Willatts P, Aggett P, Martin A, Przyrembel H, Brönstrup A, Ciok J, Gómez Ruiz JÁ, de Sesmaisons-Lecarré A, Naska A. Dietary reference values for potassium. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.4592] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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10
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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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11
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Johnson EE, Rehmann L. The role of 1,3-propanediol production in fermentation of glycerol by Clostridium pasteurianum. BIORESOURCE TECHNOLOGY 2016; 209:1-7. [PMID: 26946434 DOI: 10.1016/j.biortech.2016.02.088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Waste crude glycerol from biodiesel production can be used to produce biobutanol using Clostridium pasteurianum with the main products being n-butanol, 1,3-propanediol (PDO) and ethanol. There has been much discrepancy and mystery around the cause and effect of process parameters on the product distribution, thus a better understanding of the pathway regulation is required. This study shows that as process pH decreased, the rate of cell growth and CO2 production also decreased, resulting in slower fermentations, increased duration of butanol production and higher butanol concentrations and yields. The production rate of PDO was multi-modal and the role of PDO appears to function in redox homeostasis. The results also showed that C. pasteurianum displayed little biphasic behavior when compared to Clostridia spp. typically used in ABE fermentation due to the alternative glycolysis-independent reductive pathway of PDO production, rendering it suitable for a continuous fermentation process.
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Affiliation(s)
- Erin E Johnson
- Department of Chemical & Biochemical Engineering, The University of Western Ontario, 1151 Richmond St., London, Ontario N6A 3K7, Canada
| | - Lars Rehmann
- Department of Chemical & Biochemical Engineering, The University of Western Ontario, 1151 Richmond St., London, Ontario N6A 3K7, Canada; Department of Biochemical Engineering, AVT - Aachener Verfahrenstechnik, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany.
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12
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Wheatley RW, Juers DH, Lev BB, Huber RE, Noskov SY. Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model. Phys Chem Chem Phys 2016; 17:10899-909. [PMID: 25820412 DOI: 10.1039/c4cp04952g] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many enzymes require a specific monovalent cation (M(+)), that is either Na(+) or K(+), for optimal activity. While high selectivity M(+) sites in transport proteins have been extensively studied, enzyme M(+) binding sites generally have lower selectivity and are less characterized. Here we study the M(+) binding site of the model enzyme E. coli β-galactosidase, which is about 10 fold selective for Na(+) over K(+). Combining data from X-ray crystallography and computational models, we find the electrostatic environment predominates in defining the Na(+) selectivity. In this lower selectivity site rather subtle influences on the electrostatic environment become significant, including the induced polarization effects of the M(+) on the coordinating ligands and the effect of second coordination shell residues on the charge distribution of the primary ligands. This work expands the knowledge of ion selectivity in proteins to denote novel mechanisms important for the selectivity of M(+) sites in enzymes.
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Affiliation(s)
- Robert W Wheatley
- Division of Biochemistry, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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13
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - 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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15
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Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
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16
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Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev 2014. [PMID: 25184561 DOI: 10.1128/mmbr.00009–14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
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Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sharmistha Sinha
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sunny Chun
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Todd O Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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17
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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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18
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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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19
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Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nat Chem Biol 2014; 10:106-12. [PMID: 24362703 PMCID: PMC3939041 DOI: 10.1038/nchembio.1426] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/21/2013] [Indexed: 01/07/2023]
Abstract
7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg(2+)-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5'-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg(2+), which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified (β6/α3) protein core and an expanded cluster-binding motif, CX14CX2C.
