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Yang CW, Hsu HY, Lee YZ, Lee SJ. Vitamin B12 inhibits peptidylarginine deiminases and ameliorates rheumatoid arthritis in CAIA mice. Biochem Biophys Res Commun 2024; 704:149668. [PMID: 38401303 DOI: 10.1016/j.bbrc.2024.149668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/26/2024]
Abstract
Rheumatoid arthritis is an autoimmune disease whose early onset correlates with dysregulated citrullination, a process catalyzed by peptidylarginine deiminase isoform 4 (PADI-4). Here, we report that PADI-4 is a novel target of vitamin B12, a water-soluble vitamin that serves as a cofactor in DNA synthesis and the metabolism of fatty and amino acids. Vitamin B12 preferentially inhibited PADI-4 over PADI-2 with comparable inhibitory activity to the reference compound Cl-amidine in enzymatic inhibition assays, and reduced total cellular citrullination levels including that of histone H3 citrullination mediated by PADI-4. We also demonstrated that hydroxocobalamin, a manufactured form of vitamin B12, significantly ameliorated the severity of collagen type II antibody induced arthritis (CAIA) in mice and diminished gene expression of the rheumatoid inflammatory factors and cytokines IL17A, TNFα, IL-6, COX-II and ANXA2, as well PADI-4. Therefore, the use of vitamin B12 to treat rheumatoid arthritis merits further study.
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Affiliation(s)
- Cheng-Wei Yang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Hsing-Yu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Yue-Zhi Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Shiow-Ju Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC.
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2
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Shibata N, Higuchi Y, Kräutler B, Toraya T. 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 2022; 28:e202202196. [PMID: 35974426 DOI: 10.1002/chem.202202196] [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: 07/13/2022] [Indexed: 11/11/2022]
Abstract
The X-ray structures of coenzyme B12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH2 group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Bernhard Kräutler
- Institute of Organic Chemistry and, Center of Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
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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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Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell. Biochim Biophys Acta Gen Subj 2020; 1864:129680. [DOI: 10.1016/j.bbagen.2020.129680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
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5
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Bridwell-Rabb J, Grell TAJ, Drennan CL. A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited. Annu Rev Biochem 2019; 87:555-584. [PMID: 29925255 DOI: 10.1146/annurev-biochem-062917-012500] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.
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Affiliation(s)
- Jennifer Bridwell-Rabb
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Present address: Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tsehai A J Grell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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6
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018; 57:7830-7835. [DOI: 10.1002/anie.201803591] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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8
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Wick CR, Smith DM. Modeling the Reactions Catalyzed by Coenzyme B 12 Dependent Enzymes: Accuracy and Cost-Quality Balance. J Phys Chem A 2018; 122:1747-1755. [PMID: 29389127 DOI: 10.1021/acs.jpca.7b11798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reactions catalyzed by coenzyme B12 dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B12 system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B12 reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.
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Affiliation(s)
- Christian R Wick
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - David M Smith
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia.,Center for Computational Chemistry, FAU Erlangen-Nürnberg , Nägelsbachstrasse 25, 91052 Erlangen, Germany
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9
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A B 12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature 2017; 544:322-326. [PMID: 28346939 PMCID: PMC5398914 DOI: 10.1038/nature21689] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/03/2017] [Indexed: 11/22/2022]
Abstract
Oxetanocin-A (OXT-A, 1) is a potent antitumor, antiviral, and
antibacterial compound. Biosynthesis of OXT-A has been linked to a
plasmid-borne, Bacillus megaterium gene cluster that contains
four genes, oxsA, oxsB, oxrA,
and oxrB. Here, we show that the oxsA and
oxsB genes are both required for the production of OXT-A.
Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent
S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an
HD-domain phosphohydrolase, OxsA, revealed that OXT-A is derived from
2′-deoxyadenosine phosphate in an OxsB-catalyzed ring contraction
reaction initiated by H-atom abstraction from C2′. Hence, OxsB
represents the first biochemically characterized non-methylating Cbl-dependent
AdoMet radical enzyme. X-ray analysis of OxsB reveals the fold of a
Cbl-dependent AdoMet radical enzyme for which there are an estimated 7000
members. Overall, this work provides a framework for understanding the interplay
of AdoMet and Cbl cofactors and expands the catalytic repertoire of
Cbl-dependent AdoMet radical enzymes.
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Wang J, Jain R, Shen X, Sun X, Cheng M, Liao JC, Yuan Q, Yan Y. Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose. Metab Eng 2017; 40:148-156. [DOI: 10.1016/j.ymben.2017.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/29/2022]
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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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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13
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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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Siebert D, Wendisch VF. Metabolic pathway engineering for production of 1,2-propanediol and 1-propanol by Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:91. [PMID: 26110019 PMCID: PMC4478622 DOI: 10.1186/s13068-015-0269-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/05/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Production of the versatile bulk chemical 1,2-propanediol and the potential biofuel 1-propanol is still dependent on petroleum, but some approaches to establish bio-based production from renewable feed stocks and to avoid toxic intermediates have been described. The biotechnological workhorse Corynebacterium glutamicum has also been shown to be able to overproduce 1,2-propanediol by metabolic engineering. Additionally, C. glutamicum has previously been engineered for production of the biofuels ethanol and isobutanol but not for 1-propanol. RESULTS In this study, the improved production of 1,2-propanediol by C. glutamicum is presented. The product yield of a C. glutamicum strain expressing the heterologous genes gldA and mgsA from Escherichia coli that encode methylglyoxal synthase gene and glycerol dehydrogenase, respectively, was improved by additional expression of alcohol dehydrogenase gene yqhD from E. coli leading to a yield of 0.131 mol/mol glucose. Deletion of the endogenous genes hdpA and ldh encoding dihydroxyacetone phosphate phosphatase and lactate dehydrogenase, respectively, prevented formation of glycerol and lactate as by-products and improved the yield to 0.343 mol/mol glucose. To construct a 1-propanol producer, the operon ppdABC from Klebsiella oxytoca encoding diol dehydratase was expressed in the improved 1,2-propanediol producing strain ending up with 12 mM 1-propanol and up to 60 mM unconverted 1,2-propanediol. Thus, B12-dependent diol dehydratase activity may be limiting 1-propanol production. CONCLUSIONS Production of 1,2-propanediol by C. glutamicum was improved by metabolic engineering targeting endogenous enzymes. Furthermore, to the best of our knowledge, production of 1-propanol by recombinant C. glutamicum was demonstrated for the first time.
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Affiliation(s)
- Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Volker F. Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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15
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Jain R, Sun X, Yuan Q, Yan Y. Systematically engineering Escherichia coli for enhanced production of 1,2-propanediol and 1-propanol. ACS Synth Biol 2015; 4:746-56. [PMID: 25490349 DOI: 10.1021/sb500345t] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The biological production of high value commodity 1,2-propanediol has been established by engineering the glycolysis pathway. However, the simultaneous achievement of high titer and high yield has not been reported yet, as all efforts in increasing the titer have resulted in low yields. In this work, we overcome this limitation by employing an optimal minimal set of enzymes, channeling the carbon flux into the 1,2-propanediol pathway, increasing NADH availability, and improving the anaerobic growth of the engineered Escherichia coli strain by developing a cell adaptation method. These efforts lead to 1,2-propanediol production at a titer of 5.13 g/L with a yield of 0.48 g/g glucose in 20 mL shake flask studies. On this basis, we pursue the enhancement of 1-propanol production from the 1,2-propanediol platform. By constructing a fusion diol dehydratase and developing a dual strain process, we achieve a 1-propanol titer of 2.91 g/L in 20 mL shake flask studies. To summarize, we report the production of 1,2-propanediol at enhanced titer and enhanced yield simultaneously in E. coli for the first time. Furthermore, we establish an efficient system for the production of biofuel 1-propanol biologically.
