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Mondal A, Roy P, Carrannanto J, Datar PM, DiRocco DJ, Hunter K, Marsh ENG. Surveying the scope of aromatic decarboxylations catalyzed by prenylated-flavin dependent enzymes. Faraday Discuss 2024. [PMID: 38837123 DOI: 10.1039/d4fd00006d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The prenylated-flavin mononucleotide-dependent decarboxylases (also known as UbiD-like enzymes) are the most recently discovered family of decarboxylases. The modified flavin facilitates the decarboxylation of unsaturated carboxylic acids through a novel mechanism involving 1,3-dipolar cyclo-addition chemistry. UbiD-like enzymes have attracted considerable interest for biocatalysis applications due to their ability to catalyse (de)carboxylation reactions on a broad range of aromatic substrates at otherwise unreactive carbon centres. There are now ∼35 000 protein sequences annotated as hypothetical UbiD-like enzymes. Sequence similarity network analyses of the UbiD protein family suggests that there are likely dozens of distinct decarboxylase enzymes represented within this family. Furthermore, many of the enzymes so far characterized can decarboxylate a broad range of substrates. Here we describe a strategy to identify potential substrates of UbiD-like enzymes based on detecting enzyme-catalysed solvent deuterium exchange into potential substrates. Using ferulic acid decarboxylase (FDC) as a model system, we tested a diverse range of aromatic and heterocyclic molecules for their ability to undergo enzyme-catalysed H/D exchange in deuterated buffer. We found that FDC catalyses H/D exchange, albeit at generally very low levels, into a wide range of small, aromatic molecules that have little resemblance to its physiological substrate. In contrast, the sub-set of aromatic carboxylic acids that are substrates for FDC-catalysed decarboxylation is much smaller. We discuss the implications of these findings for screening uncharacterized UbiD-like enzymes for novel (de)carboxylase activity.
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Affiliation(s)
- Anushree Mondal
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Pronay Roy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Jaclyn Carrannanto
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Prathamesh M Datar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Daniel J DiRocco
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Katherine Hunter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Han Y, Jiang H, Huang C, Wu X, Ouyang Y, Chen H, Lan D, Wang Y, Zheng B, Xia J. Enzymatic interfacial conversion of acylglycerols in Pickering emulsions stabilized by hydrogel microparticles. J Colloid Interface Sci 2024; 661:228-236. [PMID: 38301461 DOI: 10.1016/j.jcis.2024.01.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/04/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
HYPOTHESIS A critical challenge in the enzymatic conversion of acylglycerols is the limited exposure of the enzyme dissolved in the aqueous solution to the hydrophobic substrate in the oil phase. Positioning the enzyme in a microenvironment with balanced hydrophobicity and hydrophilicity in Pickering emulsion will facilitate the acylglycerol-catalyzing reactions at the interface between the oil and liquid phases. EXPERIMENTS In this work, to overcome the challenge of biphasic catalysis, we report a method to immobilize enzymes in polyethylene glycol (PEG)-based hydrogel microparticles (HMPs) at the interface between the oil and water phases in Pickering emulsion to promote the enzymatic conversion of acylglycerols. FINDINGS 3 wt% of HMPs can stabilize the oil-in-water Pickering emulsion for at least 14 days and increase the viscosity of emulsions. Lipase-HMP conjugates showed significantly higher hydrolytic activity in Pickering emulsion; HMP-immobilized lipase SMG1 showed an activity about three times that of free lipase SMG1. Co-immobilization of a lipase and a fatty acid photodecarboxylase from Chlorella variabilis (CvFAP) in Pickering emulsion enables light-driven cascade conversion of triacylglycerols to hydrocarbons, transforming waste oil to renewable biofuels in a green and sustainable approach. HMPs stabilize the Pickering emulsion and promote interfacial biocatalysis in converting acylglycerols to renewable biofuels.
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Affiliation(s)
- Yongxu Han
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hao Jiang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chen Huang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Xue Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yinghan Ouyang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hongfei Chen
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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3
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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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4
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Tan W, Li X, Zhang P, Yao X, Li J, Jin P, Li K. A fatty acid photodecarboxylase-mimicking photonanozyme with defect-induced enzymatic substrate-binding pockets. J Colloid Interface Sci 2023; 652:1965-1973. [PMID: 37690304 DOI: 10.1016/j.jcis.2023.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/20/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Hydrocarbon synthesis hints at the significance of in-depth investigations and detailed explanations of mimicking fatty acid photodecarboxylase (FAP). Considering the importance of photodecarboxylases in hydrocarbon synthesis, we present the potential of defective semiconductor nanomaterials as a novel type of photonanozymes (PNZs) that mimic enzyme-like performance, serving as alternatives to FAP. Ferrum-doped titanium dioxide (Fe-TiO2) was synthesized to introduce appropriate amounts of surface defects including reduced Ti3+ sites and oxygen vacancies, which reduce the band gap of TiO2 and enhance the visible-light absorption, thereby facilitating efficient charge trapping. Notably, the surface defects of Fe-TiO2 PNZs singularly act as enzymatic substrate-binding pockets that enable efficient carboxylic acid adsorption during the dark process, conversely facilitating the formation of more defects and boosting the FAP-like activity for photocatalytic decarboxylation reactions. This work provides a creative strategy for designing substrate-dependent higher-concentration defects as enzyme-like binding sites on promising PNZs that mimic natural photoenzymes.
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Affiliation(s)
- Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Xuyan Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Jinzhao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Peng Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, PR China.
