1
|
Li X, Zhang FG, Ma JA, Liu Y. Computational insights into the binding modes, keto-enol tautomerization and stereo-electronically controlled decarboxylation of oxaloacetate in the active site of macrophomate synthase. Phys Chem Chem Phys 2024; 26:12331-12344. [PMID: 38598177 DOI: 10.1039/d4cp00716f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Oxaloacetic acid (OAA) is a β-ketocarboxylic acid, which plays an important role as an intermediate in some metabolic pathways, including the tricarboxylic acid cycle, gluconeogenesis and fatty acid biosynthesis. Animal studies have indicated that supplementing oxaloacetic acid shows an increase of lifespan and other substantial health benefits including mitochondrial DNA protection, and protection of retinal, neural and pancreatic tissues. Most of the chemical transformations of OAA in the metabolic pathways have been extensively studied; however, the understanding of decarboxylation of OAA at the atomic level is relatively lacking. Here, we carried out MD simulations and combined quantum mechanical/molecular mechanical (QM/MM) calculations as an example to systematically elucidate the binding modes, keto-enol tautomerization and decarboxylation of OAA in the active site of macrophomate synthase (MPS), which is a Mg(II)-dependent bifunctional enzyme that catalyzes both the decarboxylation of OAA and [4+2] cycloaddition of 2-pyrone with the decarboxylated intermediate of OAA (pyruvate enolate). On the basis of our calculations, it was found that the Mg2+-coordinated oxaloacetate may exist in enol forms and keto forms. The four keto forms can be transformed into each other by simply rotating the C2-C3 single bond, nevertheless, the keto-enol tautomerization strictly requires the assistance of pocket water molecules. In addition, the decarboxylation is stereo-electronically controlled, i.e., it is the relative orientation of the terminal carboxyl anion that determines the rate of decarboxylation. As such, the chemistry of oxaloacetate in the active site of MPS is complex. On one hand, the most stable binding mode (K-I) may undergo enol-keto tautomerization to isomerize to the enol form, which may further react with the second substrate; on the other hand, K-I may isomerize to another binding mode K-II to proceed decarboxylation to generate pyruvate enolate and CO2. Starting from K-I, the enol-keto tautomerization corresponds to a barrier of 16.2 kcal mol-1, whereas the decarboxylation is associated with an overall barrier of 19.7 kcal mol-1. These findings may provide useful information for understanding the chemistry of OAA and the catalysis of related enzymes, and they are basically in agreement with the available experimental kinetic data.
Collapse
Affiliation(s)
- Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| |
Collapse
|
2
|
Gu T, Lu H, Liu H, Zhang G, Wang Y. Function discovery of a non-ribosomal peptide synthetase-like encoding gene in the nematode-trapping fungus Arthrobotrys oligospora. Front Microbiol 2023; 14:1210288. [PMID: 37520361 PMCID: PMC10373296 DOI: 10.3389/fmicb.2023.1210288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
In this study, the function of a non-ribosomal peptide synthetase-like (NRPS-like) encoding gene AOL_s00188g306 (g306) was investigated to reveal the association between NRPS and nematocidal activity in the nematode-trapping fungus Arthrobotrys oligospora. Sequence analysis indicated that the encoded product of g306 is an adenylation domain of non-ribosomal peptide synthetases and extended short-chain dehydrogenase/reductase domain-containing proteins, and displays a wide substrate spectrum. The Δg306 mutants were more sensitive to chemical stressors than the wild type. Disruption of g306 impeded the nematocidal efficiency of A. oligospora. Metabolomics analysis showed that secondary metabolite biosynthesis and lipid metabolism were altered in the mutants. The phenotypic changes in the mutants can be attributed to the down-regulation of various metabolites, including fatty acyls, prenol lipids, steroidsand steroid derivative, and amino acid derivatives, identified in the present study. This study investigated the association between the non-ribosomal polypeptide-encoding gene g306 and nematicidal activity in A. oligospora, providing a reference for resolving the predation mechanism of nematode-trapping fungus.
