1
|
Vogel U, Beerens K, Desmet T. Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential. J Biol Chem 2022; 298:101809. [PMID: 35271853 PMCID: PMC8987622 DOI: 10.1016/j.jbc.2022.101809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Nucleotide sugar (NS) dehydratases play a central role in the biosynthesis of deoxy and amino sugars, which are involved in a variety of biological functions in all domains of life. Bacteria are true masters of deoxy sugar biosynthesis as they can produce a wide range of highly specialized monosaccharides. Indeed, deoxy and amino sugars play important roles in the virulence of gram-positive and gram-negative pathogenic species and are additionally involved in the biosynthesis of diverse macrolide antibiotics. The biosynthesis of deoxy sugars relies on the activity of NS dehydratases, which can be subdivided into three groups based on their structure and reaction mechanism. The best-characterized NS dehydratases are the 4,6-dehydratases that, together with the 5,6-dehydratases, belong to the NS-short-chain dehydrogenase/reductase superfamily. The other two groups are the less abundant 2,3-dehydratases that belong to the Nudix hydrolase superfamily and 3-dehydratases, which are related to aspartame aminotransferases. 4,6-Dehydratases catalyze the first step in all deoxy sugar biosynthesis pathways, converting nucleoside diphosphate hexoses to nucleoside diphosphate-4-keto-6-deoxy hexoses, which in turn are further deoxygenated by the 2,3- and 3-dehydratases to form dideoxy and trideoxy sugars. In this review, we give an overview of the NS dehydratases focusing on the comparison of their structure and reaction mechanisms, thereby highlighting common features, and investigating differences between closely related members of the same superfamilies.
Collapse
Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
| |
Collapse
|
2
|
Beerens K, Gevaert O, Desmet T. GDP-Mannose 3,5-Epimerase: A View on Structure, Mechanism, and Industrial Potential. Front Mol Biosci 2022; 8:784142. [PMID: 35087867 PMCID: PMC8787198 DOI: 10.3389/fmolb.2021.784142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
GDP-mannose 3,5-epimerase (GM35E, GME) belongs to the short-chain dehydrogenase/reductase (SDR) protein superfamily and catalyses the conversion of GDP-d-mannose towards GDP-l-galactose. Although the overall reaction seems relatively simple (a double epimerization), the enzyme needs to orchestrate a complex set of chemical reactions, with no less than 6 catalysis steps (oxidation, 2x deprotonation, 2x protonation and reduction), to perform the double epimerization of GDP-mannose to GDP-l-galactose. The enzyme is involved in the biosynthesis of vitamin C in plants and lipopolysaccharide synthesis in bacteria. In this review, we provide a clear overview of these interesting epimerases, including the latest findings such as the recently characterized bacterial and thermostable GM35E representative and its mechanism revision but also focus on their industrial potential in rare sugar synthesis and glycorandomization.
Collapse
Affiliation(s)
| | | | - Tom Desmet
- *Correspondence: Koen Beerens, ; Tom Desmet,
| |
Collapse
|
3
|
Alvarez Quispe C, Da Costa M, Beerens K, Desmet T. Exploration of archaeal nucleotide sugar epimerases unveils a new and highly promiscuous GDP-Gal4E subgroup. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
4
|
Da Costa M, Gevaert O, Van Overtveldt S, Lange J, Joosten HJ, Desmet T, Beerens K. Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. Biotechnol Adv 2021; 48:107705. [PMID: 33571638 DOI: 10.1016/j.biotechadv.2021.107705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare sugars and glycosides. Some family members have already been extensively characterized due to their direct implication in metabolic disorders or in the biosynthesis of virulence factors. In this review, we combine the knowledge gathered from studies that typically focused only on one NS-SDR activity with an in-depth analysis and overview of all of the different NS-SDR families (169,076 enzyme sequences). Through this structure-based multiple sequence alignment of NS-SDRs retrieved from public databases, we could identify clear patterns in conservation and correlation of crucial residues. Supported by this analysis, we suggest updating and extending the UDP-galactose 4-epimerase "hexagonal box model" to an "heptagonal box model" for all NS-SDR enzymes. This specificity model consists of seven conserved regions surrounding the NDP-sugar substrate that serve as fingerprint for each specificity. The specificity fingerprints highlighted in this review will be beneficial for functional annotation of the large group of NS-SDR enzymes and form a guide for future enzyme engineering efforts focused on the biosynthesis of rare and specialty carbohydrates.