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5
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Li ZM, Hu Z, Wang X, Chen S, Yu W, Liu J, Li Z. Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843. Int J Mol Sci 2023; 24:12198. [PMID: 37569577 PMCID: PMC10418658 DOI: 10.3390/ijms241512198] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
α-Ketoglutarate decarboxylase is a crucial enzyme in the tricarboxylic acid cycle of cyanobacteria, catalyzing the non-oxidative decarboxylation of α-ketoglutarate to produce succinate semialdehyde and CO2. The decarboxylation process is reliant on the cofactor of thiamine diphosphate. However, this enzyme's biochemical and structural properties have not been well characterized. In this work, two α-ketoglutarate decarboxylases encoded by MAE_06010 and MiAbw_01735 genes from Microcystis aeruginosa NIES-843 (MaKGD) and NIES-4325 (MiKGD), respectively, were overexpressed and purified by using an Escherichia coli expression system. It was found that MaKGD exhibited 9.2-fold higher catalytic efficiency than MiKGD, which may be attributed to the absence of glutamate decarboxylase in Microcystis aeruginosa NIES-843. Further biochemical investigation of MaKGD demonstrated that it displayed optimum activity at pH 6.5-7.0 and was most activated by Mg2+. Additionally, MaKGD showed substrate specificity towards α-ketoglutarate. Structural modeling and autodocking results revealed that the active site of MaKGD contained a distinct binding pocket where α-ketoglutarate and thiamine diphosphate interacted with specific amino acid residues via hydrophobic interactions, hydrogen bonds and salt bridges. Furthermore, the mutagenesis study provided strong evidence supporting the importance of certain residues in the catalysis of MaKGD. These findings provide new insights into the structure-function relationships of α-ketoglutarate decarboxylases from cyanobacteria.
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Affiliation(s)
- Zhi-Min Li
- College of Chemistry and Materials, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Ziwei Hu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Suhang Chen
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiyan Yu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Liu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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6
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Kaneshiro AK, Datar PM, Marsh ENG. Negative Cooperativity in the Mechanism of Prenylated-Flavin-Dependent Ferulic Acid Decarboxylase: A Proposal for a "Two-Stroke" Decarboxylation Cycle. Biochemistry 2023; 62:53-61. [PMID: 36521056 DOI: 10.1021/acs.biochem.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ferulic acid decarboxylase (FDC) catalyzes the reversible carboxylation of various substituted phenylacrylic acids to produce the correspondingly substituted styrenes and CO2. FDC is a member of the UbiD family of enzymes that use prenylated-FMN (prFMN) to catalyze decarboxylation reactions on aromatic rings and C-C double bonds. Although a growing number of prFMN-dependent enzymes have been identified, the mechanism of the reaction remains poorly understood. Here, we present a detailed pre-steady-state kinetic analysis of the FDC-catalyzed reaction of prFMN with both styrene and phenylacrylic acid. Based on the pattern of reactivity observed, we propose a "two-stroke" kinetic model in which negative cooperativity between the two subunits of the FDC homodimer plays an important and previously unrecognized role in catalysis. In this model, catalysis is initiated at the high-affinity active site, which reacts with phenylacrylate to yield, after decarboxylation, the covalently bound styrene-prFMN cycloadduct. In the second stage of the catalytic cycle, binding of the second substrate molecule to the low-affinity active site drives a conformational switch that interconverts the high-affinity and low-affinity active sites. This switching of affinity couples the energetically unfavorable cycloelimination of styrene from the first site with the energetically favorable cycloaddition and decarboxylation of phenylacrylate at the second site. We note as a caveat that, at this point, the complexity of the FDC kinetics leaves open other mechanistic interpretations and that further experiments will be needed to more firmly establish or refute our proposal.
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7
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Gokcan H, Bedoyan JK, Isayev O. Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. J Chem Inf Model 2022; 62:3463-3475. [PMID: 35797142 DOI: 10.1021/acs.jcim.2c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. The E1 component of the mitochondrial multienzyme PDC (PDC-E1) is a symmetric dimer of heterodimers (αβ/α'β') encoded by the PDHA1 and PDHB genes, with two symmetric active sites each consisting of highly conserved phosphorylation loops A and B. PDHA1 mutations are responsible for 82-88% of cases. Greater than 85% of E1α residues with disease-causing missense mutations (DMMs) are solvent-inaccessible, with ∼30% among those involved in subunit-subunit interface contact (SSIC). We performed molecular dynamics simulations of wild-type (WT) PDC-E1 and E1 variants with E1α DMMs at R349 and W185 (residues involved in SSIC), to investigate their impact on human PDC-E1 structure. We evaluated the change in E1 structure and dynamics and examined their implications on E1 function with the specific DMMs. We found that the dynamics of phosphorylation Loop A, which is crucial for E1 biological activity, changes with DMMs that are at least about 15 Å away. Because communication is essential for PDC-E1 activity (with alternating active sites), we also investigated the possible communication network within WT PDC-E1 via centrality analysis. We observed that DMMs altered/disrupted the communication network of PDC-E1. Collectively, these results indicate allosteric effect in PDC-E1, with implications for the development of novel small-molecule therapeutics for specific recurrent E1α DMMs such as replacements of R349 responsible for ∼10% of PDC deficiency due to E1α DMMs.
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Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jirair K Bedoyan
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224, United States.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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8
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Han SW, Shin JS. Aromatic L-amino acid decarboxylases: mechanistic features and microbial applications. Appl Microbiol Biotechnol 2022; 106:4445-4458. [DOI: 10.1007/s00253-022-12028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
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9
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Datar PM, Marsh ENG. Decarboxylation of Aromatic Carboxylic Acids by the Prenylated-FMN-dependent Enzyme Phenazine-1-carboxylic Acid Decarboxylase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Sheng X, Himo F. Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations. Comput Struct Biotechnol J 2021; 19:3176-3186. [PMID: 34141138 PMCID: PMC8187880 DOI: 10.1016/j.csbj.2021.05.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/18/2022] Open
Abstract
Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity. Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value‐added chemicals by CO2 fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5‐carboxyvanillate decarboxylase, γ‐resorcylate decarboxylase, 2,3‐dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.
