1
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Ma X, Sun C, Xian M, Guo J, Zhang R. Progress in research on the biosynthesis of 1,2,4-butanetriol by engineered microbes. World J Microbiol Biotechnol 2024; 40:68. [PMID: 38200399 DOI: 10.1007/s11274-024-03885-4] [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: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
1,2,4-butanetriol (BT) is a polyol with unique chemical properties, which has a stereocenter and can be divided into D-BT (the S-enantiomer) and L-BT (the R-enantiomer). BT can be used for the synthesis of 1,2,4-butanetriol trinitrate, 3-hydroxytetrahydrofuran, polyurethane, and other chemicals. It is widely used in the military industry, medicine, tobacco, polymer. At present, the BT is mainly synthesized by chemical methods, which are accompanied by harsh reaction conditions, poor selectivity, many by-products, and environmental pollution. Therefore, BT biosynthesis methods with the advantages of mild reaction conditions and green sustainability have become a current research hotspot. In this paper, the research status of microbial synthesis of BT was summarized from the following three aspects: (1) the biosynthetic pathway establishment for BT from xylose; (2) metabolic engineering strategies employed for improving BT production from xylose; (3) other substrates for BT production. Finally, the challenges and prospects of biosynthetic BT were discussed for future methods to improve competitiveness for industrial production.
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Affiliation(s)
- Xiangyu Ma
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jing Guo
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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2
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Alba-Posse EJ, Bruque CD, Gándola Y, Gasulla J, Nadra AD. From in-silico screening to in-vitro evaluation: Enhancing the detection of Microcystins with engineered PP1 mutant variants. J Struct Biol 2023; 215:108043. [PMID: 37935286 DOI: 10.1016/j.jsb.2023.108043] [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: 07/15/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023]
Abstract
Cyanotoxins produced during harmful algal blooms (CyanoHABs) have become a worldwide issue of concern. Microcystins (MC) are the most ubiquitous group of cyanotoxins and have known carcinogenic and hepatotoxic effects. The protein phosphatase inhibition assays (PPIAs), based on the inhibition of Protein Phosphatase 1/2A (PP1/PP2A) by MC, are one of the most cost-effective options for detecting MC. In this work, we aimed to design in-silico and evaluate in-vitro mutant variants of the PP1 protein, in order to enhance their capabilities as a MC biosensor. To this end, we performed an in-silico active site-saturated mutagenesis screening, followed by stability and docking affinity calculation with the MCLR cyanotoxin. Candidates with improved both affinity and stability were further tested in a fully flexible active-site docking. The best-scored mutations (19) were individually analysed regarding their locations and interactions. Four of them (p.D197F; p.Q249Y; p.S129W; p.D220Q) were selected for in-vitro expression and evaluation. Mutant p.D197F, exhibited a significant increment in inhibition by MCLR with respect to the WT, while showing a non-significant difference in stability nor activity. This successful PP1 inhibition enhancement suggests the potential of the p.D197F variant for practical MC detection applications.
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Affiliation(s)
- Ezequiel J Alba-Posse
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina
| | - Carlos David Bruque
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina; Unidad de Conocimiento Traslacional Hospitalaria Patagónica, Hospital de Alta Complejidad El Calafate - S.A.M.I.C., Jorge Newbery 453, CP9405 El Calafate, Santa Cruz, Argentina
| | - Yamila Gándola
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina
| | - Javier Gasulla
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina.
| | - Alejandro D Nadra
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina.
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3
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Li F, Yuan L, Lu H, Li G, Chen Y, Engqvist MKM, Kerkhoven EJ, Nielsen J. Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction. Nat Catal 2022. [DOI: 10.1038/s41929-022-00798-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractEnzyme turnover numbers (kcat) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured kcat data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput kcat prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture kcat changes for mutated enzymes and identify amino acid residues with a strong impact on kcat values. We applied this approach to predict genome-scale kcat values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted kcat values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.
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4
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Wang Q, Geng S, Wang L, Wen Z, Sun X, Huang H. Bacterial mandelic acid degradation pathway and its application in biotechnology. J Appl Microbiol 2022; 133:273-286. [PMID: 35294082 DOI: 10.1111/jam.15529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/22/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Shanshan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Lingru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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5
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Hirose J, Tsukimata R, Miyatake M, Yokoi H. Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1. Genes (Basel) 2020; 11:genes11121416. [PMID: 33260964 PMCID: PMC7760541 DOI: 10.3390/genes11121416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD+-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain.