Collapse
Affiliation(s)
- Matthieu Da Costa
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Joanna Lange
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Tom Desmet
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Koen Beerens
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| |
Collapse
|
5
|
Fushinobu S. Molecular evolution and functional divergence of UDP-hexose 4-epimerases. Curr Opin Chem Biol 2020; 61:53-62. [PMID: 33171387 DOI: 10.1016/j.cbpa.2020.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023]
Abstract
UDP-glucose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) and/or the interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc) in sugar metabolism. GalEs belong to the short-chain dehydrogenase/reductase superfamily, use a conserved 'transient keto intermediate' mechanism and have variable substrate specificity. GalEs have been classified into three groups based on substrate specificity: group 1 prefers UDP-Glc/Gal, group 3 prefers UDP-GlcNAc/GalNAc, and group 2 has comparable activities for both types of the substrates. The phylogenetic relationship and structural basis for the specificities of GalEs revealed possible molecular evolution of UDP-hexose 4-epimerases in various organisms. Based on the recent advances in studies on GalEs and related enzymes, an updated view of their evolutional diversification is presented.
Collapse
Affiliation(s)
- Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
| |
Collapse
|
6
|
Gevaert O, Van Overtveldt S, Da Costa M, Beerens K, Desmet T. GDP-altrose as novel product of GDP-mannose 3,5-epimerase: Revisiting its reaction mechanism. Int J Biol Macromol 2020; 165:1862-1868. [PMID: 33075338 DOI: 10.1016/j.ijbiomac.2020.10.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Abstract
GDP-mannose 3,5-epimerase (GM35E) catalyzes the double epimerization of GDP-mannose to yield GDP-l-galactose. GDP-l-gulose (C5-epimer) has previously been detected as a byproduct of this reaction, indicating that C3,5-epimerization occurs through an initial epimerization at C5. Given these products, GM35E constitutes a valuable bridge between d- and l-hexoses. In order to fully exploit this potential, the enzyme might be subjected to specificity engineering for which profound mechanistic insights are beneficial. Accordingly, this study further elucidated GM35E's reaction mechanism. For the first time, the production of the C3-epimer GDP-altrose was demonstrated, resulting in an adjustment of the acknowledged reaction mechanism. As GM35E converts GDP-mannose to GDP-l-gulose, GDP-altrose and GDP-l-galactose in a 72:4:4:20 ratio, this indicates that the enzyme does not discriminate between the C3 and C5 position as initial epimerization site. This was also confirmed by a structural investigation. Based on a mutational analysis of the active site, residues S115 and R281 were attributed a stabilizing function, which is believed to support the reactivation process of the catalytic residues. This paper eventually reflected on some engineering strategies that aim to change the enzyme towards a single specificity.
Collapse
Affiliation(s)
- Ophelia Gevaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| |
Collapse
|
7
|
Van Overtveldt S, Da Costa M, Gevaert O, Joosten HJ, Beerens K, Desmet T. Determinants of the Nucleotide Specificity in the Carbohydrate Epimerase Family 1. Biotechnol J 2020; 15:e2000132. [PMID: 32761842 DOI: 10.1002/biot.202000132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/20/2020] [Indexed: 11/09/2022]
Abstract
In recent years, carbohydrate epimerases have attracted increasing attention as promising biocatalysts for the production of specialty sugars and derivatives. The vast majority of these enzymes are active on nucleotide-activated sugars, rather than on their free counterparts. Although such epimerases are known to have a clear preference for a particular nucleotide (UDP, GDP, CDP, or ADP), very little is known about the determinants of the respective specificities. In this work, sequence motifs are identified that correlate with the different nucleotide specificities in one of the main epimerase superfamilies, carbohydrate epimerase 1 (CEP1). To confirm their relevance, GDP- and CDP-specific residues are introduced into the UDP-glucose 4-epimerase from Thermus thermophilus, resulting in a 3-fold and 13-fold reduction in KM for GDP-Glc and CDP-Glc, respectively. Moreover, several variants are severely crippled in UDP-Glc activity, which further underlines the crucial role of the identified positions. Hence, the analysis should prove to be valuable for the further exploration and application of epimerases involved in carbohydrate synthesis.