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Key Words
- 2,3-DHBD, 2,3‐dihydroxybenzoic acid decarboxylase
- 2,6-DHBD, 2,6‐dihydroxybenzoic acid decarboxylase
- 2-NR, 2-nitroresorcinol
- 5-CV, 5-carboxyvanillate
- 5-NV, 5-nitrovanillate
- 5caU, 5-carboxyuracil
- AHS, amidohydrolase superfamily
- Biocatalysis
- Decarboxylase
- Density functional theory
- IDCase, iso-orotate decarboxylase
- LigW, 5‐carboxyvanillate decarboxylase
- MIMS, membrane inlet mass spectrometry
- QM/MM, quantum mechanics/molecular mechanics
- Reaction mechanism
- Transition state
- γ-RS, γ-resorcylate
- γ-RSD, γ‐resorcylate decarboxylase
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Affiliation(s)
- Xiang Sheng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, and National Technology Innovation Center for Synthetic Biology, Tianjin 300308, PR China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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Aleku GA, Roberts GW, Titchiner GR, Leys D. Synthetic Enzyme-Catalyzed CO 2 Fixation Reactions. CHEMSUSCHEM 2021; 14:1781-1804. [PMID: 33631048 PMCID: PMC8252502 DOI: 10.1002/cssc.202100159] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/25/2021] [Indexed: 05/11/2023]
Abstract
In recent years, (de)carboxylases that catalyze reversible (de)carboxylation have been targeted for application as carboxylation catalysts. This has led to the development of proof-of-concept (bio)synthetic CO2 fixation routes for chemical production. However, further progress towards industrial application has been hampered by the thermodynamic constraint that accompanies fixing CO2 to organic molecules. In this Review, biocatalytic carboxylation methods are discussed with emphases on the diverse strategies devised to alleviate the inherent thermodynamic constraints and their application in synthetic CO2 -fixation cascades.
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Affiliation(s)
- Godwin A. Aleku
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCambridgeCB2 1GAUK
| | - George W. Roberts
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Gabriel R. Titchiner
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - David Leys
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
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12
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Kaneshiro AK, Koebke KJ, Zhao C, Ferguson KL, Ballou DP, Palfey BA, Ruotolo BT, Marsh ENG. Kinetic Analysis of Transient Intermediates in the Mechanism of Prenyl-Flavin-Dependent Ferulic Acid Decarboxylase. Biochemistry 2020; 60:125-134. [PMID: 33342208 DOI: 10.1021/acs.biochem.0c00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferulic acid decarboxylase catalyzes the decarboxylation of various substituted phenylacrylic acids to their corresponding styrene derivatives and CO2 using the recently discovered cofactor prenylated FMN (prFMN). The mechanism involves an unusual 1,3-dipolar cycloaddition reaction between prFMN and the substrate to generate a cycloadduct capable of undergoing decarboxylation. Using native mass spectrometry, we show the enzyme forms a stable prFMN-styrene cycloadduct that accumulates on the enzyme during turnover. Pre-steady state kinetic analysis of the reaction using ultraviolet-visible stopped-flow spectroscopy reveals a complex pattern of kinetic behavior, best described by a half-of-sites model involving negative cooperativity between the two subunits of the dimeric enzyme. For the reactive site, the cycloadduct of prFMN with phenylacylic acid is formed with a kapp of 131 s-1. This intermediate converts to the prFMN-styrene cycloadduct with a kapp of 75 s-1. Cycloelimination of the prFMN-styrene cycloadduct to generate styrene and free enzyme appears to determine kcat for the overall reaction, which is 11.3 s-1.
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13
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Sheng X, Himo F. Mechanism of 3-Methylglutaconyl CoA Decarboxylase AibA/AibB: Pericyclic Reaction versus Direct Decarboxylation. Angew Chem Int Ed Engl 2020; 59:22973-22977. [PMID: 32914510 PMCID: PMC7756340 DOI: 10.1002/anie.202008919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/08/2020] [Indexed: 12/11/2022]
Abstract
The enzyme 3-methylglutaconyl coenzyme A (CoA) decarboxylase (called AibA/AibB) catalyzes the decarboxylation of 3-methylglutaconyl CoA to generate 3,3-dimethylacrylyl-CoA, representing an important step in the biosynthesis of isovaleryl-coenzyme A in Myxococcus xanthus when the regular pathway is blocked. A novel mechanism involving a pericyclic transition state has previously been proposed for this enzyme, making AibA/AibB unique among decarboxylases. Herein, density functional calculations are used to examine the energetic feasibility of this mechanism. It is shown that the intramolecular pericyclic reaction is associated with a very high energy barrier that is similar to the barrier of the same reaction in the absence of the enzyme. Instead, the calculations show that a direct decarboxylation mechanism has feasible energy barriers that are in line with the experimental observations.
