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Diaz-Bárcena A, Fernandez-Pacios L, Giraldo P. Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L. Biomolecules 2023; 14:2. [PMID: 38275743 PMCID: PMC10813097 DOI: 10.3390/biom14010002] [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: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cofactors in the apo state and in three complexes with substrate (S)-reticuline in DRS and intermediate 1,2-dehydroreticuline in DRS and in DRR. Since no experimental structure exists for REPI, we used its AlphaFold model as a scaffold to build up these four systems, which were submitted to all-atom molecular dynamics (MD) simulations. A comparison of MD results for the four systems revealed key dynamic changes associated with cofactor and ligand binding and provided a dynamic picture of the evolution of their structures and interactions. We also explored the possible dynamic occurrence of tunnels and electrostatic highways potentially involved in alternative mechanisms for channeling the intermediate from DRS to DRR.
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Affiliation(s)
- Alba Diaz-Bárcena
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (L.F.-P.); (P.G.)
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2
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Liao J, Lederer V, Bardhi A, Zou Z, Hoffmann TD, Sun G, Song C, Hoffmann T, Schwab W. Acceptors and Effectors Alter Substrate Inhibition Kinetics of a Plant Glucosyltransferase NbUGT72AY1 and Its Mutants. Int J Mol Sci 2023; 24:ijms24119542. [PMID: 37298492 DOI: 10.3390/ijms24119542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
One of the main obstacles in biocatalysis is the substrate inhibition (SI) of enzymes that play important roles in biosynthesis and metabolic regulation in organisms. The promiscuous glycosyltransferase UGT72AY1 from Nicotiana benthamiana is strongly substrate-inhibited by hydroxycoumarins (inhibitory constant Ki < 20 µM), but only weakly inhibited when monolignols are glucosylated (Ki > 1000 µM). Apocarotenoid effectors reduce the inherent UDP-glucose glucohydrolase activity of the enzyme and attenuate the SI by scopoletin derivatives, which could also be achieved by mutations. Here, we studied the kinetic profiles of different phenols and used the substrate analog vanillin, which has shown atypical Michaelis-Menten kinetics in previous studies, to examine the effects of different ligands and mutations on the SI of NbUGT72AY1. Coumarins had no effect on enzymatic activity, whereas apocarotenoids and fatty acids strongly affected SI kinetics by increasing the inhibition constant Ki. Only the F87I mutant and a chimeric version of the enzyme showed weak SI with the substrate vanillin, but all mutants exhibited mild SI when sinapaldehyde was used as an acceptor. In contrast, stearic acid reduced the transferase activity of the mutants to varying degrees. The results not only confirm the multi-substrate functionality of NbUGT72AY1, but also reveal that the enzymatic activity of this protein can be fine-tuned by external metabolites such as apocarotenoids and fatty acids that affect SI. Since these signals are generated during plant cell destruction, NbUGT72AY1 likely plays an important role in plant defense by participating in the production of lignin in the cell wall and providing direct protection through the formation of toxic phytoalexins.
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Affiliation(s)
- Jieren Liao
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Veronika Lederer
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Alba Bardhi
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Zhiwei Zou
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Guangxin Sun
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei 230036, China
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
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3
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High-level expression of an acetaldehyde dehydrogenase from Lactiplantibacillus plantarum and preliminary evaluation of its potential as a functional food additive. ELECTRON J BIOTECHN 2023. [DOI: 10.1016/j.ejbt.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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4
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Ozber N, Yu L, Hagel JM, Facchini PJ. Strong Feedback Inhibition of Key Enzymes in the Morphine Biosynthetic Pathway from Opium Poppy Detectable in Engineered Yeast. ACS Chem Biol 2023; 18:419-430. [PMID: 36735832 DOI: 10.1021/acschembio.2c00873] [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: 02/05/2023]
Abstract
Systematic screening of morphine pathway intermediates in engineered yeast revealed key biosynthetic enzymes displaying potent feedback inhibition: 3'-hydroxy-N-methylcoclaurine 4'-methyltransferase (4'OMT), which yields (S)-reticuline, and the coupled salutaridinol-7-O-acetyltransferase (SalAT) and thebaine synthase (THS2) enzyme system that produces thebaine. The addition of deuterated reticuline-d1 to a yeast strain able to convert (S)-norcoclaurine to (S)-reticuline showed reduced product accumulation in response to the feeding of all four successive pathway intermediates. Similarly, the addition of deuterated thebaine-d3 to a yeast strain able to convert salutaridine to thebaine showed reduced product accumulation from exogenous salutaridine or salutaridinol. In vitro analysis showed that reticuline is a noncompetitive inhibitor of 4'OMT, whereas thebaine exerts mixed inhibition on SalAT/THS2. In a yeast strain capable of de novo morphine biosynthesis, the addition of reticuline and thebaine resulted in the accumulation of several pathway intermediates. In contrast, morphine had no effect, suggesting that circumventing the interaction of reticuline and thebaine with 4'OMT and SalAT/THS2, respectively, could substantially increase opiate alkaloid titers in engineered yeast.