Collapse
Affiliation(s)
- Tiantian Gu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Hengqian Lu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Huiwen Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Guanghui Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| |
Collapse
|
3
|
Dulin CC, Sharma P, Frigo L, Voehler MW, Iverson TM, Bachmann BO. EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster. J Biol Chem 2023:104893. [PMID: 37286037 PMCID: PMC10338323 DOI: 10.1016/j.jbc.2023.104893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023] Open
Abstract
The everninomicins are bacterially produced antibiotic octasaccharides characterized by the presence of two interglycosidic spirocyclic ortho-δ-lactone (orthoester) moieties. The terminating G- and H-ring sugars, L-lyxose and C-4 branched sugar β-D-eurekanate, are proposed to be biosynthetically derived from nucleotide diphosphate pentose sugar pyranosides; however, the identity of these precursors and their biosynthetic origin remain to be determined. Herein we identify a new glucuronic acid decarboxylase from Micromonospora belonging to the superfamily of short-chain dehydrogenase/reductase enzymes, EvdS6. Biochemical characterization demonstrated that EvdS6 is an NAD+-dependent bifunctional enzyme that produces a mixture of two products, differing in the sugar C-4 oxidation state. This product distribution is atypical for glucuronic acid decarboxylating enzymes, most of which favor production of the reduced sugar and a minority of which favor release of the oxidized product. Spectroscopic and stereochemical analysis of reaction products revealed that the first product released is the oxidatively produced 4-keto-D-xylose and the second product is the reduced D-xylose. X-ray crystallographic analysis of EvdS6 at 1.51 Å resolution with bound co-factor and TDP demonstrated that the overall geometry of the EvdS6 active site is conserved with other SDR enzymes and enabled studies probing structural determinants for the reductive half of the net neutral catalytic cycle. Critical active site threonine and aspartate residues were unambiguously identified as essential in the reductive step of the reaction and resulted in enzyme variants producing almost exclusively the keto sugar. This work defines potential precursors for the G-ring L-lyxose and resolves likely origins of the H-ring β-D-eurekanate sugar precursor.
Collapse
Affiliation(s)
- Callie C Dulin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Laura Frigo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
4
|
Cowled MS, Li H, Gilchrist CLM, Lacey E, Chooi YH, Piggott AM. Stereodivergent Hydroxylation of Berkeleylactones by Penicillium turbatum. JOURNAL OF NATURAL PRODUCTS 2023; 86:541-549. [PMID: 36524608 DOI: 10.1021/acs.jnatprod.2c00946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Penicillium turbatum has previously been reported to produce A26771B, a 16-membered macrocyclic polyketide with activity against Gram-positive bacteria, mycoplasma, and fungi, as well as the structurally related compounds berkeleylactone E and berkeleylactones I-O. In this work, large-scale cultivation of P. turbatum NRRL 5630 on rice yielded seven new berkeleylactone analogues, berkeleylactone E methyl ester, 14-epi-berkeleylactone F, berkeleylactones P-R, 12-epi-berkeleylactone Q, and 13-epi-berkeleylactone R, and six previously reported analogues, A26771B and berkeleylactones E-G and J-K. The structures of the berkeleylactones were elucidated by detailed analysis of spectroscopic data, molecular modeling, and comparison with literature values. Interestingly, six of the berkeleylactone analogues were isolated as pairs of hydroxy epimers, highlighting how Nature can exploit stereodivergence in biosynthetic pathways to increase chemical diversity. The genome of P. turbatum was sequenced, and a putative gene cluster (bekl) responsible for the biosynthesis of the berkeleylactones was identified. The new berkeleylactone analogues exhibited no significant biological activity against a panel of bacteria, fungi, the parasite Giardia duodenalis, or NS-1 murine myeloma cells, suggesting a hitherto undiscovered biological role.
Collapse
Affiliation(s)
- Michael S Cowled
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Ernest Lacey
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
5
|
Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatische C4-Epimerisierung von UDP-Glucuronsäure: präzise gesteuerte Rotation eines transienten 4-Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202211937. [PMID: 38515538 PMCID: PMC10952283 DOI: 10.1002/ange.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 03/23/2024]
Abstract
AbstractUDP‐Glucuronsäure(UDP‐GlcA)‐4‐Epimerase repräsentiert eine wichtige Fragestellung in der Enzymkatalyse: die Balance zwischen konformativer Flexibilität und genauer Positionierung. Das Enzym koordiniert die C4‐Oxidation des Substrats durch NAD+ mit der Rotation eines leicht decarboxylierbaren β‐Ketosäure‐Intermediats im aktiven Zentrum zur Ermöglichung der stereoinvertierenden Reduktion der Ketogruppe durch NADH. Wir zeigen hier die nur schwer erfassbare Rotationskoordinate des 4‐Ketointermediats. Distorsion des Zuckerrings in eine Boot‐Konformation erzeugt torsionale Mobilität in der Bindungstasche des Enzyms. Die Endpunkte der Rotation zeigen den 4‐Ketozucker in einer unverformten 4C1‐Sesselkonformation. Die äquatorial positionierte Carboxylatgruppe ist ungünstig für die 4‐Ketozucker‐Decarboxylierung. Varianten der Epimerase zeigen Decarboxylierung, wenn sie die Bindung mit der Carboxylatgruppe im entgegengesetzten Rotationsisomer des Substrats entfernen. R185A/D‐Substitutionen wandeln die Epimerase in UDP‐Xylose‐Synthasen um, welche UDP‐GlcA in stereospezifischen, konfigurationserhaltenden Reaktionen decarboxylieren.