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Affiliation(s)
- Xiang Sheng
- Department of Organic ChemistryArrhenius LaboratoryStockholm UniversitySE-10691StockholmSweden
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm UniversitySE-10691StockholmSweden
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14
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Sheng X, Himo F. Mechanism of 3‐Methylglutaconyl CoA Decarboxylase AibA/AibB: Pericyclic Reaction versus Direct Decarboxylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry Arrhenius Laboratory Stockholm University SE-10691 Stockholm Sweden
| | - Fahmi Himo
- Department of Organic Chemistry Arrhenius Laboratory Stockholm University SE-10691 Stockholm Sweden
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15
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Goryanova B, Amyes TL, Richard JP. Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization. J Am Chem Soc 2019; 141:13468-13478. [PMID: 31365243 PMCID: PMC6735427 DOI: 10.1021/jacs.9b04823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Kinetic
parameters kex (s–1)
and kex/Kd (M–1 s–1) are reported
for exchange
for deuterium in D2O of the C-6 hydrogen of 5-fluororotidine
5′-monophosphate (FUMP) catalyzed by the Q215A,
Y217F, and Q215A/Y217F variants of yeast orotidine 5′-monophosphate
decarboxylase (ScOMPDC) at pD 8.1, and by the Q215A
variant at pD 7.1–9.3. The pD rate profiles for wildtype ScOMPDC and the Q215A variant are identical, except for
a 2.5 log unit downward displacement in the profile for the Q215A
variant. The Q215A, Y217F and Q215A/Y217F substitutions cause 1.3–2.0
kcal/mol larger increases in the activation barrier for wildtype ScOMPDC-catalyzed deuterium exchange compared with decarboxylation,
because of the stronger apparent side chain interaction with the transition
state for the deuterium exchange reaction. The stabilization of the
transition state for the OMPDC-catalyzed deuterium exchange reaction
of FUMP is ca. 19 kcal/mol smaller than the transition
state for decarboxylation of OMP, and ca. 8 kcal/mol
smaller than for OMPDC-catalyzed deprotonation of FUMP to form the vinyl carbanion intermediate common to OMPDC-catalyzed
reactions OMP/FOMP and UMP/FUMP. We propose
that ScOMPDC shows similar stabilizing interactions
with the common portions of decarboxylation and deprotonation transition
states that lead to formation of this vinyl carbanion intermediate,
and that there is a large ca. (19–8) = 11 kcal/mol stabilization
of the former transition state from interactions with the nascent
CO2 of product. The effects of Q215A and Y217F substitutions
on kcat/Km for decarboxylation of OMP are expressed mainly as
an increase in Km for the reactions catalyzed
by the variant enzymes, while the effects on kex/Kd for deuterium exchange are
expressed mainly as an increase in kex. This shows that the Q215 and Y217 side chains stabilize the Michaelis
complex to OMP for the decarboxylation reaction, compared
with the complex to FUMP for the deuterium exchange reaction.
These results provide strong support for the conclusion that interactions
which stabilize the transition state for ScOMPDC-catalyzed
decarboxylation at a nonpolar enzyme active site dominate over interactions
that destabilize the ground-state Michaelis complex.
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Affiliation(s)
- Bogdana Goryanova
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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16
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Claes L, Janssen M, De Vos DE. Organocatalytic Decarboxylation of Amino Acids as a Route to Bio‐based Amines and Amides. ChemCatChem 2019. [DOI: 10.1002/cctc.201900800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Laurens Claes
- Department of Microbial and Molecular Systems Centre for Membrane Separations, Adsorption, Catalysis, and Spectroscopy forSustainable Solutions (cMACS) KU Leuven Celestijnenlaan 200F box 2454 3001 Leuven Belgium
| | - Michiel Janssen
- Department of Microbial and Molecular Systems Centre for Membrane Separations, Adsorption, Catalysis, and Spectroscopy forSustainable Solutions (cMACS) KU Leuven Celestijnenlaan 200F box 2454 3001 Leuven Belgium
| | - Dirk E. De Vos
- Department of Microbial and Molecular Systems Centre for Membrane Separations, Adsorption, Catalysis, and Spectroscopy forSustainable Solutions (cMACS) KU Leuven Celestijnenlaan 200F box 2454 3001 Leuven Belgium
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17
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Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
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Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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18
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De Schouwer F, Claes L, Vandekerkhove A, Verduyckt J, De Vos DE. Protein-Rich Biomass Waste as a Resource for Future Biorefineries: State of the Art, Challenges, and Opportunities. CHEMSUSCHEM 2019; 12:1272-1303. [PMID: 30667150 DOI: 10.1002/cssc.201802418] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Protein-rich biomass provides a valuable feedstock for the chemical industry. This Review describes every process step in the value chain from protein waste to chemicals. The first part deals with the physicochemical extraction of proteins from biomass, hydrolytic degradation to peptides and amino acids, and separation of amino acid mixtures. The second part provides an overview of physical and (bio)chemical technologies for the production of polymers, commodity chemicals, pharmaceuticals, and other fine chemicals. This can be achieved by incorporation of oligopeptides into polymers, or by modification and defunctionalization of amino acids, for example, their reduction to amino alcohols, decarboxylation to amines, (cyclic) amides and nitriles, deamination to (di)carboxylic acids, and synthesis of fine chemicals and ionic liquids. Bio- and chemocatalytic approaches are compared in terms of scope, efficiency, and sustainability.
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Affiliation(s)
- Free De Schouwer
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, Celestijnenlaan 200F, post box 2461, 3001, Heverlee, Belgium
| | - Laurens Claes
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, Celestijnenlaan 200F, post box 2461, 3001, Heverlee, Belgium
| | - Annelies Vandekerkhove
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, Celestijnenlaan 200F, post box 2461, 3001, Heverlee, Belgium
| | - Jasper Verduyckt
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, Celestijnenlaan 200F, post box 2461, 3001, Heverlee, Belgium
| | - Dirk E De Vos
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, Celestijnenlaan 200F, post box 2461, 3001, Heverlee, Belgium
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19
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Human 2-Oxoglutarate Dehydrogenase and 2-Oxoadipate Dehydrogenase Both Generate Superoxide/H 2O 2 in a Side Reaction and Each Could Contribute to Oxidative Stress in Mitochondria. Neurochem Res 2019; 44:2325-2335. [PMID: 30847859 DOI: 10.1007/s11064-019-02765-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/30/2022]
Abstract
According to recent findings, the human 2-oxoglutarate dehydrogenase complex (hOGDHc) could be an important source of the reactive oxygen species in the mitochondria and could contribute to mitochondrial abnormalities associated with multiple neurodegenerative diseases, including Alzheimer's disease, Huntington disease, and Parkinson's disease. The human 2-oxoadipate dehydrogenase (hE1a) is a novel protein, which is encoded by the DHTKD1 gene. Both missence and nonsense mutations were identified in the DHTKD1 that lead to alpha-aminoadipic and alpha-oxoadipic aciduria, a metabolic disorder with a wide variety of the neurological abnormalities, and Charcot-Marie-Tooth disease type 2Q, an inherited neurological disorder affecting the peripheral nervous system. Recently, the rare pathogenic mutations in DHTKD1 and an increased H2O2 production were linked to the genetic ethiology of Eosinophilic Esophagitis (EoE), a chronic allergic inflammatory esophageal disorder. In view of the importance of hOGDHc in the tricarboxylic acid cycle (TCA cycle) and hE1a on the L-lysine, L-hydroxylysine and L-tryptophan degradation pathway in mitochondria, and to enhance our current understanding of the mechanism of superoxide/H2O2 generation by hOGDHc, and by human 2-oxoadipate dehydrogenase complex (hOADHc), this review focuses on several novel and unanticipated recent findings in vitro that emerged from the Jordan group's research. Most significantly, the hE1o and hE1a now join the hE3 as being able to generate the superoxide/H2O2 in mitochondria.