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6
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Chakraborty J, Nemeria NS, Zhang X, Nareddy PR, Szostak M, Farinas E, Jordan F. Engineering 2‐
oxoglutarate
dehydrogenase to a 2‐oxo
aliphatic
dehydrogenase complex by optimizing consecutive components. AIChE J 2019. [DOI: 10.1002/aic.16769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joydeep Chakraborty
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark New Jersey
| | | | - Xu Zhang
- Department of Chemistry Rutgers University Newark New Jersey
| | | | - Michal Szostak
- Department of Chemistry Rutgers University Newark New Jersey
| | - Edgardo Farinas
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark New Jersey
| | - Frank Jordan
- Department of Chemistry Rutgers University Newark New Jersey
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7
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Wei Z, Wilkinson RC, Rashid GMM, Brown D, Fülöp V, Bugg TDH. Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 Involved in Degradation of Aryl C 2 Lignin Degradation Fragments. Biochemistry 2019; 58:5281-5293. [PMID: 30946572 DOI: 10.1021/acs.biochem.9b00177] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A thiamine diphosphate-dependent enzyme annotated as a benzoylformate decarboxylase is encoded by gene cluster ro02984-ro02986 in Rhodococcus jostii RHA1 previously shown to generate vanillin and 4-hydroxybenzaldehyde from lignin oxidation, and a closely related gene cluster is also found in the genome of Pseudomonas fluorescens Pf-5. Two hypotheses for possible pathways involving a thiamine diphosphate-dependent cleavage, either C-C cleavage of a ketol or diketone aryl C3 substrate or decarboxylation of an aryl C2 substrate, were investigated by expression and purification of the recombinant enzymes and expression of dehydrogenase and oxidase enzymes also found in the gene clusters. The ThDP-dependent enzymes showed no activity for cleavage of aryl C3 ketol or diketone substrates but showed activity for decarboxylation of benzoylformate and 4-hydroxybenzoylformate. A flavin-dependent oxidase encoded by gene ro02984 was found to oxidize either mandelic acid or phenylglyoxal. The crystal structure of the P. fluorescens decarboxylase enzyme was determined at 1.69 Å resolution, showing similarity to structures of known benzoylformate decarboxylase enzymes. The P. fluorescens decarboxylase enzyme showed enhanced carboligase activity between vanillin and acetaldehyde, rationalized by the presence of alanine versus serine at residue 73 in the enzyme active site, which was investigated further by site-directed mutagenesis of this residue. A hypothesis for a pathway for degradation of aryl C2 fragments arising from oxidative cleavage of phenylcoumaran and diarylpropane structures in lignin is proposed.
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Affiliation(s)
- Zhen Wei
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | | | - Goran M M Rashid
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | - David Brown
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | - Vilmos Fülöp
- School of Life Sciences , University of Warwick , Coventry CV4 7AL , U.K
| | - Timothy D H Bugg
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
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8
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Planas F, McLeish MJ, Himo F. Computational Study of Enantioselective Carboligation Catalyzed by Benzoylformate Decarboxylase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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9
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Hartman MD, Minen RI, Iglesias AA, Figueroa CM. Cofactor Specificity Switch on Peach Glucitol Dehydrogenase. Biochemistry 2019; 58:1287-1294. [PMID: 30726068 DOI: 10.1021/acs.biochem.8b01240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most oxidoreductases that use NAD+ or NADP+ to transfer electrons in redox reactions display a strong preference for the cofactor. The catalytic efficiency of peach glucitol dehydrogenase (GolDHase) for NAD+ is 1800-fold higher than that for NADP+. Herein, we combined structural and kinetic data to reverse the cofactor specificity of this enzyme. Using site-saturation mutagenesis, we obtained the D216A mutant, which uses both NAD+ and NADP+, although with different catalytic efficiencies (1000 ± 200 and 170 ± 30 M-1 s-1, respectively). This mutant was used as a template to introduce further mutations by site-directed mutagenesis, using information from the fruit fly NADP-dependent GolDHase. The D216A/V217R/D218S triple mutant displayed a 2-fold higher catalytic efficiency with NADP+ than with NAD+. Overall, our results indicate that the triple mutant has the potential to be used for metabolic and cellular engineering and for cofactor recycling in industrial processes.