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Affiliation(s)
- Natali Ozber
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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5
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He JJ, Liu XX, Li Y, Wang Z, Shi HL, Kan YC, Yao LG, Tang CD. High level expression of nicotinamide nucleoside kinase from Saccharomyces cerevisiae and its purification and immobilization by one-step method. Front Bioeng Biotechnol 2023; 11:1134152. [PMID: 36873348 PMCID: PMC9975500 DOI: 10.3389/fbioe.2023.1134152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Nicotinamide riboside kinase (NRK) plays an important role in the synthesis of β -nicotinamide nucleotide (NMN). NMN is a key intermediate of NAD+ synthesis, and it actually contribute to the well-being of our health. In this study, gene mining technology was used to clone nicotinamide nucleoside kinase gene fragments from S. cerevisiae, and the ScNRK1 was achieved a high level of soluble expression in E. coli BL21. Then, the reScNRK1 was immobilized by metal affinity label to optimize the enzyme performance. The results showed that the enzyme activity in the fermentation broth was 14.75 IU/mL, and the specific enzyme activity after purification was 2252.59 IU/mg. After immobilization, the optimum temperature of the immobilized enzyme was increased by 10°C compared with the free enzyme, and the temperature stability was improved with little change in pH. Moreover, the activity of the immobilized enzyme remained above 80% after four cycles of immobilized reScNRK1, which makes the enzyme more advantageous in the enzymatic synthesis of NMN.
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Affiliation(s)
- Jian-Ju He
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Xin-Xin Liu
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Ying Li
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Zhe Wang
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Hong-Ling Shi
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Yun-Chao Kan
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Lun-Guang Yao
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Cun-Duo Tang
- Henan Provincial Key Laboratory of Funiu Mountain Insect Biology and Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China.,College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
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6
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Tang CD, Zhang X, Shi HL, Liu XX, Wang HY, Lu YF, Zhang SP, Kan YC, Yao LG. Improving catalytic activity of Lactobacillus harbinensis -mandelate dehydrogenase toward -o-chloromandelic acid by laboratory evolution. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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Yang S, Bai M, Hao G, Guo H, Fu B. Transcriptomics analysis of field-droughted pear ( Pyrus spp.) reveals potential drought stress genes and metabolic pathways. PeerJ 2022; 10:e12921. [PMID: 35321406 PMCID: PMC8935990 DOI: 10.7717/peerj.12921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/20/2022] [Indexed: 01/11/2023] Open
Abstract
Drought acts as a major abiotic stress that hinders plant growth and crop productivity. It is critical, as such, to discern the molecular response of plants to drought in order to enhance agricultural yields under droughts as they occur with increasing frequency. Pear trees are among the most crucial deciduous fruit trees worldwide, and yet the molecular mechanisms of drought tolerance in field-grown pear remain unclear. In this study, we analyzed the differences in transcriptome profiles of pear leaves, branches, and young fruits in irrigation vs field-drought conditions over the growing seasons. In total, 819 differentially expressed genes (DEGs) controlling drought response were identified, among which 427 DEGs were upregulated and 392 DEGs were downregulated. Drought responsive genes were enriched significantly in monoterpenoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis. Fourteen phenylpropanoid, five flavonoid, and four monoterpenoid structural genes were modulated by field drought stress, thereby indicating the transcriptional regulation of these metabolic pathways in fruit exposed to drought. A total of 4,438 transcription factors (TFs) belonging to 30 TF families were differentially expressed between drought and irrigation, and such findings signal valuable information on transcriptome changes in response to drought. Our study revealed that pear trees react to drought by modulating several secondary metabolic pathways, particularly by stimulating the production of phenylpropanoids as well as volatile organic compounds like monoterpenes. Our findings are of practical importance for agricultural breeding programs, while the resulting data is a resource for improving drought tolerance through genetic engineering of non-model, but economically important, perennial plants.
