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Zheng Y, Zhao S, Zhang M, Yang L, Wu X, Tan R, Jiang H. Progress based on a multi-omics research strategy in the biosynthesis and modernization of active ingredients of Herpetospermum pedunculosum seeds. Fitoterapia 2024; 177:106113. [PMID: 38971329 DOI: 10.1016/j.fitote.2024.106113] [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: 05/07/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Herpetospermum pedunculosum seeds also known as Herpetospermum caudigerum Wall. is the mature seed of the Herpetospermum pedunculosum(Ser.) C. B. Clarke,Cucurbitaceae. Modern pharmacological studies have shown that H. pedunculosum has hepatoprotective, anti-inflammatory, anti-gout and antibacterial pharmacological activities. The biologically active chemical components include lignin compounds such as Herpetin, Herpetetrone, Herpetoriol and so on. The natural product displays considerable skeletal diversity and structural complexity, offering significant opportunities for novel drug discovery. Based on the multi-omics research strategy and the 'gene-protein-metabolite' research framework, the biosynthetic pathway of terpenoids and lignans in H. pedunculosum has has been elucidated at multiple levels. These approaches provide comprehensive genetic information for cloning and identification of pertinent enzyme genes. Furthermore, the application of multi-omics integrative approaches provides a scientific means to elucidate entire secondary metabolic pathways. We investigated the biosynthetic pathways of lignin and terpene components in H. pedunculosum and conducted bioinformatics analysis of the crucial enzyme genes involved in the biosynthetic process using genomic and transcriptomic data. We identified candidate genes for six key enzymes in the biosynthetic pathway. This review reports on the current literature on pharmacological investigations of H. pedunculosum, proposing its potential as an antidiabetic agent. Moreover, we conclude, for the first time, the identification of key enzyme genes potentially involved in the biosynthesis of active compounds in H. pedunculosum. This review provides a scientific foundation for the discovery of novel therapeutic agents from natural sources.
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Affiliation(s)
- Yating Zheng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Siyu Zhao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Mengyu Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Lijiao Yang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Xiaoqing Wu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Rui Tan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China.
| | - Hezhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China.
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2
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Zhao H. Recent advances in enzymatic carbon-carbon bond formation. RSC Adv 2024; 14:25932-25974. [PMID: 39161440 PMCID: PMC11331486 DOI: 10.1039/d4ra03885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.
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Affiliation(s)
- Hua Zhao
- Department of Bioproducts and Biosystems Engineering, University of Minnesota St. Paul MN 55108 USA
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3
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Jeong YJ, Seo MJ, Sung BH, Kim JS, Yeom SJ. Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans. BIORESOUR BIOPROCESS 2024; 11:9. [PMID: 38647973 PMCID: PMC10992282 DOI: 10.1186/s40643-024-00727-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/03/2024] [Indexed: 04/25/2024] Open
Abstract
The bioconversion of 4-hydroxy-2-keto acid derivatives via aldol condensation of formaldehyde and pyruvate has received substantial attention as potential source of chemicals for production of amino acids, hydroxy carboxylic acids, and chiral aldehydes. We developed an environmentally friendly biocatalyst consisting of a novel thermostable class II pyruvate aldolase from Deinococcus radiodurans with maltose-binding protein (MBP-DrADL), which has specific activity of 46.3 µmol min-1 mg-1. Surprisingly, MBP-DrADL maintained over 60% of enzyme activity for 4 days at 50 to 65 °C, we used MBP-DrADL as the best candidate enzyme to produce 2-keto-4-hydroxybutyrate (2-KHB) from formaldehyde and pyruvate via aldol condensation. The optimum reaction conditions for 2-KHB production were 50 °C, pH 8.0, 5 mM Mg2+, 100 mM formaldehyde, and 200 mM pyruvate. Under these optimized conditions, MBP-DrADL produced 76.5 mM (8.94 g L-1) 2-KHB over 60 min with a volumetric productivity of 8.94 g L-1 h-1 and a specific productivity of 357.6 mg mg-enzyme-1 h-1. Furthermore, 2-KHB production was improved by continuous addition of substrates, which produced approximately 124.8 mM (14.6 g L-1) of 2-KHB over 60 min with a volumetric productivity and specific productivity of 14.6 g L-1 h-1 and 583.4 mg mg-enzyme-1 h-1, respectively. MBP-DrADL showed the highest specific productivity for 2-KHB production yet reported. Our study provides a highly efficient biocatalyst for the synthesis of 2-KHB and lays the foundation for large-scale production and application of high-value compounds from formaldehyde.
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Affiliation(s)
- Yeon-Ju Jeong
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Soo-Jin Yeom
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, Republic of Korea.
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea.