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Affiliation(s)
- Matías D Hartman
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB , 3000 Santa Fe , Argentina
| | - Romina I Minen
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB , 3000 Santa Fe , Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB , 3000 Santa Fe , Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB , 3000 Santa Fe , Argentina
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10
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Mohammadi Nargesi B, Sprenger GA, Youn JW. Metabolic Engineering of Escherichia coli for para-Amino-Phenylethanol and para-Amino-Phenylacetic Acid Biosynthesis. Front Bioeng Biotechnol 2019; 6:201. [PMID: 30662895 PMCID: PMC6328984 DOI: 10.3389/fbioe.2018.00201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/10/2018] [Indexed: 11/24/2022] Open
Abstract
Aromatic amines are an important class of chemicals which are used as building blocks for the synthesis of polymers and pharmaceuticals. In this study we establish a de novo pathway for the biosynthesis of the aromatic amines para-amino-phenylethanol (PAPE) and para-amino-phenylacetic acid (4-APA) in Escherichia coli. We combined a synthetic para-amino-l-phenylalanine pathway with the fungal Ehrlich pathway. Therefore, we overexpressed the heterologous genes encoding 4-amino-4-deoxychorismate synthase (pabAB from Corynebacterium glutamicum), 4-amino-4-deoxychorismate mutase and 4-amino-4-deoxyprephenate dehydrogenase (papB and papC from Streptomyces venezuelae) and ThDP-dependent keto-acid decarboxylase (aro10 from Saccharomyces cerevisiae) in E. coli. The resulting para-amino-phenylacetaldehyde either was reduced to PAPE or oxidized to 4-APA. The wild type strain E. coli LJ110 with a plasmid carrying these four genes produced (in shake flask cultures) 11 ± 1.5 mg l−1 of PAPE from glucose (4.5 g l−1). By the additional cloning and expression of feaB (phenylacetaldehyde dehydrogenase from E. coli) 36 ± 5 mg l−1 of 4-APA were obtained from 4.5 g l−1 glucose. Competing reactions, such as the genes for aminotransferases (aspC and tyrB) or for biosynthesis of L-phenylalanine and L-tyrosine (pheA, tyrA) and for the regulator TyrR were removed. Additionally, the E. coli genes aroFBL were cloned and expressed from a second plasmid. The best producer strains of E. coli showed improved formation of PAPE and 4-APA, respectively. Plasmid-borne expression of an aldehyde reductase (yahK from E. coli) gave best values for PAPE production, whereas feaB-overexpression led to best values for 4-APA. In fed-batch cultivation, the best producer strains achieved 2.5 ± 0.15 g l−1 of PAPE from glucose (11% C mol mol-1 glucose) and 3.4 ± 0.3 g l−1 of 4-APA (17% C mol mol−1 glucose), respectively which are the highest values for recombinant strains reported so far.
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11
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Tripathi R, Noetzel J, Marx D. Exposing catalytic versatility of GTPases: taking reaction detours in mutants of hGBP1 enzyme without additional energetic cost. Phys Chem Chem Phys 2019; 21:859-867. [DOI: 10.1039/c8cp06343e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Our study reveals that the replacement of catalytically competent residues by the inert amino acid alanine, S73A and E99A, in hGBP1 opens a plethora of molecularly different reaction pathways featuring very similar energy barriers as the wild type.
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Affiliation(s)
- Ravi Tripathi
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Jan Noetzel
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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12
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Planas F, Sheng X, McLeish MJ, Himo F. A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism. Front Chem 2018; 6:205. [PMID: 29998094 PMCID: PMC6028569 DOI: 10.3389/fchem.2018.00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/18/2018] [Indexed: 01/27/2023] Open
Abstract
Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.