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Affiliation(s)
- Sheng Yang
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China,Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China
| | - Mudan Bai
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China,Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China
| | - Guowei Hao
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Huangping Guo
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Baochun Fu
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China,Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China
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8
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Jamieson CS, Misa J, Tang Y, Billingsley JM. Biosynthesis and synthetic biology of psychoactive natural products. Chem Soc Rev 2021; 50:6950-7008. [PMID: 33908526 PMCID: PMC8217322 DOI: 10.1039/d1cs00065a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychoactive natural products play an integral role in the modern world. The tremendous structural complexity displayed by such molecules confers diverse biological activities of significant medicinal value and sociocultural impact. Accordingly, in the last two centuries, immense effort has been devoted towards establishing how plants, animals, and fungi synthesize complex natural products from simple metabolic precursors. The recent explosion of genomics data and molecular biology tools has enabled the identification of genes encoding proteins that catalyze individual biosynthetic steps. Once fully elucidated, the "biosynthetic pathways" are often comparable to organic syntheses in elegance and yield. Additionally, the discovery of biosynthetic enzymes provides powerful catalysts which may be repurposed for synthetic biology applications, or implemented with chemoenzymatic synthetic approaches. In this review, we discuss the progress that has been made toward biosynthetic pathway elucidation amongst four classes of psychoactive natural products: hallucinogens, stimulants, cannabinoids, and opioids. Compounds of diverse biosynthetic origin - terpene, amino acid, polyketide - are identified, and notable mechanisms of key scaffold transforming steps are highlighted. We also provide a description of subsequent applications of the biosynthetic machinery, with an emphasis placed on the synthetic biology and metabolic engineering strategies enabling heterologous production.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. and Invizyne Technologies, Inc., Monrovia, CA, USA
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9
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Wang HY, Xie YL, Shi X, Shi HL, Xu JH, Tang CD, Yao LG, Kan YC. Directed evolution of a D-mandelate dehydrogenase toward D-o-chloromandelic acid and insight into the molecular basis for its catalytic performance. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Shang YP, Chen Q, Li AT, Quan S, Xu JH, Yu HL. Attenuated substrate inhibition of a haloketone reductase via structure-guided loop engineering. J Biotechnol 2020; 308:141-147. [PMID: 31866427 DOI: 10.1016/j.jbiotec.2019.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/26/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
Abstract
Substrate inhibition of enzymes is one of the main obstacles encountered frequently in industrial biocatalysis. Haloketone reductase SsCR was seriously inhibited by substrate 2,2',4'-trichloroacetophenone. In this study, two essential loops were found that have a relationship with substrate binding by conducting X-ray crystal structure analysis. Three key residues were selected from the tips of the loops and substituted with amino acids with lower hydrophobicity to weaken the hydrophobic interactions that bridge the two loops, resulting in a remarkable reduction of substrate inhibition. Among these variants, L211H showed a significant attenuation of substrate inhibition, with a Ki of 16 mM, which was 16 times that of the native enzyme. The kinetic parameter kcat/Km of L211H was 3.1 × 103 s-1 mM-1, showing the comparable catalytic efficiency to that of the wild-type enzyme (WT). At the substrate loading of 100 mM, the space time yield of variant L211H in asymmetric reduction of the haloketone was 3-fold higher than that of the WT.
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Affiliation(s)
- Yue-Peng Shang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China.
| | - Ai-Tao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, 368 Youyi Road, Wuchang, Wuhan, 430062, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China.