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20
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Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus. J Bacteriol 2013; 195:1689-96. [PMID: 23378508 DOI: 10.1128/jb.02185-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Glutamate is usually synthesized from acetyl coenzyme A (acetyl-CoA) via citrate, isocitrate, and 2-oxoglutarate. Genome analysis revealed that in Syntrophus aciditrophicus, the gene for Si-citrate synthase is lacking. An alternative pathway starting from the catabolic intermediate glutaconyl-CoA via 2-hydroxyglutarate could be excluded by genomic analysis. On the other hand, a putative gene (SYN_02536; NCBI gene accession no. CP000252.1) annotated as coding for isopropylmalate/citramalate/homocitrate synthase has been shown to share 49% deduced amino acid sequence identity with the gene encoding Re-citrate synthase of Clostridium kluyveri. We cloned and overexpressed this gene in Escherichia coli together with the genes encoding the chaperone GroEL. The recombinant homotetrameric enzyme with a C-terminal Strep-tag (4 × 72,892 Da) was separated from GroEL on a Strep-Tactin column by incubation with ATP, K(+), and Mg(2+). The pure Re-citrate synthase used only acetyl-CoA and oxaloacetate as the substrates. As isolated, the enzyme contained stoichiometric amounts of Ca(2+) (0.9 Ca/73 kDa) but achieved higher specific activities in the presence of Mn(2+) (1.2 U/mg) or Co(2+) (2.0 U/mg). To determine the stereospecificity of the enzyme, [(14)C]citrate was enzymatically synthesized from oxaloacetate and [1-(14)C]acetyl-CoA; the subsequent cleavage by Si-citrate lyase yielded unlabeled acetate and labeled oxaloacetate, demonstrating that the enzyme is a Re-citrate synthase. The production of Re-citrate synthase by S. aciditrophicus grown axenically on crotonate was revealed by synthesis of [(14)C]citrate in a cell extract followed by stereochemical analysis. This result was supported by detection of transcripts of the Re-citrate synthase gene in axenic as well as in syntrophic cultures using quantitative reverse transcriptase PCR (qRT-PCR).
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21
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A novel cell modification method used in biotransformation of glycerol to 3-HPA by Lactobacillus reuteri. Appl Microbiol Biotechnol 2013; 97:4325-32. [PMID: 23359000 DOI: 10.1007/s00253-013-4723-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/12/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
The aim of the present study was to develop a new cell modification method to facilitate the cell separation from broth. In order to reduce the transfer limitation of substrate and product caused by general immobilization methods in the following biotransformation of glycerol, the carboxyl-functioned superparamagnetic nanoparticle (MNP) was directly attached to the surface of Lactobacillus reuteri for 3-hydroxypropionealdehyde producing. The modification process could be finished in several minutes by just adding MNP fluid into the bulk fermentation broth. The modified cells could be rapidly separated from the solution with the aid of magnetic field. The interaction between cell and MNP was shown by electron microscopy. The efficiency of the cells attached by MNPs for transformation of various concentrations of glycerol (100-400 mM) was studied at various temperatures (25-40 °C) and pH levels (5.8-7.5) with different cell concentrations (7.5-30 g/L). The 3- hydroxypropionealdehyde (HPA)/glycerol molar conversion under optimal condition (30 °C and pH 7) reached 70 %. The inactive modified cell could be reactivated easily by fresh medium and recovered the ability of glycerol conversion. MNPS distributing on cell surface had little adverse effect on cell activity. The modification method simplified the two-step production of 3-HPA by resting L. reuteri. The method of MNPs attached to cell surface is totally different from the traditional immobilization method in which the cell is attached to or entrapped in big carrier. The results obtained in this study showed that carboxyl-functioned MNP could be directly used as cell modification particle and realized cell recycle with the aid of magnetic field in bioprocess.
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22
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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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23
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Doitomi K, Kamachi T, Toraya T, Yoshizawa K. Inactivation Mechanism of Glycerol Dehydration by Diol Dehydratase from Combined Quantum Mechanical/Molecular Mechanical Calculations. Biochemistry 2012; 51:9202-10. [DOI: 10.1021/bi300488u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuki Doitomi
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Tetsuo Toraya
- Graduate School of Natural Science
and Technology, Okayama University, Okayama
700-8530, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering
and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
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24
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Yoshizawa K. [Analysis of enzymatic reactions by quantum chemical calculations]. YAKUGAKU ZASSHI 2012; 132:863-71. [PMID: 22864343 DOI: 10.1248/yakushi.132.863] [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) is now extensively used as a research tool for the investigation of structure and reactivity of biological systems; however, its high computational demands still restrict the applicability of DFT to systems of a few tens up to one hundred atoms. A combined quantum mechanical/molecular mechanical (QM/MM) approach is applicable as an important method to study whole enzyme systems more than ten thousands atoms. We have investigated methane monooxygenase, dopamenie β-monooxygenase, tyrosinase, B12 dependent diol dehydratase, etc. using DFT and QM/MM calculations. In particular, we have done some computational mutation analyses about the amino acid residues at the active site of diol dehydratase. Our DFT and QM/MM calculations can correctly describe the structures and activation barriers of intermediates and transition states in the protein environment, and therefore, we successfully revealed the catalytic role of amino acid residues at the active site of diol dehydratase. Predicted relative activities of mutants are consistent with experimentally observed reaction rates. These results encourage us to apply QM/MM research to enzymatic reactions, functional analysis of active-site residues, and rational design of enzymes with new catalytic functions.