Collapse
Affiliation(s)
- Stevie Van Overtveldt
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, Nijmegen, 6511 AA, The Netherlands
| | - Koen Beerens
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| |
Collapse
|
8
|
Characterization of the First Bacterial and Thermostable GDP-Mannose 3,5-Epimerase. Int J Mol Sci 2019; 20:ijms20143530. [PMID: 31330931 PMCID: PMC6678494 DOI: 10.3390/ijms20143530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023] Open
Abstract
GDP-mannose 3,5-epimerase (GM35E) catalyzes the conversion of GDP-mannose towards GDP-l-galactose and GDP-l-gulose. Although this reaction represents one of the few enzymatic routes towards the production of l-sugars and derivatives, it has not yet been exploited for that purpose. One of the reasons is that so far only GM35Es from plants have been characterized, yielding biocatalysts that are relatively unstable and difficult to express heterologously. Through the mining of sequence databases, we succeeded in identifying a promising bacterial homologue. The gene from the thermophilic organism Methylacidiphilum fumariolicum was codon optimized for expression in Escherichia coli, resulting in the production of 40 mg/L of recombinant protein. The enzyme was found to act as a self-sufficient GM35E, performing three chemical reactions in the same active site. Furthermore, the biocatalyst was highly stable at temperatures up to 55 °C, making it well suited for the synthesis of new carbohydrate products with application in the pharma industry.
Collapse
|
9
|
Shvarev D, Nishi CN, Maldener I. Glycolipid composition of the heterocyst envelope of Anabaena sp. PCC 7120 is crucial for diazotrophic growth and relies on the UDP-galactose 4-epimerase HgdA. Microbiologyopen 2019; 8:e00811. [PMID: 30803160 PMCID: PMC6692557 DOI: 10.1002/mbo3.811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 01/05/2023] Open
Abstract
The nitrogenase complex in the heterocysts of the filamentous freshwater cyanobacterium Anabaenasp. PCC 7120 fixes atmospheric nitrogen to allow diazotrophic growth. The heterocyst cell envelope protects the nitrogenase from oxygen and consists of a polysaccharide and a glycolipid layer that are formed by a complex process involving the recruitment of different proteins. Here, we studied the function of the putative nucleoside‐diphosphate‐sugar epimerase HgdA, which along with HgdB and HgdC is essential for deposition of the glycolipid layer and growth without a combined nitrogen source. Using site‐directed mutagenesis and single homologous recombination approach, we performed a thoroughly functional characterization of HgdA and confirmed that the glycolipid layer of the hgdAmutant heterocyst is aberrant as shown by transmission electron microscopy and chemical analysis. The hgdA gene was expressed during late stages of the heterocyst differentiation. GFP‐tagged HgdA protein localized inside the heterocysts. The purified HgdA protein had UDP‐galactose 4‐epimerase activity in vitro. This enzyme could be responsible for synthesis of heterocyst‐specific glycolipid precursors, which could be transported over the cell wall by the ABC transporter components HgdB/HgdC.
Collapse
Affiliation(s)
- Dmitry Shvarev
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Carolina N Nishi
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Iris Maldener
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany
| |
Collapse
|
10
|
Chen LL, Han DL, Zhai YF, Wang JH, Wang YF, Chen M. Characterization and mutational analysis of two UDP-galactose 4-epimerases in Streptococcus pneumoniae TIGR4. BIOCHEMISTRY (MOSCOW) 2018. [DOI: 10.1134/s0006297918010054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Beerens K, Van Overtveldt S, Desmet T. The “epimerring” highlights the potential of carbohydrate epimerases for rare sugar production. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1306738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Koen Beerens
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Stevie Van Overtveldt
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| |
Collapse
|
12
|
Beerens K, Soetaert W, Desmet T. UDP-hexose 4-epimerases: a view on structure, mechanism and substrate specificity. Carbohydr Res 2015; 414:8-14. [PMID: 26162744 DOI: 10.1016/j.carres.2015.06.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 06/09/2015] [Accepted: 06/13/2015] [Indexed: 12/19/2022]
Abstract
UDP-sugar 4-epimerase (GalE) belongs to the short-chain dehydrogenase/reductase (SDR) superfamily of proteins and is one of enzymes in the Leloir pathway. They have been shown to be important virulence factors in a number of Gram-negative pathogens and to be involved in the biosynthesis of different polysaccharide structures. The metabolic disease type III galactosemia is caused by detrimental mutations in the human GalE. GalE and related enzymes display unusual enzymologic, chemical, and stereochemical properties; including irreversible binding of the cofactor NAD and uridine nucleotide-induced activation of this cofactor. These epimerases have been found active on UDP-hexoses, the N-acetylated and uronic acid forms thereof as well as UDP-pentoses. As they are involved in different pathways and functions, a deeper understanding of the enzymes, and their substrate promiscuity and/or selectivity, could lead to drug and vaccine design as well as antibiotic and probiotic development. This review summarizes the research performed on UDP-sugar 4-epimerases' structure, mechanism and substrate promiscuity.
Collapse
Affiliation(s)
- Koen Beerens
- Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Tom Desmet
- Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| |
Collapse
|