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Affiliation(s)
- Ferran Planas
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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13
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Wechsler C, Meyer D, Loschonsky S, Funk LM, Neumann P, Ficner R, Brodhun F, Müller M, Tittmann K. Tuning and Switching Enantioselectivity of Asymmetric Carboligation in an Enzyme through Mutational Analysis of a Single Hot Spot. Chembiochem 2015; 16:2580-4. [DOI: 10.1002/cbic.201500529] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Cindy Wechsler
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Danilo Meyer
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Sabrina Loschonsky
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Lisa-Marie Funk
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Piotr Neumann
- Abt. Molekulare Strukturbiologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Ralf Ficner
- Abt. Molekulare Strukturbiologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Florian Brodhun
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Kai Tittmann
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
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14
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Andrews FH, Horton JD, Shin D, Yoon HJ, Logsdon MG, Malik AM, Rogers MP, Kneen MM, Suh SW, McLeish MJ. The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1001-9. [DOI: 10.1016/j.bbapap.2015.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/05/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
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15
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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: 20] [Impact Index Per Article: 2.0] [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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Andrews FH, Rogers MP, Paul LN, McLeish MJ. Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer. Biochemistry 2014; 53:4358-67. [PMID: 24956165 PMCID: PMC4215898 DOI: 10.1021/bi500081r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The X-ray structure of benzoylformate
decarboxylase (BFDC) from Pseudomonas putida ATCC
12633 shows it to be a tetramer.
This was believed to be typical of all thiamin diphosphate-dependent
decarboxylases until recently when the structure of KdcA, a branched-chain
2-keto acid decarboxylase from Lactococcus lactis, showed it to be a homodimer. This lent credence to earlier unfolding
experiments on pyruvate decarboxylase from Saccharomyces cerevisiae that indicated that it might be active as a dimer. To investigate
this possibility in BFDC, we sought to shift the equilibrium toward
dimer formation. Point mutations were made in the noncatalytic monomer–monomer
interfaces, but these had a minimal effect on both tetramer formation
and catalytic activity. Subsequently, the R141E/Y288A/A306F variant
was shown by analytical ultracentrifugation to be partially dimeric.
It was also found to be catalytically inactive. Further experiments
revealed that just two mutations, R141E and A306F, were sufficient
to markedly alter the dimer–tetramer equilibrium and to provide
an ∼450-fold decrease in kcat.
Equilibrium denaturation studies suggested that the residual activity
was possibly due to the presence of residual tetramer. The structures
of the R141E and A306F variants, determined to <1.5 Å resolution,
hinted that disruption of the monomer interfaces will be accompanied
by movement of a loop containing Leu109 and Leu110. As these residues
contribute to the hydrophobicity of the active site and the correct
positioning of the substrate, it seems that tetramer formation may
well be critical to the catalytic activity of BFDC.
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Affiliation(s)
- Forest H Andrews
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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Andrews FH, McLeish MJ. Using site-saturation mutagenesis to explore mechanism and substrate specificity in thiamin diphosphate-dependent enzymes. FEBS J 2013; 280:6395-411. [DOI: 10.1111/febs.12459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Forest H. Andrews
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; IN USA
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; IN USA
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Jordan F, Patel H. Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples. ACS Catal 2013; 3:1601-1617. [PMID: 23914308 DOI: 10.1021/cs400272x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This review is focused on three types of enzymes decarboxylating very different substrates: (1) Thiamin diphosphate (ThDP)-dependent enzymes reacting with 2-oxo acids; (2) Pyridoxal phosphate (PLP)-dependent enzymes reacting with α-amino acids; and (3) An enzyme with no known co-factors, orotidine 5'-monophosphate decarboxylase (OMPDC). While the first two classes have been much studied for many years, during the past decade studies of both classes have revealed novel mechanistic insight challenging accepted understanding. The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 1017-fold rate acceleration in the absence of cofactors or even metal ions. A comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences. The field of decarboxylases remains an interesting and challenging one for the mechanistic enzymologist notwithstanding the large amount of information already available.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
| | - Hetalben Patel
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
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Phelan RM, Townsend CA. Mechanistic insights into the bifunctional non-heme iron oxygenase carbapenem synthase by active site saturation mutagenesis. J Am Chem Soc 2013; 135:7496-502. [PMID: 23611403 PMCID: PMC3683866 DOI: 10.1021/ja311078s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The carbapenem class of β-lactam antibiotics is known for its remarkable potency, antibacterial spectrum, and resistance to β-lactamase-mediated inactivation. While the biosynthesis of structurally "complex" carbapenems, such as thienamycin, share initial biochemical steps with carbapenem-3-carboxylate ("simple" carbapenem), the requisite inversion at C5 and formation of the characteristic α,β-unsaturated carboxylate are different in origin between the two groups. Here, we consider carbapenem synthase, a mechanistically distinct bifunctional non-heme iron α-ketoglutarate-dependent enzyme responsible for the terminal reactions, C5 epimerization and desaturation, in simple carbapenem production. Interestingly, this enzyme accepts two stereoisomeric substrates and transforms each to a common active antibiotic. Owing both to enzyme and product instability, resorting to saturation mutagenesis of active site and selected second-sphere residues gave clearly differing profiles of CarC tolerance to structural modification. Guided by a crystal structure and the mutational data, in silico docking was used to suggest the positioning of each disastereomeric substrate in the active site. The two orientations relative to the reactive iron-oxo center are manifest in the two distinct reactions, C5-epimerization and C2/3-desaturation. These observations favor a two-step reaction scheme involving two complete oxidative cycles as opposed to a single catalytic cycle in which an active site tyrosine, Tyr67, after hydrogen donation to achieve bicyclic ring inversion, is further hypothesized to serve as a radical carrier.