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11
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Mallette E, Kimber MS. Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis. Biochemistry 2018; 57:3780-3789. [PMID: 29757625 DOI: 10.1021/acs.biochem.8b00464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
S-(+)-1-Amino-2-propanol dehydrogenase (APDH) is a short-chain dehydrogenase/reductase associated with the incompletely characterized Rhodococcus and Mycobacterium bacterial microcompartment (RMM). We enzymatically characterized the APDH from M. smegmatis and showed it is highly selective, with a low micromolar Km for S-(+)-1-amino-2-propanol and specificity for NADP(H). A paralogous enzyme from a nonmicrocompartment-associated operon in the same organism was also shown to have a similar activity. We determined the structure of APDH in both apo form (at 1.7 Å) and as a ternary enzyme complex with NADP+ and aminoacetone (at 1.9 Å). Recognition of aminoacetone was mediated by strong hydrogen bonds to the amino group by Thr145 and by Glu251 from the C-terminus of an adjacent protomer. The substrate binding site entirely encloses the substrate, with close contacts between the aminoacetone methyl group and Phe95, Trp154, and Leu195. Kinetic characterization of several of these residues confirm their importance in enzyme functioning. Bioinformatics analysis of APDH homologues implies that many nonmicrocompartment APDH orthologues partake in an aminoacetone degradation pathway that proceeds via an aminopropanol O-phosphate phospholyase. RMM microcompartments may mediate a similar pathway, though possibly with differences in the details of the pathway that necessitates encapsulation behind a shell.
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Affiliation(s)
- Evan Mallette
- Department of Molecular and Cellular Biology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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12
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Xu Y, Chen G, Greer MS, Caldo KMP, Ramakrishnan G, Shah S, Wu L, Lemieux MJ, Ozga J, Weselake RJ. Multiple mechanisms contribute to increased neutral lipid accumulation in yeast producing recombinant variants of plant diacylglycerol acyltransferase 1. J Biol Chem 2017; 292:17819-17831. [PMID: 28900030 DOI: 10.1074/jbc.m117.811489] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/07/2017] [Indexed: 11/06/2022] Open
Abstract
The apparent bottleneck in the accumulation of oil during seed development in some oleaginous plant species is the formation of triacylglycerol (TAG) by the acyl-CoA-dependent acylation of sn-1,2-diacylglycerol catalyzed by diacylglycerol acyltransferase (DGAT, EC 2.3.1.20). Improving DGAT activity using protein engineering could lead to improvements in seed oil yield (e.g. in canola-type Brassica napus). Directed evolution of B. napus DGAT1 (BnaDGAT1) previously revealed that one of the regions where amino acid residue substitutions lead to higher performance in BnaDGAT1 is in the ninth predicted transmembrane domain (PTMD9). In this study, several BnaDGAT1 variants with amino acid residue substitutions in PTMD9 were characterized. Among these enzyme variants, the extent of yeast TAG production was affected by different mechanisms, including increased enzyme activity, increased polypeptide accumulation, and possibly reduced substrate inhibition. The kinetic properties of the BnaDGAT1 variants were affected by the amino acid residue substitutions, and a new kinetic model based on substrate inhibition and sigmoidicity was generated. Based on sequence alignment and further biochemical analysis, the amino acid residue substitutions that conferred increased TAG accumulation were shown to be present in the DGAT1-PTMD9 region of other higher plant species. When amino acid residue substitutions that increased BnaDGAT1 enzyme activity were introduced into recombinant Camelina sativa DGAT1, they also improved enzyme performance. Thus, the knowledge generated from directed evolution of DGAT1 in one plant species can be transferred to other plant species and has potentially broad applications in genetic engineering of oleaginous crops and microorganisms.
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Affiliation(s)
- Yang Xu
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Guanqun Chen
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Michael S Greer
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Kristian Mark P Caldo
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5.,the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, and
| | - Geetha Ramakrishnan
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Saleh Shah
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Limin Wu
- Crop Pathology and Biotechnology, InnoTech Alberta, Vegreville, Alberta T9C 1T4, Canada
| | - M Joanne Lemieux
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, and
| | - Jocelyn Ozga
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Randall J Weselake
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5,
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13
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Suástegui M, Shao Z. Yeast factories for the production of aromatic compounds: from building blocks to plant secondary metabolites. J Ind Microbiol Biotechnol 2016; 43:1611-1624. [PMID: 27581441 DOI: 10.1007/s10295-016-1824-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/02/2016] [Indexed: 12/23/2022]
Abstract
The aromatic amino acid biosynthesis pathway is a source to a plethora of commercially relevant chemicals with very diverse industrial applications. Tremendous efforts in microbial engineering have led to the production of compounds ranging from small aromatic molecular building blocks all the way to intricate plant secondary metabolites. Particularly, the yeast Saccharomyces cerevisiae has been a great model organism given its superior capability to heterologously express long metabolic pathways, especially the ones containing cytochrome P450 enzymes. This review contains a collection of state-of-the-art metabolic engineering work devoted towards unraveling the mechanisms for enhancing the flux of carbon into the aromatic pathway. Some of the molecules discussed include the polymer precursor muconic acid, as well as important nutraceuticals (flavonoids and stilbenoids), and opium-derived drugs (benzylisoquinoline alkaloids).