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Nishiyama R, Ojima T, Ohnishi Y, Kumaki Y, Aizawa T, Inoue A. An oxidative metabolic pathway of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU) from alginate in an alginate-assimilating bacterium. Commun Biol 2021; 4:1254. [PMID: 34728789 PMCID: PMC8563752 DOI: 10.1038/s42003-021-02786-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
Alginate-assimilating bacteria degrade alginate into an unsaturated monosaccharide, which is converted into 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU). DEHU is reduced to 2-keto-3-deoxy-D-gluconate by a DEHU-specific reductase using NAD(P)H. This is followed by pyruvate production via the Entner-Doudoroff pathway. Previously, we identified FlRed as a DEHU reductase in an alginate-assimilating bacterium, Flavobacterium sp. strain UMI-01. Here, we showed that FlRed can also catalyze the oxidation of DEHU with NAD+, producing 2-keto-3-deoxy-D-glucarate (KDGR). FlRed showed a predilection for NADH and NAD+ over NADPH and NADP+, respectively, and the Km value for NADH was approximately 2.6-fold less than that for NAD+. Furthermore, we identified two key enzymes, FlDet and FlDeg, for KDGR catabolism. FlDet was identified as an enzyme of the ribonuclease activity regulator A family, which converts KDGR to α-ketoglutaric semialdehyde (α-KGSA). FlDeg, a type II α-KGSA dehydrogenase, generated α-ketoglutaric acid by oxidizing the aldehyde group of α-KGSA using NAD(P)+. Consequently, unlike the conventional DEHU reduction pathway, DEHU can be directly converted to α-ketoglutaric acid without consuming NAD(P)H. Alginate upregulated the expression of not only FlRed and two enzymes of the DEHU-reduction pathway, but also FlDet and FlDeg. These results revealed dual pathways of DEHU metabolism involving reduction or oxidation by FlRed.
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Affiliation(s)
- Ryuji Nishiyama
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
| | - Takao Ojima
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
| | - Yuki Ohnishi
- grid.39158.360000 0001 2173 7691Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Yasuhiro Kumaki
- grid.39158.360000 0001 2173 7691Faculty of Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tomoyasu Aizawa
- grid.39158.360000 0001 2173 7691Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Akira Inoue
- grid.39158.360000 0001 2173 7691Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido Japan
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Hogancamp TN, Cory SA, Barondeau DP, Raushel FM. Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin. Biochemistry 2019; 58:3494-3503. [PMID: 31339729 DOI: 10.1021/acs.biochem.9b00549] [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
LigU from Novosphingobium sp. strain KA1 catalyzes the isomerization of (4E)-oxalomesaconate (OMA) to (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH) as part of the protocatechuate (PCA) 4,5-cleavage pathway during the degradation of lignin. The three-dimensional structure of the apo form of the wild-type enzyme was determined by X-ray crystallography, and the structure of the K66M mutant enzyme was determined in the presence of the substrate OMA. LigU is a homodimer requiring no cofactors or metal ions with a diaminopimelate epimerase structural fold, consisting of two domains with similar topologies. Each domain has a central α-helix surrounded by a β-barrel composed of antiparallel β-strands. The active site is at the cleft of the two domains. 1H nuclear magnetic resonance spectroscopy demonstrated that the enzyme catalyzes the exchange of the pro-S hydrogen at C5 of KCH with D2O during the isomerization reaction. Solvent-deuterium exchange experiments demonstrated that mutation of Lys-66 eliminated the isotope exchange at C5 and that mutation of C100 abolished exchange at C3. The positioning of these two residues in the active site of LigU is consistent with a reaction mechanism that is initiated by the abstraction of the pro-S hydrogen at C3 of OMA by the thiolate anion of Cys-100 and the donation of a proton at C5 of the proposed enolate anion intermediate by the side chain of Lys-66 to form the product KCH. The 1,3-proton transfer is suprafacial.
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Affiliation(s)
- Tessily N Hogancamp
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Seth A Cory
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David P Barondeau
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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6
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Marsden SR, Mestrom L, Bento I, Hagedoorn P, McMillan DGG, Hanefeld U. CH‐π Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stefan R. Marsden
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Luuk Mestrom
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Isabel Bento
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Peter‐Leon Hagedoorn
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
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Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess M. A 2.08 Å resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315. Protein Sci 2019; 28:794-799. [PMID: 30687968 DOI: 10.1002/pro.3582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 11/05/2022]
Abstract
Cellulases play a significant role in the degradation of complex carbohydrates. In the human gut, anaerobic bacteria are essential to the well-being of the host by producing these essential enzymes that convert plant polymers into simple sugars that can then be further metabolized by the host. Here, we report the 2.08 Å resolution structure of HLB5, a chemically verified cellulase that was identified previously from an anaerobic gut bacterium and that has no structural cellulase homologues in PDB nor possesses any conserved region typical for glycosidases. We anticipate that the information presented here will facilitate the identification of additional cellulases for which no homologues have been identified to date and enhance our understanding how these novel cellulases bind and hydrolyze their substrates.