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20
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Leys D. Flavin metamorphosis: cofactor transformation through prenylation. Curr Opin Chem Biol 2018; 47:117-125. [PMID: 30326424 DOI: 10.1016/j.cbpa.2018.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/28/2022]
Abstract
Prenylated flavin (prFMN) is a recently discovered cofactor that underpins catalysis in the ubiquitous microbial UbiDX system. UbiX acts as a flavin prenyltransferase while UbiD is a prFMN-dependent reversible (de)carboxylase. The extensive modification of flavin by prenylation, and the consecutive oxidation to the prFMNiminium azomethine ylide, leads to cofactor metamorphosis. While prFMN is no longer able to perform N5-based classical flavin chemistry, it is capable of forming cycloadducts with dipolarophiles, long-lived C4a-based radical species as well as undergoing extensive light driven isomerization. An ever-expanding range of distinct prFMN forms hints at the possibility of novel prFMN driven biochemistry yet to be discovered.
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Affiliation(s)
- David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, UK.
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21
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Novak WRP, West KHJ, Kirkman LMD, Brandt GS. Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target. Acta Crystallogr F Struct Biol Commun 2018; 74:664-668. [PMID: 30279319 PMCID: PMC6168774 DOI: 10.1107/s2053230x18010610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/23/2018] [Indexed: 11/11/2022] Open
Abstract
The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69-78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate. Here, the re-refinement of a set of three structures, the apo enzyme and two versions of the product-bound form (PDB entries 2za1, 2za2 and 2za3), is reported. The improved geometry and fit of these structures to the observed electron density will enhance their utility in antimalarial drug design.
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Affiliation(s)
- Walter R. P. Novak
- Chemistry Department, Wabash College, 301 West Wabash Avenue, Crawfordsville, IN 47933, USA
| | - Korbin H. J. West
- Chemistry Department, Wabash College, 301 West Wabash Avenue, Crawfordsville, IN 47933, USA
| | - Lucy M. D. Kirkman
- Chemistry Department, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
| | - Gabriel S. Brandt
- Chemistry Department, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
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22
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Nanjo T, Kato N, Takemoto Y. Oxidative Decarboxylation Enables Chemoselective, Racemization-Free Esterification: Coupling of α-Ketoacids and Alcohols Mediated by Hypervalent Iodine(III). Org Lett 2018; 20:5766-5769. [PMID: 30168722 DOI: 10.1021/acs.orglett.8b02466] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An α-ketoacid could be converted into a reactive acylating agent by treatment with hypervalent iodine(III) species, and in so doing, we discovered a novel decarboxylative acylation of alcohols that affords a variety of esters in excellent yields. The esterification has been applied to a sterol bearing a free carboxylic acid and shows unique chemoselectivity. The procedure is racemization-free and operates under mild conditions.
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Affiliation(s)
- Takeshi Nanjo
- Graduate School of Pharmaceutical Sciences , Kyoto University , Yoshida, Sakyo-ku, Kyoto 606-8501 , Japan
| | - Natsuki Kato
- Graduate School of Pharmaceutical Sciences , Kyoto University , Yoshida, Sakyo-ku, Kyoto 606-8501 , Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences , Kyoto University , Yoshida, Sakyo-ku, Kyoto 606-8501 , Japan
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23
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Qin M, Song H, Dai X, Chan C, Chan W, Guo Z. Single‐Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate‐Dependent Catalysis in Vitamin K Biosynthesis. Chembiochem 2018; 19:1514-1522. [DOI: 10.1002/cbic.201800143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mingming Qin
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Haigang Song
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Present address: Division of Structural BiologyWellcome Trust Centre of Human GenomicsUniversity of Oxford Roosevelt Drive Oxford OX3 7BN UK
| | - Xin Dai
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Chi‐Kong Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Wan Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Zhihong Guo
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
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24
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Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002. Int J Biol Macromol 2018; 114:188-193. [PMID: 29574001 DOI: 10.1016/j.ijbiomac.2018.03.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/22/2022]
Abstract
α-Ketoglutarate decarboxylase (α-KGD), one member of α-keto acid decarboxylases, catalyzing non-oxidative decarboxylation of α-ketoglutarate to form succinic semialdehyde, was proposed to play critical role in completing tricarboxylic acid (TCA) cycle of cyanobacteria. Although the catalytic function of α-KGD from Synechococcus sp. PCC7002 was demonstrated previously, there was no detailed biochemical characterization of α-KGD from Synechococcus sp. PCC7002 yet. In this study, the gene encoding α-KGD from Synechococcus sp. PCC7002 was amplified and soluble expression of recombinant α-KGD was achieved by coexpressing with pTf16 chaperone plasmid in E. coli BL21 (DE3). Kinetic analysis showed that the activity of α-KGD was dependent on cofactors of thiamine pyrophosphate and divalent cation. Meanwhile this α-KGD was specific for α-ketoglutarate with respect to the decarboxylation activity despite of the pretty low activity of acetolactate synthase. The catalytic efficiency of α-KGD (the values of kcat and kcat/Km for α-ketoglutarate were 1.2s-1 and 6.3×103M-1s-1, respectively) might provide evidence for its physiological role in TCA cycle of Synechococcus sp. PCC7002.