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Affiliation(s)
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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16
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Menon BRK, Menon N, Fisher K, Rigby SEJ, Leys D, Scrutton NS. Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. FEBS J 2015; 282:1242-55. [PMID: 25627283 PMCID: PMC4413051 DOI: 10.1111/febs.13215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B12 potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.
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Affiliation(s)
- Binuraj R K Menon
- Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, UK
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17
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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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18
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Kumar V, Ashok S, Park S. Recent advances in biological production of 3-hydroxypropionic acid. Biotechnol Adv 2013; 31:945-61. [DOI: 10.1016/j.biotechadv.2013.02.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/13/2013] [Accepted: 02/24/2013] [Indexed: 11/16/2022]
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19
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Chen ZG, Ziętek MA, Russell HJ, Tait S, Hay S, Jones AR, Scrutton NS. Dynamic, electrostatic model for the generation and control of high-energy radical intermediates by a coenzyme B₁₂-dependent enzyme. Chembiochem 2013; 14:1529-33. [PMID: 23959797 PMCID: PMC4155860 DOI: 10.1002/cbic.201300420] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Zhi-Gang Chen
- College of Food and Science Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095 (P.R. China)
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20
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Jones AR, Levy C, Hay S, Scrutton NS. Relating localized protein motions to the reaction coordinate in coenzyme B12-dependent enzymes. FEBS J 2013; 280:2997-3008. [DOI: 10.1111/febs.12223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 01/27/2023]
Affiliation(s)
| | - Colin Levy
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
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21
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Makins C, Pickering AV, Mariani C, Wolthers KR. Mutagenesis of a conserved glutamate reveals the contribution of electrostatic energy to adenosylcobalamin co-C bond homolysis in ornithine 4,5-aminomutase and methylmalonyl-CoA mutase. Biochemistry 2013; 52:878-88. [PMID: 23311430 DOI: 10.1021/bi3012719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of substrate to ornithine 4,5-aminomutase (OAM) and methylmalonyl-CoA mutase (MCM) leads to the formation of an electrostatic interaction between a conserved glutamate side chain and the adenosyl ribose of the adenosylcobalamin (AdoCbl) cofactor. The contribution of this residue (Glu338 in OAM from Clostridium sticklandii and Glu392 in human MCM) to AdoCbl Co-C bond labilization and catalysis was evaluated by substituting the residue with a glutamine, aspartate, or alanine. The OAM variants, E338Q, E338D, and E338A, showed 90-, 380-, and 670-fold reductions in catalytic turnover and 20-, 60-, and 220-fold reductions in k(cat)/K(m), respectively. Likewise, the MCM variants, E392Q, E392D, and E392A, showed 16-, 330-, and 12-fold reductions in k(cat), respectively. Binding of substrate to OAM is unaffected by the single-amino acid mutation as stopped-flow absorbance spectroscopy showed that the rates of external aldimine formation in the OAM variants were similar to that of the native enzyme. The decrease in the level of catalysis is instead linked to impaired Co-C bond rupture, as UV-visible spectroscopy did not show detectable AdoCbl homolysis upon binding of the physiological substrate, d-ornithine. AdoCbl homolysis was also not detected in the MCM mutants, as it was for the native enzyme. We conclude from these results that a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for Co-C bond homolysis, thereby pointing to a key role for the conserved polar glutamate residue in controlling the initial generation of radical species.