Collapse
Affiliation(s)
- Annika J. E. Borg
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Derzeitige Adresse: Nostrum BiodiscoveryAv. De Josep Tarradellas, 8–1008029BarcelonaSpanien
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys, 2308010BarcelonaSpanien
| | - Bernd Nidetzky
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
- Austrian Center of Industrial Biotechnology (acib)Krenngasse 378010GrazÖsterreich
| |
Collapse
|
6
|
Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation. Angew Chem Int Ed Engl 2023; 62:e202211937. [PMID: 36308301 PMCID: PMC10107529 DOI: 10.1002/anie.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.
Collapse
Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Present address: Nostrum Biodiscovery, Av. De Josep Tarradellas, 8-10, 08029, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria.,Austrian Center of Industrial Biotechnology (acib), Krenngasse 37, 8010, Graz, Austria
| |
Collapse
|
7
|
Enhancing Acetophenone Tolerance of Anti-Prelog Short-Chain Dehydrogenase/Reductase EbSDR8 Using a Whole-Cell Catalyst by Directed Evolution. Catalysts 2022. [DOI: 10.3390/catal12091071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The short-chain dehydrogenase/reductase (SDR) from Empedobacter brevis ZJUY-1401 (EbSDR8, GenBank: ALZ42979.1) is a promising biocatalyst for the reduction of acetophenone to (R)-1-phenylethanol, but its industrial application is restricted by its insufficient tolerance to acetophenone. In this paper, we developed a chromogenic reaction-based high-throughput screening method and employed directed evolution to enhance the acetophenone tolerance of EbSDR8. The resulting variant, M190V, showed 74.8% improvement over the wild-type in specific activity when catalyzing the reduction of 200 mM acetophenone. Kinetic analysis revealed a 70% enhancement in its catalytic efficiency (kcat/Km). Molecular docking was conducted to reveal the possible mechanism behind the improved acetophenone tolerance, and the result implied that the M190V mutation is conducive to the binding and release of coenzyme. Aside from the improved catalytic performance when dealing with a high concentration of acetophenone, other features of M190V, such as a broad pH range (6.0 to 10.5), low optimal cosubstrate concentration (1% isopropanol), and a temperature optimum close to that of E. coli cells (35 °C), also contribute to its practical application as a whole-cell catalyst. In this study, we first designed a directed evolution means to engineer the enzyme and obtained the positive variant which has a high activity under high concentrations of acetophenone. After that, we optimized the catalytic performance of the variant to adapt to industrial applications.
Collapse
|
8
|
A colorimetric assay for the screening and kinetic analysis of nucleotide sugar 4,6-dehydratases. Anal Biochem 2022; 655:114870. [PMID: 36027972 DOI: 10.1016/j.ab.2022.114870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/22/2022]
Abstract
Nucleotide sugar 4,6-dehydratases belong to the Short-chain Dehydrogenase/Reductase (SDR) superfamily and catalyze the conversion of an NDP-hexose to an NDP-4-keto-6-deoxy hexose, a key step in the biosynthesis of a plethora of deoxy and amino sugars. Here, we present a colorimetric assay for the detection of their reaction products (NDP-4-keto-6-deoxy hexoses) using concentrated sulfuric acid and an ethanolic resorcinol solution. Under these conditions, the keto-function of the dehydratase product reacts specifically with resorcinol to form an orange-red or pink complex for NDP-glucose/GDP-mannose and UDP-N-acetylglucosamine, respectively, with an absorption maximum at 510 nm. The presented assay allows reliable product detection at low concentrations and can be applied in microtiter plates. It thus allows the determination of kinetic enzyme parameters like the optimal temperature, pH, Vmax, KM and kcat, as well as the miniaturization for screening purposes with crude cell extracts. As such, this detection assay opens new possibilities for the characterization and screening of these dehydratases in 96-well plates for different research goals.