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25
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Alcázar R, Tiburcio AF. Determination of Arginine and Ornithine Decarboxylase Activities in Plants. Methods Mol Biol 2018; 1694:117-122. [PMID: 29080161 DOI: 10.1007/978-1-4939-7398-9_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In plants, putrescine is synthesized directly from the decarboxylation of ornithine and/or by the alternative arginine decarboxylase pathway. The prevalence of one or the other depends on the tissue and stress conditions. In both amino acid decarboxylation reactions, the corresponding enzymes use pyridoxal phosphate (PLP) as co-factor. PLP combines with the α-amino acid to form a Schiff base, which acts as substrate in the carboxyl group removal and CO2 formation. We describe the methodology employed for the determination of ODC and ADC activities in plant tissues by detecting the release of (C14) CO2 using (C14) labelled substrates (ornithine or arginine).
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Affiliation(s)
- Rubén Alcázar
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Avda Joan XXIII 27-31, 08028, Barcelona, Spain.
| | - Antonio F Tiburcio
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Section of Plant Physiology, University of Barcelona, Avda Joan XXIII 27-31, 08028, Barcelona, Spain
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26
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Bailey SS, Payne KAP, Fisher K, Marshall SA, Cliff MJ, Spiess R, Parker DA, Rigby SEJ, Leys D. The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis. J Biol Chem 2017; 293:2272-2287. [PMID: 29259125 PMCID: PMC5818171 DOI: 10.1074/jbc.ra117.000881] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/13/2017] [Indexed: 02/03/2023] Open
Abstract
The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu–Arg–Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMNketimine and prFMNiminium, have been observed. It also has been suggested that only the prFMNiminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMNiminium to prFMNketimine is a light-dependent process that is largely independent of the Glu277–Arg173–Glu282 network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu–Arg–Glu network, as only Glu → Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMNiminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu–Arg–Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu–Arg–Glu network in both catalysis and oxidative maturation.
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Affiliation(s)
- Samuel S Bailey
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - Karl A P Payne
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - Karl Fisher
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - Stephen A Marshall
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - Matthew J Cliff
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - Reynard Spiess
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - David A Parker
- Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, Houston, Texas 77082-3101
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
| | - David Leys
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and
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27
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Slusarczyk M, Ferla S, Brancale A, McGuigan C. Synthesis and biological evaluation of 6-substituted-5-fluorouridine ProTides. Bioorg Med Chem 2017; 26:551-565. [PMID: 29277307 DOI: 10.1016/j.bmc.2017.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/29/2022]
Abstract
A new family of thirteen phosphoramidate prodrugs (ProTides) of different 6-substituted-5-fluorouridine nucleoside analogues were synthesized and evaluated as potential anticancer agents. In addition, antiviral activity against Chikungunya (CHIKV) virus was evaluated using a cytopathic effect inhibition assay. Although a carboxypeptidase Y assay supported a putative mechanism of activation of ProTides built on 5-fluorouridine with such C6-modifications, the Hint docking studies revealed a compromised substrate-activity for the Hint phosphoramidase-type enzyme that is likely responsible for phosphoramidate bioactivation through P-N bond cleavage and free nucleoside 5'-monophosphate delivery. Our observations may support and explain to some extent the poor in vitro biological activity generally demonstrated by the series of 6-substituted-5-fluorouridine phosphoramidates (ProTides) and will be of guidance for the design of novel phosphoramidate prodrugs.
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Affiliation(s)
- Magdalena Slusarczyk
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK.
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Christopher McGuigan
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
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28
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Wang X, Lei G, Wu X, Wang F, Lai C, Li Z. Expression, purification and characterization of sll1981 protein from cyanobacterium Synechocystis sp. PCC6803. Protein Expr Purif 2017; 139:21-28. [DOI: 10.1016/j.pep.2017.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/14/2017] [Accepted: 07/17/2017] [Indexed: 11/26/2022]
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29
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The UbiX-UbiD system: The biosynthesis and use of prenylated flavin (prFMN). Arch Biochem Biophys 2017; 632:209-221. [DOI: 10.1016/j.abb.2017.07.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
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30
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Ferguson KL, Eschweiler JD, Ruotolo BT, Marsh ENG. Evidence for a 1,3-Dipolar Cyclo-addition Mechanism in the Decarboxylation of Phenylacrylic Acids Catalyzed by Ferulic Acid Decarboxylase. J Am Chem Soc 2017; 139:10972-10975. [PMID: 28753302 DOI: 10.1021/jacs.7b05060] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ferulic acid decarboxylase catalyzes the decarboxylation of phenylacrylic acid using a newly identified cofactor, prenylated flavin mononucleotide (prFMN). The proposed mechanism involves the formation of a putative pentacyclic intermediate formed by a 1,3 dipolar cyclo-addition of prFMN with the α-β double bond of the substrate, which serves to activate the substrate toward decarboxylation. However, enzyme-catalyzed 1,3 dipolar cyclo-additions are unprecedented and other mechanisms are plausible. Here we describe the use of a mechanism-based inhibitor, 2-fluoro-2-nitrovinylbenzene, to trap the putative cyclo-addition intermediate, thereby demonstrating that prFMN can function as a dipole in a 1,3 dipolar cyclo-addition reaction as the initial step in a novel type of enzymatic reaction.