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Affiliation(s)
- Caitlyn Makins
- Department of Chemistry, University of British Columbia, 3333 University Way, Kelowna, BC, Canada
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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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Russell HJ, Jones AR, Hay S, Greetham GM, Towrie M, Scrutton NS. Protein Motions Are Coupled to the Reaction Chemistry in Coenzyme B 12-Dependent Ethanolamine Ammonia Lyase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Russell HJ, Jones AR, Hay S, Greetham GM, Towrie M, Scrutton NS. Protein Motions Are Coupled to the Reaction Chemistry in Coenzyme B12-Dependent Ethanolamine Ammonia Lyase. Angew Chem Int Ed Engl 2012; 51:9306-10. [DOI: 10.1002/anie.201202502] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/13/2012] [Indexed: 11/12/2022]
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26
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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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27
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Speranza G, Buckel W, Golding BT. CoenzymeB12-dependent enzymatic dehydration of 1,2-diols: simple reaction, complex mechanism! J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conversion of glycerol to acrolein is an undesirable event in whisky production, caused by infection of the broth with Klebsiella pneumoniae. This organism uses glycerol dehydratase to transform glycerol into 3-hydroxypropanal, which affords acrolein on distillation. The enzyme requires adenosylcobalamin (coenzyme B12) as cofactor and a monovalent cation (e.g. K+). Diol dehydratase is a similar enzyme that converts 1,2-diols ( C2- C4) including glycerol into an aldehyde and water. The subtle stereochemical features of these enzymes are exemplified by propane-1,2-diol: both enantiomers are substrates but different hydrogen and oxygen atoms are abstracted. The mechanism of action of the dehydratases has been elucidated by protein crystallography and ab initio molecular orbital calculations, aided by stereochemical and model studies. The 5'-deoxyadenosyl (adenosyl) radical from homolysis of the coenzyme's Co - C σ-bond abstracts a specific hydrogen atom from C -1 of diol substrate giving a substrate radical that rearranges to a product radical by 1,2-shift of hydroxyl from C -2 to C -1. The rearrangement mechanism involves an acid-base 'push-pull' in which migration of OH is facilitated by partial protonation by Hisα143, synergistically assisted by partial deprotonation of the non-migrating ( C -1) OH by the carboxylate of Gluα170. The active site K+ion holds the two hydroxyl groups in the correct conformation, whilst not significantly contributing to catalysis. Recently, diol dehydratases not dependent on coenzyme B12have been discovered. These enzymes utilize the same kind of diol radical chemistry as the coenzyme B12-dependent enzymes and they also use the adenosyl radical as initiator, but this is generated from S-adenosylmethionine.
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Affiliation(s)
- Giovanna Speranza
- Dipartimento di Chimica Organica e Industriale, Università di Milano, via Venezian 21, 20133 Milano, Italia
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, D-35032 Marburg, Germany
| | - Bernard T. Golding
- School of Natural Sciences - Chemistry, Bedson Building, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, United Kingdom
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28
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Jones AR, Hardman SJO, Hay S, Scrutton NS. Is There a Dynamic Protein Contribution to the Substrate Trigger in Coenzyme B12-Dependent Ethanolamine Ammonia Lyase? Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Jones AR, Hardman SJO, Hay S, Scrutton NS. Is there a dynamic protein contribution to the substrate trigger in coenzyme B12-dependent ethanolamine ammonia lyase? Angew Chem Int Ed Engl 2011; 50:10843-6. [PMID: 21948289 DOI: 10.1002/anie.201105132] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Alex R Jones
- Faculty of Life Sciences, Photon Science Institute and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
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30
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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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31
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Maervoet VET, De Mey M, Beauprez J, De Maeseneire S, Soetaert WK. Enhancing the Microbial Conversion of Glycerol to 1,3-Propanediol Using Metabolic Engineering. Org Process Res Dev 2010. [DOI: 10.1021/op1001929] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Veerle E. T. Maervoet
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Marjan De Mey
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Joeri Beauprez
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Sofie De Maeseneire
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Wim K. Soetaert
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
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32
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Larsson KM, Logan DT, Nordlund P. Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases. ACS Chem Biol 2010; 5:933-42. [PMID: 20672854 DOI: 10.1021/cb1000845] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.