Collapse
|
9
|
Rapp C, Nidetzky B. Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate. ACS Catal 2022; 12:6816-6830. [PMID: 35747200 PMCID: PMC9207888 DOI: 10.1021/acscatal.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/12/2022] [Indexed: 11/29/2022]
Abstract
![]()
Transient oxidation–reduction
through hydride transfer with
tightly bound NAD coenzyme is used by a large class of sugar nucleotide
epimerases to promote configurational inversion of carbon stereocenters
in carbohydrate substrates. A requirement for the epimerases to coordinate
hydride abstraction and re-addition with substrate rotation in the
binding pocket poses a challenge for dynamical protein conformational
selection linked to enzyme catalysis. Here, we studied the thermophilic
C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose
substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride
transfer toward environmental fluctuations affected by temperature
(20–80 °C). We determined noncompetitive primary kinetic
isotope effects (KIE) due to 2H at the glucose C2 and showed
that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of
the hydrogen abstraction to enzyme-NAD+ in a rate-limiting
transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C)
and 3.3 at high temperature (80 °C). The temperature profiles
for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically
important breakpoint (∼40 °C), suggesting an equilibrium
shift to an impaired conformational landscape relevant for catalysis
in the low-temperature region. Full Marcus-like model fits of the
rate and KIE profiles provided evidence for a high-temperature reaction
via low-frequency conformational sampling associated with a broad
distribution of hydride donor–acceptor distances (long-distance
population centered at 3.31 ± 0.02 Å), only poorly suitable
for quantum mechanical tunneling. Collectively, dynamical characteristics
of TaCPa2E-catalyzed hydride transfer during transient
oxidation of CDP-glucose reveal important analogies to mechanistically
simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase.
A loose-fit substrate (in TaCPa2E) resembles structural
variants of these enzymes by extensive dynamical sampling to balance
conformational flexibility and catalytic efficiency.
Collapse
Affiliation(s)
- Christian Rapp
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
10
|
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
|
11
|
Zou G, Ren J, Wu D, Zhang H, Gong M, Li W, Zhang J, Yang Y. Characterization and Heterologous Expression of UDP-Glucose 4-Epimerase From a Hericium erinaceus Mutant with High Polysaccharide Production. Front Bioeng Biotechnol 2021; 9:796278. [PMID: 34900974 PMCID: PMC8655778 DOI: 10.3389/fbioe.2021.796278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/03/2021] [Indexed: 02/02/2023] Open
Abstract
Hericium erinaceus is an important medicinal fungus in traditional Chinese medicine because of its polysaccharides and other natural products. Compared terpenoids and polyketides, the analysis of synthetic pathway of polysaccharides is more difficult because of the many genes involved in central metabolism. In previous studies, A6180, encoding a putative UDP-glucose 4-epimerase (UGE) in an H. erinaceus mutant with high production of active polysaccharides, was significantly upregulated. Since there is no reliable genetic manipulation technology for H. erinaceus, we employed Escherichia coli and Saccharomyces cerevisiae to study the function and activity of A6180. The recombinant overexpression vector pET22b-A6180 was constructed for heterologous expression in E. coli. The enzymatic properties of the recombinant protein were investigated. It showed that the recombinant A6180 could strongly convert UDP-α-D-glucose into UDP-α-D-galactose under optimal conditions (pH 6.0, 30°C). In addition, when A6180 was introduced into S. cerevisiae BY4742, xylose was detected in the polysaccharide composition of the yeast transformant. This suggested that the protein coded by A6180 might be a multifunctional enzyme. The generated polysaccharides with a new composition of sugars showed enhanced macrophage activity in vitro. These results indicate that A6180 plays an important role in the structure and activity of polysaccharides. It is a promising strategy for producing polysaccharides with higher activity by introducing A6180 into polysaccharide-producing mushrooms.