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Affiliation(s)
- Ryan M. Phelan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
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Andrews FH, Tom AR, Gunderman PR, Novak WRP, McLeish MJ. A Bulky Hydrophobic Residue Is Not Required To Maintain the V-Conformation of Enzyme-Bound Thiamin Diphosphate. Biochemistry 2013; 52:3028-30. [DOI: 10.1021/bi400368j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Forest H. Andrews
- Department of Chemistry and
Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Alan R. Tom
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Peter R. Gunderman
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Walter R. P. Novak
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Michael J. McLeish
- Department of Chemistry and
Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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Klvaňa M, Murphy DL, Jeřábek P, Goodman MF, Warshel A, Sweasy JB, Florián J. Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment. Biochemistry 2012; 51:8829-43. [PMID: 23013478 DOI: 10.1021/bi300783t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We carried out free-energy calculations and transient kinetic experiments for the insertion of the right (dC) and wrong (dA) nucleotides by wild-type (WT) and six mutant variants of human DNA polymerase β (Pol β). Since the mutated residues in the point mutants, I174S, I260Q, M282L, H285D, E288K, and K289M, were not located in the Pol β catalytic site, we assumed that the WT and its point mutants share the same dianionic phosphorane transition-state structure of the triphosphate moiety of deoxyribonucleotide 5'-triphosphate (dNTP) substrate. On the basis of this assumption, we have formulated a thermodynamic cycle for calculating relative dNTP insertion efficiencies, Ω = (k(pol)/K(D))(mut)/(k(pol)/K(D))(WT) using free-energy perturbation (FEP) and linear interaction energy (LIE) methods. Kinetic studies on five of the mutants have been published previously using different experimental conditions, e.g., primer-template sequences. We have performed a presteady kinetic analysis for the six mutants for comparison with wild-type Pol β using the same conditions, including the same primer/template DNA sequence proximal to the dNTP insertion site used for X-ray crystallographic studies. This consistent set of kinetic and structural data allowed us to eliminate the DNA sequence from the list of factors that can adversely affect calculated Ω values. The calculations using the FEP free energies scaled by 0.5 yielded 0.9 and 1.1 standard deviations from the experimental log Ω values for the insertion of the right and wrong dNTP, respectively. We examined a hybrid FEP/LIE method in which the FEP van der Waals term for the interaction of the mutated amino acid residue with its surrounding environment was replaced by the corresponding van der Waals term calculated using the LIE method, resulting in improved 0.4 and 1.0 standard deviations from the experimental log Ω values. These scaled FEP and FEP/LIE methods were also used to predict log Ω for R283A and R283L Pol β mutants.
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Affiliation(s)
- Martin Klvaňa
- Department of Chemistry, Loyola University, Chicago, Illinois 60626, United States
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Random mutagenesis MAPPIT analysis identifies binding sites for Vif and Gag in both cytidine deaminase domains of Apobec3G. PLoS One 2012; 7:e44143. [PMID: 22970171 PMCID: PMC3438196 DOI: 10.1371/journal.pone.0044143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 08/01/2012] [Indexed: 11/19/2022] Open
Abstract
The mammalian two-hybrid system MAPPIT allows the detection of protein-protein interactions in intact human cells. We developed a random mutagenesis screening strategy based on MAPPIT to detect mutations that disrupt the interaction of one protein with multiple protein interactors simultaneously. The strategy was used to detect residues of the human cytidine deaminase Apobec3G that are important for its homodimerization and its interaction with the HIV-1 Gag and Vif proteins. The strategy is able to identify the previously described head-to-head homodimerization interface in the N-terminal domain of Apobec3G. Our analysis further detects two new potential interaction surfaces in the N-and C-terminal domain of Apobec3G for interaction with Vif and Gag or for Apobec3G dimerization.