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Affiliation(s)
- Karl-Magnus Larsson
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Pär Nordlund
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 77 Stockholm, Sweden
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33
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Shibata N, Tamagaki H, Hieda N, Akita K, Komori H, Shomura Y, Terawaki SI, Mori K, Yasuoka N, Higuchi Y, Toraya T. Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. J Biol Chem 2010; 285:26484-93. [PMID: 20519496 PMCID: PMC2924083 DOI: 10.1074/jbc.m110.125112] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/17/2010] [Indexed: 11/06/2022] Open
Abstract
N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase beta-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83-93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (alphabeta)(2) dimer. The active site is in the (beta/alpha)(8) barrel of the alpha-subunit; the beta-subunit covers the lower part of the cobalamin that is bound in the interface of the alpha- and beta-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Argalpha(160) contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co-C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Glualpha(287), one of the substrate-binding residues, has a direct contact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co-C bond.
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Affiliation(s)
- Naoki Shibata
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- the RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan, and
| | - Hiroko Tamagaki
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Naoki Hieda
- the Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
| | - Keita Akita
- the Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
| | - Hirofumi Komori
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yasuhito Shomura
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shin-ichi Terawaki
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Koichi Mori
- the Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
| | - Noritake Yasuoka
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- From the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- the RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan, and
| | - Tetsuo Toraya
- the Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
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34
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Kozlowski PM, Kamachi T, Kumar M, Nakayama T, Yoshizawa K. Theoretical Analysis of the Diradical Nature of Adenosylcobalamin Cofactor−Tyrosine Complex in B12-Dependent Mutases: Inspiring PCET-Driven Enzymatic Catalysis. J Phys Chem B 2010; 114:5928-39. [DOI: 10.1021/jp100573b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomonori Nakayama
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
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35
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Durbeej B, Sandala GM, Bucher D, Smith DM, Radom L. On the importance of ribose orientation in the substrate activation of the coenzyme B12-dependent mutases. Chemistry 2009; 15:8578-8585. [PMID: 19630017 DOI: 10.1002/chem.200901002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The degree to which the corrin ring portion of coenzyme B(12) can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B(12). In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3', are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol(-1) in the transition structure (TS) complex corresponding to orientation B (TS(B)CorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TS(B)CorIm appears to be the result of favorable interactions involving O3' and the corrin ring, including a C-HO hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co-C distance. Our calculations show that any potential stabilization afforded to the H-atom-abstraction step by coenzyme B(12) is sensitive to the orientation of the ribose moiety.
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Affiliation(s)
- Bo Durbeej
- 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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36
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Kamachi T, Takahata M, Toraya T, Yoshizawa K. What is the Identity of the Metal Ions in the Active Sites of Coenzyme B12-Dependent Diol Dehydratase? A Computational Mutation Analysis. J Phys Chem B 2009; 113:8435-8. [DOI: 10.1021/jp9001737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Masanori Takahata
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
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37
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Abstract
This chapter reviews the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyl transfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
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Affiliation(s)
- Rowena G Matthews
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor MI 48109-2216, USA
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38
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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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39
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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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40
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Kinoshita K, Kawata M, Ogura KI, Yamasaki A, Watanabe T, Komoto N, Hieda N, Yamanishi M, Tobimatsu T, Toraya T. Histidine-α143 Assists 1,2-Hydroxyl Group Migration and Protects Radical Intermediates in Coenzyme B12-Dependent Diol Dehydratase. Biochemistry 2008; 47:3162-73. [DOI: 10.1021/bi7018095] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Koichiro Kinoshita