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Affiliation(s)
- Kazunari Yoshizawa
- Institute for Materials Chemistry and Engneering, Kyushu University, Fukuoka, Japan.
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25
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Adenosylcobalamin enzymes: theory and experiment begin to converge. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1154-64. [PMID: 22516318 DOI: 10.1016/j.bbapap.2012.03.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/04/2012] [Accepted: 03/27/2012] [Indexed: 11/21/2022]
Abstract
Adenosylcobalamin (coenzyme B(12)) serves as the cofactor for a group of enzymes that catalyze unusual rearrangement or elimination reactions. The role of the cofactor as the initiator of reactive free radicals needed for these reactions is well established. Less clear is how these enzymes activate the coenzyme towards homolysis and control the radicals once generated. The availability of high resolution X-ray structures combined with detailed kinetic and spectroscopic analyses have allowed several adenosylcobalamin enzymes to be computationally modeled in some detail. Computer simulations have generally obtained good agreement with experimental data and provided valuable insight into the mechanisms of these unusual reactions. Importantly, atomistic modeling of the enzymes has allowed the role of specific interactions between protein, substrate and coenzyme to be explored, leading to mechanistic predictions that can now be tested experimentally. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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26
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Yamanishi M, Kinoshita K, Fukuoka M, Saito T, Tanokuchi A, Ikeda Y, Obayashi H, Mori K, Shibata N, Tobimatsu T, Toraya T. Redesign of coenzyme B12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. FEBS J 2012; 279:793-804. [DOI: 10.1111/j.1742-4658.2012.08470.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Jiang D, Barata-Vallejo S, Golding BT, Ferreri C, Chatgilialoglu C. Revisiting the reaction of hydroxyl radicals with vicinal diols in water. Org Biomol Chem 2012; 10:1102-7. [DOI: 10.1039/c1ob06538f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Gruber K, Puffer B, Kräutler B. Vitamin B12-derivatives-enzyme cofactors and ligands of proteins and nucleic acids. Chem Soc Rev 2011; 40:4346-63. [PMID: 21687905 DOI: 10.1039/c1cs15118e] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
B(12)-cofactors play important roles in the metabolism of microorganisms, animals and humans. Microorganisms are the only natural sources of B(12)-derivatives, and the latter are "vitamins" for other B(12)-requiring organisms. Some B(12)-dependent enzymes catalyze complex isomerisation reactions, such as methylmalonyl-CoA mutase. They need coenzyme B(12), an organometallic B(12)-derivative, to induce enzymatic radical reactions. Another group of widely relevant enzymes catalyzes the transfer of methyl groups, such as methionine synthase, which uses methylcobalamin as cofactor. This tutorial review covers structure and reactivity of B(12)-derivatives and structural aspects of their interactions with proteins and nucleotides, which are crucial for the efficient catalysis by the important B(12)-dependent enzymes, and for achieving and regulating uptake and transport of B(12)-derivatives.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50/3, Graz, A-8010, Austria
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29
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Shibata N, Higuchi Y, Toraya T. How Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase Deals with Both Enantiomers of 2-Amino-1-propanol as Substrates: Structure-Based Rationalization,,. Biochemistry 2010; 50:591-8. [DOI: 10.1021/bi101696h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, 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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30
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Abstract
Vitamin B₁₂ is produced only by prokaryotes and utilized by animals as an essential micronutrient. Genetic complementation analysis of cell lines from patients indicated that at least eight gene products are involved in intracellular B₁₂ metabolism and utilization. We have investigated bacterial adenosylcobalamin-dependent enzymes and elucidated their structure-based fine mechanisms. They tend to undergo mechanism-based inactivation during catalysis, because they use highly reactive radicals for catalyzing chemically difficult reactions. We have discovered molecular chaperone-like reactivating factors for these enzymes that release a damaged cofactor forming apoenzyme. Methylcobalamin-dependent methionine synthase also undergoes inactivation, because it utilizes cob (I) alamin, a super nucleophile, for catalysis. Methionine synthase reductase is a reactivating partner for this enzyme. Recent studies suggested that activity-maintaining systems for B₁₂ enzymes are present in animal cells as well, and thus hints for designing therapeutic agents for B₁₂-related metabolic disorders might be obtained from the investigations of microbial B₁₂ metabolism.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.
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