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23
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Pompeu YA, Sullivan B, Walton AZ, Stewart JD. Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200213] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Shim DJ, Nemeria NS, Balakrishnan A, Patel H, Song J, Wang J, Jordan F, Farinas ET. Assignment of function to histidines 260 and 298 by engineering the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase complex; substitutions that lead to acceptance of substrates lacking the 5-carboxyl group. Biochemistry 2011; 50:7705-9. [PMID: 21809826 DOI: 10.1021/bi200936n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first component (E1o) of the Escherichia coli 2-oxoglutarate dehydrogenase complex (OGDHc) was engineered to accept substrates lacking the 5-carboxylate group by subjecting H260 and H298 to saturation mutagenesis. Apparently, H260 is required for substrate recognition, but H298 could be replaced with hydrophobic residues of similar molecular volume. To interrogate whether the second component would allow synthesis of acyl-coenzyme A derivatives, hybrid complexes consisting of recombinant components of OGDHc (o) and pyruvate dehydrogenase (p) enzymes were constructed, suggesting that a different component is the "gatekeeper" for specificity for these two multienzyme complexes in bacteria, E1p for pyruvate but E2o for 2-oxoglutarate.
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Affiliation(s)
- Da Jeong Shim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, University Heights, Newark, New Jersey 07102, United States
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Reetz MT. Gerichtete Evolution stereoselektiver Enzyme: Eine ergiebige Katalysator‐Quelle für asymmetrische Reaktionen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000826] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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Reetz MT. Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Ed Engl 2010; 50:138-74. [DOI: 10.1002/anie.201000826] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study. BMC Bioinformatics 2009; 10 Suppl 12:S3. [PMID: 19828079 PMCID: PMC2762068 DOI: 10.1186/1471-2105-10-s12-s3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background The design of mutants in protein functional regions, such as the ligand binding sites, is a powerful approach to recognize the determinants of specific protein activities in cellular pathways. For an exhaustive analysis of selected positions of protein structure large scale mutagenesis techniques are often employed, with laborious and time consuming experimental set-up. 'In silico' mutagenesis and screening simulation represents a valid alternative to laboratory methods to drive the 'in vivo' testing toward more focused objectives. Results We present here a high performance computational procedure for large-scale mutant modelling and subsequent evaluation of the effect on ligand binding affinity. The mutagenesis was performed with a 'saturation' approach, where all 20 natural amino acids were tested in positions involved in ligand binding sites. Each modelled mutant was subjected to molecular docking simulation and stability evaluation. The simulated protein-ligand complexes were screened for their impairment of binding ability based on change of calculated Ki compared to the wild-type. An example of application to the Endothelial Protein C Receptor residues involved in lipid binding is reported. Conclusion The computational pipeline presented in this work is a useful tool for the design of structurally stable mutants with altered affinity for ligand binding, considerably reducing the number of mutants to be experimentally tested. The saturation mutagenesis procedure does not require previous knowledge of functional role of the residues involved and allows extensive exploration of all possible substitutions and their pairwise combinations. Mutants are screened by docking simulation and stability evaluation followed by a rationally driven selection of those presenting the required characteristics. The method can be employed in molecular recognition studies and as a preliminary approach to select models for experimental testing.
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Topal KG, Atilgan C, Demir AS, Aviyente V. Understanding the mode of action of ThDP in benzoylformate decarboxylase. Biopolymers 2009; 93:32-46. [PMID: 19688812 DOI: 10.1002/bip.21291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26, and H281 are catalytically active amino acids. H281 functions as a base to accept H(donor) in the first nucleophilic attack and as an acid in the second, to donate the proton back to O(acceptor). S26 assists H281 in deprotonation of the donor aldehyde and protonation of the acceptor aldehyde. In both the first and second nucleophilic attacks, H70 interacts with O(aldehyde) and aligns it toward the nucleophilic center. H70 has been found to have an electrostatic effect on the approaching aldehyde whose absence would block the initiation of the reaction. The reactivity difference between benzaldehyde (BA) and acetaldehyde (AA) is mainly explained by the steric interactions of the acceptor aldehyde with the surrounding amino acids in the active center of the enzyme.