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Masahiro Kawata
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Ken-ichi Ogura
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Ai Yamasaki
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Takeshi Watanabe
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Noriaki Komoto
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Naoki Hieda
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Mamoru Yamanishi
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
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41
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Kamachi T, Toraya T, Yoshizawa K. Computational Mutation Analysis of Hydrogen Abstraction and Radical Rearrangement Steps in the Catalysis of Coenzyme B12-Dependent Diol Dehydratase. Chemistry 2007; 13:7864-73. [PMID: 17614304 DOI: 10.1002/chem.200601466] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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42
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Schwartz PA, Frey PA. Dioldehydrase: an essential role for potassium ion in the homolytic cleavage of the cobalt-carbon bond in adenosylcobalamin. Biochemistry 2007; 46:7293-301. [PMID: 17516630 PMCID: PMC2516201 DOI: 10.1021/bi700078z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex of dioldehydrase with adenosylcobalamin (coenzyme B12) and potassium ion reacts with molecular oxygen in the absence of a substrate to oxidize coenzyme and inactivate the complex. In this article, high performance liquid chromatography and mass spectral analysis are used to identify the nucleoside products resulting from oxygen inactivation. The product profile indicates that oxygen inactivation proceeds by direct reaction of molecular oxygen with the 5'-deoxyadenosyl radical and cob(II)alamin. Formation of 5'-peroxyadenosine as the initial nucleoside product chemically correlates this reaction with aerobic, aqueous photoinduced homolytic cleavage of adenosylcobalamin (Schwartz, P. A., and Frey, P. A., (2007) Biochemistry, in press), indicating that both reactions proceed through similar chemical intermediates. The oxygen inactivation of the enzyme-coenzyme complex shows an absolute requirement for the same monocations required in catalysis by dioldehydrase. Measurements of the dissociation constants for adenosylcobalamin from potassium-free (Kd = 16 +/- 2 microM) or potassium-bound dioldehydrase (Kd = 0.8 +/- 0.2 microM) reveal that the effect of the monocation in stimulating oxygen sensitivity cannot be explained by an effect on the binding of coenzyme to the enzyme. Cross-linking experiments suggest that the full quaternary structure is assembled in the absence of potassium ion under the experimental conditions. The results indicate that dioldehydrase likely harvests the binding energy of the activating monocation to stimulate the homolytic cleavage of the Co-C5' bond in adenosylcobalamin.
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Affiliation(s)
- Phillip A Schwartz
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
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43
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Kozlowski PM, Andruniow T, Jarzecki AA, Zgierski MZ, Spiro TG. DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors. Inorg Chem 2007; 45:5585-90. [PMID: 16813422 PMCID: PMC2773831 DOI: 10.1021/ic052069j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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44
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Rovira C, Kozlowski PM. First Principles Study of Coenzyme B12. Crystal Packing Forces Effect on Axial Bond Lengths. J Phys Chem B 2007; 111:3251-7. [PMID: 17388442 DOI: 10.1021/jp0660029] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we analyze the structure of coenzyme B12 (AdoCbl) by means of periodic density functional theory (DFT) in order to elucidate the influence of the corrin side chains and the crystalline environment on the properties of axial bonds. The Co-Nax axial bond is very weak and its strength of less than 8 kcal/mol is four times smaller than Co-C which in solution is approximately 31 kcal/mol. The proper description of the Co-Nax distance has been problematic in previous DFT calculations and the source of disagreement between experiment and theory remained unexplained. To resolve this discrepancy, periodic DFT calculations within the Car-Parrinello molecular dynamics (CPMD) framework were carried out on three different structural models of increased complexity. The simplest model (DBI-Ado+) contains the naked corrin ring with a total of 96 atoms. The second model is the full coenzyme B12 (AdoCbl) with 209 atoms which has been taken from crystallographic analysis. To understand the extent to which the crystal packing forces influence the structural properties of AdoCbl the complete crystal consisting of four AdoCbl molecules plus 48 water molecules periodically repeated in space was analyzed (1008 atoms). The results show that the properties associated with the Co-C bond can be well reproduced using truncated models. This does not apply to the Co-Nax axial bond and the presence of the local environment appears to be essential for the correct prediction of its bond length. The most interesting outcome of the present analysis is the finding that the actual length of the Co-Nax bond (2.262 A) is largely influenced by crystal packing forces.