Collapse
Affiliation(s)
- Gen Zou
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Juanbao Ren
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.,College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Di Wu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Henan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ming Gong
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jingsong Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Yang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
12
|
Wang Y, Shi Y, Li K, Yang D, Liu N, Zhang L, Zhao L, Zhang X, Liu Y, Gao L, Xia T, Wang P. Roles of the 2-Oxoglutarate-Dependent Dioxygenase Superfamily in the Flavonoid Pathway: A Review of the Functional Diversity of F3H, FNS I, FLS, and LDOX/ANS. Molecules 2021; 26:molecules26216745. [PMID: 34771153 PMCID: PMC8588099 DOI: 10.3390/molecules26216745] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
The 2-oxoglutarate-dependent dioxygenase (2-OGD) superfamily is one of the largest protein families in plants. The main oxidation reactions they catalyze in plants are hydroxylation, desaturation, demethylation, epimerization, and halogenation. Four members of the 2-OGD superfamily, i.e., flavonone 3β-hydroxylase (F3H), flavones synthase I (FNS I), flavonol synthase (FLS), and anthocyanidin synthase (ANS)/leucoanthocyanidin dioxygenase (LDOX), are present in the flavonoid pathway, catalyzing hydroxylation and desaturation reactions. In this review, we summarize the recent research progress on these proteins, from the discovery of their enzymatic activity, to their functional verification, to the analysis of the response they mediate in plants towards adversity. Substrate diversity analysis indicated that F3H, FNS Ⅰ, ANS/LDOX, and FLS perform their respective dominant functions in the flavonoid pathway, despite the presence of functional redundancy among them. The phylogenetic tree classified two types of FNS Ⅰ, one mainly performing FNS activity, and the other, a new type of FNS present in angiosperms, mainly involved in C-5 hydroxylation of SA. Additionally, a new class of LDOXs is highlighted, which can catalyze the conversion of (+)-catechin to cyanidin, further influencing the starter and extension unit composition of proanthocyanidins (PAs). The systematical description of the functional diversity and evolutionary relationship among these enzymes can facilitate the understanding of their impacts on plant metabolism. On the other hand, it provides molecular genetic evidence of the chemical evolution of flavonoids from lower to higher plants, promoting plant adaptation to harsh environments.
Collapse
Affiliation(s)
- Yueyue Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Yufeng Shi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China;
| | - Kaiyuan Li
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Dong Yang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Nana Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Lingjie Zhang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (Y.L.)
| | - Lei Zhao
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
| | - Yajun Liu
- School of Life Science, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (Y.L.)
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (Y.L.)
- Correspondence: (L.G.); (T.X.); (P.W.)
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China;
- Correspondence: (L.G.); (T.X.); (P.W.)
| | - Peiqiang Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (K.L.); (D.Y.); (N.L.); (L.Z.); (X.Z.)
- Correspondence: (L.G.); (T.X.); (P.W.)
| |
Collapse
|
13
|
Griffiths WA, Spencer KD, Thoden JB, Holden HM. Biochemical investigation of an N-acetyltransferase from Helicobacter pullorum. Protein Sci 2021; 30:2418-2432. [PMID: 34651380 DOI: 10.1002/pro.4207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/08/2022]
Abstract
N-acetylated sugars are often found, for example, on the lipopolysaccharides of Gram-negative bacteria, on the S-layers of Gram-positive bacteria, and on the capsular polysaccharides. Key enzymes involved in their biosynthesis are the sugar N-acetyltransferases. Here, we describe a structural and functional analysis of one such enzyme from Helicobacter pullorum, an emerging pathogen that may be associated with gastroenteritis and gallbladder and liver diseases. For this analysis, the gene BA919-RS02330 putatively encoding an N-acetyltransferase was cloned, and the corresponding protein was expressed and purified. A kinetic analysis demonstrated that the enzyme utilizes dTDP-3-amino-3,6-dideoxy-d-glucose as a substrate as well as dTDP-3-amino-3,6-dideoxy-d-galactose, albeit at a reduced rate. In addition to this kinetic analysis, a similar enzyme from Helicobacter bilis was cloned and expressed, and its kinetic parameters were determined. Seven X-ray crystallographic structures of various complexes of the H. pullorum wild-type enzyme (or the C80T variant) were determined to resolutions of 1.7 Å or higher. The overall molecular architecture of the H. pullorum N-acetyltransferase places it into the Class II left-handed-β-helix superfamily (LβH). Taken together, the data presented herein suggest that 3-acetamido-3,6-dideoxy-d-glucose (or the galactose derivative) is found on either the H. pullorum O-antigen or in another of its complex glycoconjugates. A BLAST search suggests that more than 50 non-pylori Helicobacter spp. have genes encoding N-acetyltransferases. Given that there is little information concerning the complex glycans in non-pylori Helicobacter spp. and considering their zoonotic potential, our results provide new biochemical insight into these pathogens.
Collapse
Affiliation(s)
- William A Griffiths
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Keelan D Spencer
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| |
Collapse
|
14
|
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
|