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Affiliation(s)
- Miguel Suástegui
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50010, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50010, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50010, USA. .,Microbiology Interdisciplinary Program, Iowa State University, Ames, IA, 50010, USA. .,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50010, USA.
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14
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Galanie S, Thodey K, Trenchard IJ, Filsinger Interrante M, Smolke CD. Complete biosynthesis of opioids in yeast. Science 2015; 349:1095-100. [PMID: 26272907 DOI: 10.1126/science.aac9373] [Citation(s) in RCA: 638] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/05/2015] [Indexed: 12/25/2022]
Abstract
Opioids are the primary drugs used in Western medicine for pain management and palliative care. Farming of opium poppies remains the sole source of these essential medicines, despite diverse market demands and uncertainty in crop yields due to weather, climate change, and pests. We engineered yeast to produce the selected opioid compounds thebaine and hydrocodone starting from sugar. All work was conducted in a laboratory that is permitted and secured for work with controlled substances. We combined enzyme discovery, enzyme engineering, and pathway and strain optimization to realize full opiate biosynthesis in yeast. The resulting opioid biosynthesis strains required the expression of 21 (thebaine) and 23 (hydrocodone) enzyme activities from plants, mammals, bacteria, and yeast itself. This is a proof of principle, and major hurdles remain before optimization and scale-up could be achieved. Open discussions of options for governing this technology are also needed in order to responsibly realize alternative supplies for these medically relevant compounds.
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Affiliation(s)
- Stephanie Galanie
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kate Thodey
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Isis J Trenchard
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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15
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He XJ, Chen SY, Wu JP, Yang LR, Xu G. Highly efficient enzymatic synthesis of tert-butyl (S)-6-chloro-5-hydroxy-3-oxohexanoate with a mutant alcohol dehydrogenase of Lactobacillus kefir. Appl Microbiol Biotechnol 2015; 99:8963-75. [DOI: 10.1007/s00253-015-6675-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 03/27/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
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16
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Fossati E, Narcross L, Ekins A, Falgueyret JP, Martin VJJ. Synthesis of Morphinan Alkaloids in Saccharomyces cerevisiae. PLoS One 2015; 10:e0124459. [PMID: 25905794 PMCID: PMC4408053 DOI: 10.1371/journal.pone.0124459] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/06/2015] [Indexed: 12/20/2022] Open
Abstract
Morphinan alkaloids are the most powerful narcotic analgesics currently used to treat moderate to severe and chronic pain. The feasibility of morphinan synthesis in recombinant Saccharomyces cerevisiae starting from the precursor (R,S)-norlaudanosoline was investigated. Chiral analysis of the reticuline produced by the expression of opium poppy methyltransferases showed strict enantioselectivity for (S)-reticuline starting from (R,S)-norlaudanosoline. In addition, the P. somniferum enzymes salutaridine synthase (PsSAS), salutaridine reductase (PsSAR) and salutaridinol acetyltransferase (PsSAT) were functionally co-expressed in S. cerevisiae and optimization of the pH conditions allowed for productive spontaneous rearrangement of salutaridinol-7-O-acetate and synthesis of thebaine from (R)-reticuline. Finally, we reconstituted a 7-gene pathway for the production of codeine and morphine from (R)-reticuline. Yeast cell feeding assays using (R)-reticuline, salutaridine or codeine as substrates showed that all enzymes were functionally co-expressed in yeast and that activity of salutaridine reductase and codeine-O-demethylase likely limit flux to morphine synthesis. The results of this study describe a significant advance for the synthesis of morphinans in S. cerevisiae and pave the way for their complete synthesis in recombinant microbes.