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Affiliation(s)
- Carme Rovira
- Centre de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
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45
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46
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Kozlowski P, Kamachi T, Toraya T, Yoshizawa K. Does Cob(II)alamin Act as a Conductor in Coenzyme B12 Dependent Mutases? Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200602977] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Kozlowski PM, Kamachi T, Toraya T, Yoshizawa K. Does Cob(II)alamin Act as a Conductor in Coenzyme B12 Dependent Mutases? Angew Chem Int Ed Engl 2007; 46:980-3. [PMID: 17171745 DOI: 10.1002/anie.200602977] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA.
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48
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Abstract
Metal complexation is a key mediator or modifier of enzyme structure and function. In addition to divalent and polyvalent metals, group IA metals Na+and K+play important and specific roles that assist function of biological macromolecules. We examine the diversity of monovalent cation (M+)-activated enzymes by first comparing coordination in small molecules followed by a discussion of theoretical and practical aspects. Select examples of enzymes that utilize M+as a cofactor (type I) or allosteric effector (type II) illustrate the structural basis of activation by Na+and K+, along with unexpected connections with ion transporters. Kinetic expressions are derived for the analysis of type I and type II activation. In conclusion, we address evolutionary implications of Na+binding in the trypsin-like proteases of vertebrate blood coagulation. From this analysis, M+complexation has the potential to be an efficient regulator of enzyme catalysis and stability and offers novel strategies for protein engineering to improve enzyme function.
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Affiliation(s)
- Michael J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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49
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Kawata M, Kinoshita K, Takahashi S, Ogura KI, Komoto N, Yamanishi M, Tobimatsu T, Toraya T. Survey of catalytic residues and essential roles of glutamate-alpha170 and aspartate-alpha335 in coenzyme B12-dependent diol dehydratase. J Biol Chem 2006; 281:18327-34. [PMID: 16571729 DOI: 10.1074/jbc.m601910200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The importance of each active-site residue in adenosylcobalamin-dependent diol dehydratase of Klebsiella oxytoca was estimated using mutant enzymes in which one of the residues interacting with substrate and/or K(+) was mutated to Ala or another amino acid residue. The Ealpha170A and Dalpha335A mutants were totally inactive, and the Halpha143A mutant showed only a trace of activity, indicating that Glu-alpha170, Asp-alpha335, and His-alpha143 are catalytic residues. The Qalpha141A, Qalpha296A, and Salpha362A mutants showed partial activity. It was suggested from kinetic parameters that Gln-alpha296 is important for substrate binding and Gln-alpha296 and Gln-alpha141 for preventing the enzyme from mechanism-based inactivation. The Ealpha221A, Ealpha170H, and Dalpha335A did not form the (alphabetagamma)(2) complex, suggesting that these mutations indirectly disrupt subunit contacts. Among other Glu-alpha170 and Asp-alpha335 mutants, Ealpha170D and Ealpha170Q were 2.2 +/- 0.3% and 0.02% as active as the wild-type enzyme, respectively, whereas Dalpha335N was totally inactive. Kinetic analysis indicated that the presence and the position of a carboxyl group in the residue alpha170 are essential for catalysis as well as for the continuous progress of catalytic cycles. It was suggested that the roles of Glu-alpha170 and Asp-alpha335 are to participate in the binding of substrate and intermediates and keep them appropriately oriented and to function as a base in the dehydration of the 1,1-diol intermediate. In addition, Glu-alpha170 seems to stabilize the transition state for the hydroxyl group migration from C2 to C1 by accepting the proton of the spectator hydroxyl group on C1.
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Affiliation(s)
- Masahiro Kawata
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
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50
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, 45701, USA.
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