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Affiliation(s)
- Kyle L Ferguson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Joseph D Eschweiler
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.,Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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31
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Schäfer M, Peckelsen K, Paul M, Martens J, Oomens J, Berden G, Berkessel A, Meijer AJHM. Hydrogen Tunneling above Room Temperature Evidenced by Infrared Ion Spectroscopy. J Am Chem Soc 2017; 139:5779-5786. [PMID: 28282985 DOI: 10.1021/jacs.6b10348] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While hydrogen tunneling at elevated temperatures has, for instance, often been postulated in biochemical processes, spectroscopic proof is thus far limited to cryogenic conditions, under which thermal reactivity is negligible. We report spectroscopic evidence for H-tunneling in the gas phase at temperatures around 320-350 K observed in the isomerization reaction of a hydroxycarbene into an aldehyde. The charge-tagged carbene was generated in situ in a tandem mass spectrometer by decarboxylation of oxo[4-(trimethylammonio)phenyl]acetic acid upon collision induced dissociation. All ion structures involved are characterized by infrared ion spectroscopy and quantum chemical calculations. The charge-tagged phenylhydroxycarbene undergoes a 1,2-H-shift to the corresponding aldehyde with an half-life of about 10 s, evidenced by isomer-selective two-color (IR-IR) spectroscopy. In contrast, the deuterated (OD) carbene analogue showed much reduced 1,2-D-shift reactivity with an estimated half-life of at least 200 s under the experimental conditions, and provides clear evidence for hydrogen atom tunneling in the H-isotopologue. This is the first spectroscopic confirmation of hydrogen atom tunneling governing 1,2-H-shift reactions at noncryogenic temperatures, which is of broad significance for a range of (bio)chemical processes, including enzymatic transformations and organocatalysis.
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Affiliation(s)
- Mathias Schäfer
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstraße 4, 50939 Cologne, Germany
| | - Katrin Peckelsen
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstraße 4, 50939 Cologne, Germany
| | - Mathias Paul
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstraße 4, 50939 Cologne, Germany
| | - Jonathan Martens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Giel Berden
- Radboud University , Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Albrecht Berkessel
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstraße 4, 50939 Cologne, Germany
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32
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Baud D, Peruch O, Saaidi PL, Fossey A, Mariage A, Petit JL, Salanoubat M, Vergne-Vaxelaire C, de Berardinis V, Zaparucha A. Biocatalytic Approaches towards the Synthesis of Chiral Amino Alcohols from Lysine: Cascade Reactions Combining alpha-Keto Acid Oxygenase Hydroxylation with Pyridoxal Phosphate- Dependent Decarboxylation. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201600934] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damien Baud
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
- Department of Chemistry; University College of London; 20 Gordon Street London WC1H 0AJ U.K
| | - Olivier Peruch
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Pierre-Loïc Saaidi
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Aurélie Fossey
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Aline Mariage
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Jean-Louis Petit
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Marcel Salanoubat
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Carine Vergne-Vaxelaire
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Véronique de Berardinis
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
| | - Anne Zaparucha
- CEA, DRF, IG, Genoscope; 2 rue Gaston Crémieux 91057 Evry France
- CNRS-UMR8030 Génomique Métabolique; 2 rue Gaston Crémieux 91057 Evry France
- Université Evry Val d'Essonne; Boulevard François Mitterrand 91025 Evry France
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33
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Marshall SA, Fisher K, Ní Cheallaigh A, White MD, Payne KAP, Parker DA, Rigby SEJ, Leys D. Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. J Biol Chem 2017; 292:4623-4637. [PMID: 28057757 DOI: 10.1074/jbc.m116.762732] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/20/2016] [Indexed: 11/06/2022] Open
Abstract
The activity of the reversible decarboxylase enzyme Fdc1 is dependent on prenylated FMN (prFMN), a recently discovered cofactor. The oxidized prFMN supports a 1,3-dipolar cycloaddition mechanism that underpins reversible decarboxylation. Fdc1 is a distinct member of the UbiD family of enzymes, with the canonical UbiD catalyzing the (de)carboxylation of para-hydroxybenzoic acid-type substrates. Here we show that the Escherichia coli UbiD enzyme, which is implicated in ubiquinone biosynthesis, cannot be isolated in an active holoenzyme form despite the fact active holoFdc1 is readily obtained. Formation of holoUbiD requires reconstitution in vitro of the apoUbiD with reduced prFMN. Furthermore, although the Fdc1 apoenzyme can be readily reconstituted and activated, in vitro oxidation to the mature prFMN cofactor stalls at formation of a radical prFMN species in holoUbiD. Further oxidative maturation in vitro occurs only at alkaline pH, suggesting a proton-coupled electron transfer precedes formation of the fully oxidized prFMN. Crystal structures of holoUbiD reveal a relatively open active site potentially occluded from solvent through domain motion. The presence of a prFMN sulfite-adduct in one of the UbiD crystal structures confirms oxidative maturation does occur at ambient pH on a slow time scale. Activity could not be detected for a range of putative para-hydroxybenzoic acid substrates tested. However, the lack of an obvious hydrophobic binding pocket for the octaprenyl tail of the proposed ubiquinone precursor substrate does suggest UbiD might act on a non-prenylated precursor. Our data reveals an unexpected variation occurs in domain mobility, prFMN binding, and maturation by the UbiD enzyme family.
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Affiliation(s)
- Stephen A Marshall
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - Karl Fisher
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - Aisling Ní Cheallaigh
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - Mark D White
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - Karl A P Payne
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - D A Parker
- Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, Houston, Texas 77082-3101
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
| | - David Leys
- From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, United Kingdom and
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34
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Verduyckt J, De Vos DE. Controlled defunctionalisation of biobased organic acids. Chem Commun (Camb) 2017; 53:5682-5693. [DOI: 10.1039/c7cc01380a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Considerable progress has been made in the field of hydrogenation, decarboxylation and deamination of both citric and amino acids to valuable chemicals, which is why they should be (re)considered as valid biobased platform chemicals.