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Affiliation(s)
- Elena Fossati
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
| | - Andrew Ekins
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
| | - Jean-Pierre Falgueyret
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
| | - Vincent J. J. Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, Canada
- * E-mail:
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17
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Neau DB, Bender G, Boeglin WE, Bartlett SG, Brash AR, Newcomer ME. Crystal structure of a lipoxygenase in complex with substrate: the arachidonic acid-binding site of 8R-lipoxygenase. J Biol Chem 2014; 289:31905-31913. [PMID: 25231982 DOI: 10.1074/jbc.m114.599662] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lipoxygenases (LOX) play critical roles in mammalian biology in the generation of potent lipid mediators of the inflammatory response; consequently, they are targets for the development of isoform-specific inhibitors. The regio- and stereo-specificity of the oxygenation of polyunsaturated fatty acids by the enzymes is understood in terms of the chemistry, but structural observation of the enzyme-substrate interactions is lacking. Although several LOX crystal structures are available, heretofore the rapid oxygenation of bound substrate has precluded capture of the enzyme-substrate complex, leaving a gap between chemical and structural insights. In this report, we describe the 2.0 Å resolution structure of 8R-LOX in complex with arachidonic acid obtained under anaerobic conditions. Subtle rearrangements, primarily in the side chains of three amino acids, allow binding of arachidonic acid in a catalytically competent conformation. Accompanying experimental work supports a model in which both substrate tethering and cavity depth contribute to positioning the appropriate carbon at the catalytic machinery.
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Affiliation(s)
- David B Neau
- Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Gunes Bender
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - William E Boeglin
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Sue G Bartlett
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Alan R Brash
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Marcia E Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803,.
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18
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Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Appl Environ Microbiol 2014; 80:3992-4002. [PMID: 24747910 DOI: 10.1128/aem.00215-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Inhibition of enzyme activity by high concentrations of substrate and/or cofactor is a general phenomenon demonstrated in many enzymes, including aldehyde dehydrogenases. Here we show that the uncharacterized protein BetB (SA2613) from Staphylococcus aureus is a highly specific betaine aldehyde dehydrogenase, which exhibits substrate inhibition at concentrations of betaine aldehyde as low as 0.15 mM. In contrast, the aldehyde dehydrogenase YdcW from Escherichia coli, which is also active against betaine aldehyde, shows no inhibition by this substrate. Using the crystal structures of BetB and YdcW, we performed a structure-based mutational analysis of BetB and introduced the YdcW residues into the BetB active site. From a total of 32 mutations, those in five residues located in the substrate binding pocket (Val288, Ser290, His448, Tyr450, and Trp456) greatly reduced the substrate inhibition of BetB, whereas the double mutant protein H448F/Y450L demonstrated a complete loss of substrate inhibition. Substrate inhibition was also reduced by mutations of the semiconserved Gly234 (to Ser, Thr, or Ala) located in the BetB NAD(+) binding site, suggesting some cooperativity between the cofactor and substrate binding sites. Substrate docking analysis of the BetB and YdcW active sites revealed that the wild-type BetB can bind betaine aldehyde in both productive and nonproductive conformations, whereas only the productive binding mode can be modeled in the active sites of YdcW and the BetB mutant proteins with reduced substrate inhibition. Thus, our results suggest that the molecular mechanism of substrate inhibition of BetB is associated with the nonproductive binding of betaine aldehyde.
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19
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Farrow SC, Facchini PJ. Dioxygenases catalyze O-demethylation and O,O-demethylenation with widespread roles in benzylisoquinoline alkaloid metabolism in opium poppy. J Biol Chem 2013; 288:28997-9012. [PMID: 23928311 DOI: 10.1074/jbc.m113.488585] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In opium poppy, the antepenultimate and final steps in morphine biosynthesis are catalyzed by the 2-oxoglutarate/Fe(II)-dependent dioxygenases, thebaine 6-O-demethylase (T6ODM) and codeine O-demethylase (CODM). Further investigation into the biochemical functions of CODM and T6ODM revealed extensive and unexpected roles for such enzymes in the metabolism of protopine, benzo[c]phenanthridine, and rhoeadine alkaloids. When assayed with a wide range of benzylisoquinoline alkaloids, CODM, T6ODM, and the functionally unassigned paralog DIOX2, renamed protopine O-dealkylase, showed novel and efficient dealkylation activities, including regio- and substrate-specific O-demethylation and O,O-demethylenation. Enzymes catalyzing O,O-demethylenation, which cleave a methylenedioxy bridge leaving two hydroxyl groups, have previously not been reported in plants. Similar cleavage of methylenedioxy bridges on substituted amphetamines is catalyzed by heme-dependent cytochromes P450 in mammals. Preferred substrates for O,O-demethylenation by CODM and protopine O-dealkylase were protopine alkaloids that serve as intermediates in the biosynthesis of benzo[c]phenanthridine and rhoeadine derivatives. Virus-induced gene silencing used to suppress the abundance of CODM and/or T6ODM transcripts indicated a direct physiological role for these enzymes in the metabolism of protopine alkaloids, and they revealed their indirect involvement in the formation of the antimicrobial benzo[c]phenanthridine sanguinarine and certain rhoeadine alkaloids in opium poppy.