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Yep A, McLeish MJ. Engineering the Substrate Binding Site of Benzoylformate Decarboxylase. Biochemistry 2009; 48:8387-95. [DOI: 10.1021/bi9008402] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alejandra Yep
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109
| | - Michael J. McLeish
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry and Chemical Biology, IUPUI, Indianapolis, Indiana 46202
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Bruning M, Berheide M, Meyer D, Golbik R, Bartunik H, Liese A, Tittmann K. Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate. Biochemistry 2009; 48:3258-68. [PMID: 19182954 DOI: 10.1021/bi801957d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiamin diphosphate- (ThDP-) dependent enzyme benzoylformate decarboxylase (BFDC) catalyzes the nonoxidative decarboxylation of benzoylformic acid to benzaldehyde and carbon dioxide. To date, no structural information for a cofactor-bound reaction intermediate in BFDC is available. For kinetic analysis, a chromophoric substrate analogue was employed that produces various absorbing intermediates during turnover but is a poor substrate with a 10(4)-fold compromised kcat. Here, we have analyzed the steady-state distribution of native intermediates by a combined chemical quench/1H NMR spectroscopic approach and estimated the net rate constants of elementary catalytic steps. At substrate saturation, carbonyl addition of the substrate to the cofactor (k' approximately 500 s-1 at 30 degrees C) and elimination of benzaldehyde (k' approximately 2.400 s-1) were found to be partially rate-determining for catalysis, whereas decarboxylation of the transient 2-mandelyl-ThDP intermediate is 1 order of magnitude faster with k' approximately 16.000 s-1, the largest rate constant of decarboxylation in any thiamin enzyme characterized so far. The X-ray structure of a predecarboxylation intermediate analogue was determined to 1.6 A after cocrystallization of BFDC from Pseudomonas putida with benzoylphosphonic acid methyl ester. In contrast to the free acid, for which irreversible phosphorylation of active center Ser26 was reported, the methyl ester forms a covalent adduct with ThDP with a similar configuration at C2alpha as observed for other thiamin enzymes. The C2-C2alpha bond of the intermediate analogue is out of plane by 7degrees, indicating strain. The phosphonate part of the adduct forms hydrogen bonds with Ser26 and His281, and the 1-OH group is held in place by interactions with His70 and the 4'-amino group of ThDP. The phenyl ring accommodates in a hydrophobic pocket formed by Phe464, Phe397, Leu109, and Leu403. A comparison with the previously determined structure of BFDC in noncovalent complex with the inhibitor (R)-mandelate suggests a least motion mechanism. Binding of benzoylphosphonic acid methyl ester to BFDC was further characterized by CD spectroscopy and stopped-flow kinetics, indicating a two-step binding mechanism with a 200-fold slower carbonyl addition to ThDP than determined for benzoylformic acid, in line with the observed slight structural reorganization of Phe464 due to steric clashes with the phosphonate moiety.
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Affiliation(s)
- Marc Bruning
- Institute of Technical Biocatalysis, Hamburg UniVersity of Technology, Denickestrasse 15, D-21073 Hamburg, Germany
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Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry 2009; 48:3247-57. [PMID: 19320438 DOI: 10.1021/bi801950k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
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Affiliation(s)
- Gabriel S Brandt
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
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Nemeria NS, Chakraborty S, Balakrishnan A, Jordan F. Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps. FEBS J 2009; 276:2432-46. [PMID: 19476485 DOI: 10.1111/j.1742-4658.2009.06964.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We summarize the currently available information regarding the state of ionization and tautomerization of the 4'-aminopyrimidine ring of the thiamine diphosphate on enzymes requiring this coenzyme. This coenzyme forms a series of covalent intermediates with its substrates as an electrophilic catalyst, and the coenzyme itself also carries out intramolecular proton transfers, which is virtually unprecedented in coenzyme chemistry. An understanding of the state of ionization and tautomerization of the 4'-aminopyrimidine ring in each of these intermediates provides important details about proton movements during catalysis. CD spectroscopy, both steady-state and time-resolved, has proved crucial for obtaining this information because no other experimental method has provided such atomic detail so far.
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Affiliation(s)
- Natalia S Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, USA.
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Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry 2009; 48:981-94. [PMID: 19140682 DOI: 10.1021/bi801810h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.
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Affiliation(s)
- Sumit Chakraborty
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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Kluger R, Rathgeber S. Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation. FEBS J 2008; 275:6089-100. [DOI: 10.1111/j.1742-4658.2008.06739.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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: 45] [Impact Index Per Article: 2.4] [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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