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Affiliation(s)
- Jasper Verduyckt
- Centre for Surface Chemistry and Catalysis
- Department of Microbial and Molecular Systems
- KU Leuven – University of Leuven
- Leuven Chem&Tech
- 3001 Heverlee
| | - Dirk E. De Vos
- Centre for Surface Chemistry and Catalysis
- Department of Microbial and Molecular Systems
- KU Leuven – University of Leuven
- Leuven Chem&Tech
- 3001 Heverlee
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35
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Ferguson KL, Arunrattanamook N, Marsh ENG. Mechanism of the Novel Prenylated Flavin-Containing Enzyme Ferulic Acid Decarboxylase Probed by Isotope Effects and Linear Free-Energy Relationships. Biochemistry 2016; 55:2857-63. [DOI: 10.1021/acs.biochem.6b00170] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kyle L. Ferguson
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nattapol Arunrattanamook
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department
of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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36
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Sheng X, Lind MES, Himo F. Theoretical study of the reaction mechanism of phenolic acid decarboxylase. FEBS J 2015; 282:4703-13. [PMID: 26408050 DOI: 10.1111/febs.13525] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]
Abstract
The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.
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Affiliation(s)
- Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Maria E S Lind
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
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37
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Lin F, Ferguson KL, Boyer DR, Lin XN, Marsh ENG. Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase. ACS Chem Biol 2015; 10:1137-44. [PMID: 25647642 DOI: 10.1021/cb5008103] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The decarboxylation of antimicrobial aromatic acids such as phenylacrylic acid (cinnamic acid) and ferulic acid by yeast requires two enzymes described as phenylacrylic acid decarboxylase (PAD1) and ferulic acid decarboxylase (FDC). These enzymes are of interest for various biotechnological applications, such as the production of chemical feedstocks from lignin under mild conditions. However, the specific role of each protein in catalyzing the decarboxylation reaction remains unknown. To examine this, we have overexpressed and purified both PAD1 and FDC from E. coli. We demonstrate that PAD1 is a flavin mononucleotide (FMN)-containing protein. However, it does not function as a decarboxylase. Rather, PAD1 catalyzes the formation of a novel, diffusible cofactor required by FDC for decarboxylase activity. Coexpression of FDC and PAD1 results in the production of FDC with high levels cofactor bound. Holo-FDC catalyzes the decarboxylation of phenylacrylic acid, coumaric acid and ferulic acid with apparent kcat ranging from 1.4-4.6 s(-1). The UV-visible and mass spectra of the cofactor indicate that it appears to be a novel, modified form of reduced FMN; however, its instability precluded determination of its structure. The E. coli enzymes UbiX and UbiD are related by sequence to PAD1 and FDC respectively and are involved in the decarboxylation of 4-hydroxy-3-octaprenylbenzoic acid, an intermediate in ubiquinone biosynthesis. We found that endogenous UbiX can also activate FDC. This implies that the same cofactor is required for decarboxylation of 4-hydroxy-3-polyprenylbenzoic acid by UbiD and suggests a wider role for this cofactor in metabolism.
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Affiliation(s)
- Fengming Lin
- Department of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyle L. Ferguson
- Department of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David R. Boyer
- Department of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xiaoxia Nina Lin
- Department of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department of Chemistry, ‡Department of Chemical Engineering,
and §Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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38
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Li J, Khairallah GN, Steinmetz V, Maitre P, O'Hair RAJ. Copper mediated decyano decarboxylative coupling of cyanoacetate ligands: Pesci versus Lewis acid mechanism. Dalton Trans 2015; 44:9230-40. [DOI: 10.1039/c5dt00942a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of gas-phase ion trap multistage mass spectrometry (MSn) experiments and density functional theory (DFT) calculations have been used to examine the mechanisms of the sequential decomposition reactions of copper cyanoacetate anions, [(NCCH2CO2)2Cu]−.
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Affiliation(s)
- Jiawei Li
- School of Chemistry
- University of Melbourne
- Australia
- Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
| | - George N. Khairallah
- School of Chemistry
- University of Melbourne
- Australia
- Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- UMR8000 CNRS
- Université Paris-Sud
- Orsay
- France
| | - Philippe Maitre
- Laboratoire de Chimie Physique
- UMR8000 CNRS
- Université Paris-Sud
- Orsay
- France
| | - Richard A. J. O'Hair
- School of Chemistry
- University of Melbourne
- Australia
- Bio21 Institute of Molecular Science and Biotechnology
- The University of Melbourne
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39
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Jordan F, Nemeria NS. Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 2014; 57:251-262. [PMID: 25228115 DOI: 10.1016/j.bioorg.2014.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/11/2014] [Indexed: 11/26/2022]
Abstract
Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
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40
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Abstract
ODCase is a highly proficient enzyme responsible for the decarboxylation of orotidine monophosphate to generate uridine monophosphate. ODCase has attracted early attention due to its interesting mechanism of catalysis. In order to exploit therapeutic advantages due to the inhibition of ODCase, one must have selective inhibitors of this enzyme from the pathogen, or a dysregulated molecular mechanism involving ODCase. ODCase inhibitors have potential applications as anticancer agents, antiviral agents, antimalarial agents and potentially act against other parasitic diseases. A variety of C6-substituted uridine monophosphate derivatives have shown excellent inhibition of ODCase. 6-iodouridine is a potent inhibitor of the malaria parasite, and its monophosphate form covalently inhibits ODCase. A variety of inhibitors of ODCase with potential applications as therapeutic agents are discussed in this review.
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41
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Jordan F, Nemeria NS. Experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 2005; 33:190-215. [PMID: 15888311 PMCID: PMC4189838 DOI: 10.1016/j.bioorg.2005.02.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 02/08/2005] [Accepted: 02/10/2005] [Indexed: 11/27/2022]
Abstract
Thiamin diphosphate (ThDP), the vitamin B1 coenzyme, is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/C2-carbanion of the thiazolium ring and the C2alpha-carbanion (or enamine) once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state (X-ray) methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of a several intermediates which are stable under acidic conditions, and circular dichroism detection of the 1',4'-imino tautomer of ThDP in some of the intermediates. Some of these methods also enable the investigator to determine the rate-limiting step in the complex series of steps.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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