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Affiliation(s)
- Scott C Farrow
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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20
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Hagel JM, Facchini PJ. Benzylisoquinoline alkaloid metabolism: a century of discovery and a brave new world. PLANT & CELL PHYSIOLOGY 2013; 54:647-72. [PMID: 23385146 DOI: 10.1093/pcp/pct020] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Benzylisoquinoline alkaloids (BIAs) are a structurally diverse group of plant specialized metabolites with a long history of investigation. Although the ecophysiological functions of most BIAs are unknown, the medicinal properties of many compounds have been exploited for centuries. These include the narcotic analgesics codeine and morphine, the antimicrobial agents sanguinarine and berberine, and the antitussive and anticancer drug noscapine. BIA biosynthesis involves a restricted number of enzyme types that catalyze landmark coupling reactions and subsequent functional group modifications. A pathogenesis-related (PR)10/Bet v1 'Pictet-Spenglerase', several O-methyl-, N-methyl- and O-acetyltransferases, cytochromes P450, FAD-dependent oxidases, non-heme dioxygenases and NADPH-dependent reductases have been implicated in the multistep pathways leading to structurally diverse alkaloids. A small number of plant species, including opium poppy (Papaver somniferum) and other members of the Ranunculales, have emerged as model systems to study BIA metabolism. The expansion of resources to include a wider range of plant species is creating an opportunity to investigate previously uncharacterized BIA pathways. Contemporary knowledge of BIA metabolism reflects over a century of research coupled with the development of key innovations such as radioactive tracing, enzyme isolation and molecular cloning, and functional genomics approaches such as virus-induced gene silencing. Recently, the emergence of transcriptomics, proteomics and metabolomics has expedited the discovery of new BIA biosynthetic genes. The growing repository of BIA biosynthetic genes is providing the parts required to apply emerging synthetic biology platforms to the development of production systems in microbes as an alternative to plants as a commecial source of valuable BIAs.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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21
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Higashi Y, Kutchan TM, Smith TJ. Atomic structure of salutaridine reductase from the opium poppy (Papaver somniferum). J Biol Chem 2011; 286:6532-41. [PMID: 21169353 PMCID: PMC3057844 DOI: 10.1074/jbc.m110.168633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 12/02/2010] [Indexed: 11/06/2022] Open
Abstract
The opium poppy (Papaver somniferum L.) is one of the oldest known medicinal plants. In the biosynthetic pathway for morphine and codeine, salutaridine is reduced to salutaridinol by salutaridine reductase (SalR; EC 1.1.1.248) using NADPH as coenzyme. Here, we report the atomic structure of SalR to a resolution of ∼1.9 Å in the presence of NADPH. The core structure is highly homologous to other members of the short chain dehydrogenase/reductase family. The major difference is that the nicotinamide moiety and the substrate-binding pocket are covered by a loop (residues 265-279), on top of which lies a large "flap"-like domain (residues 105-140). This configuration appears to be a combination of the two common structural themes found in other members of the short chain dehydrogenase/reductase family. Previous modeling studies suggested that substrate inhibition is due to mutually exclusive productive and nonproductive modes of substrate binding in the active site. This model was tested via site-directed mutagenesis, and a number of these mutations abrogated substrate inhibition. However, the atomic structure of SalR shows that these mutated residues are instead distributed over a wide area of the enzyme, and many are not in the active site. To explain how residues distal to the active site might affect catalysis, a model is presented whereby SalR may undergo significant conformational changes during catalytic turnover.
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Affiliation(s)
- Yasuhiro Higashi
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Toni M. Kutchan
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Thomas J. Smith
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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