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Affiliation(s)
- Changsoo Chang
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Jamey Mack
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
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Hogancamp TN, Mabanglo MF, Raushel FM. Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry 2018; 57:5841-5850. [PMID: 30207699 DOI: 10.1021/acs.biochem.8b00713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LigJ from the soil bacterium Sphingobium sp. SYK-6 catalyzes the reversible hydration of (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) in the degradation of lignin in the protocatechuate 4,5-cleavage pathway. LigJ is a member of the amidohydrolase superfamily and an enzyme in cog2159. The three-dimensional crystal structure of wild-type LigJ was determined in the presence [Protein Data Bank (PDB) entry 6DXQ ] and absence of the product CHA (PDB entry 6DWV ). The protein folds as a distorted (β/α)8-barrel, and a single zinc ion is bound in the active site at the C-terminal end of the central β-barrel. The product CHA is ligated to the zinc ion in the active site via the displacement of a single water molecule from the coordination shell of the metal center in LigJ. The product-bound structure reveals that the enzyme catalyzes the hydration of KCH with the formation of a chiral center at C4 with S stereochemistry. The E284Q mutant was unable to catalyze the hydration of KCH to CHA, and the structure of this mutant was determined in the presence of the substrate KCH (PDB entry 6DXS ). On the basis of the structure of LigJ in the presence of KCH and CHA, it is proposed that the side chain carboxylate of Glu-284 functions as a general base in the abstraction of a proton from a bound water molecule for nucleophilic attack at C4 of the substrate. The reaction is facilitated by the delocalization of the negative charge to the metal center via the carbonyl group at C2 of the substrate. C3 of the substrate is subsequently protonated by Glu-284 functioning as a general acid. The overall reaction occurs by the syn addition of water to the double bond between C4 and C3 of the substrate KCH. The kinetic constants for the hydration of KCH to CHA by LigJ at pH 8.0 are 25 s-1 ( kcat) and 2.6 × 106 M-1 s-1 ( kcat/ Km).
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Affiliation(s)
- Tessily N Hogancamp
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mark F Mabanglo
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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9
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Hogancamp TN, Raushel FM. Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6. Biochemistry 2018; 57:2837-2845. [DOI: 10.1021/acs.biochem.8b00295] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tessily N. Hogancamp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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10
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Razeq FM, Jurak E, Stogios PJ, Yan R, Tenkanen M, Kabel MA, Wang W, Master ER. A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:74. [PMID: 29588659 PMCID: PMC5863359 DOI: 10.1186/s13068-018-1074-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/09/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Acetylated 4-O-(methyl)glucuronoxylan (GX) is the main hemicellulose in deciduous hardwood, and comprises a β-(1→4)-linked xylopyranosyl (Xylp) backbone substituted by both acetyl groups and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Whereas enzymes that target singly acetylated Xylp or doubly 2,3-O-acetyl-Xylp have been well characterized, those targeting (2-O-MeGlcpA)3-O-acetyl-Xylp structures in glucuronoxylan have remained elusive. RESULTS An unclassified carbohydrate esterase (FjoAcXE) was identified as a protein of unknown function from a polysaccharide utilization locus (PUL) otherwise comprising carbohydrate-active enzyme families known to target xylan. FjoAcXE was shown to efficiently release acetyl groups from internal (2-O-MeGlcpA)3-O-acetyl-Xylp structures, an activity that has been sought after but lacking in known carbohydrate esterases. FjoAcXE action boosted the activity of α-glucuronidases from families GH67 and GH115 by five and nine times, respectively. Moreover, FjoAcXE activity was not only restricted to GX, but also deacetylated (3-O-Araf)2-O-acetyl-Xylp of feruloylated xylooligomers, confirming the broad substrate range of this new carbohydrate esterase. CONCLUSION This study reports the discovery and characterization of the novel carbohydrate esterase, FjoAcXE. In addition to cleaving singly acetylated Xylp, and doubly 2,3-O-acetyl-Xylp, FjoAcXE efficiently cleaves internal 3-O-acetyl-Xylp linkages in (2-O-MeGlcpA)3-O-acetyl-Xylp residues along with densely substituted and branched xylooligomers; activities that until now were missing from the arsenal of enzymes required for xylan conversion.
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Affiliation(s)
- Fakhria M. Razeq
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Edita Jurak
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
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11
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Huang GT, Yu JSK. Catalytic Roles of Histidine and Arginine in Pyruvate Class II Aldolase: A Perspective from QM/MM Metadynamics. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gou-Tao Huang
- Department of Biological Science and Technology, ‡Institute of Bioinformatics and Systems
Biology, and ¶Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan
| | - Jen-Shiang K. Yu
- Department of Biological Science and Technology, ‡Institute of Bioinformatics and Systems
Biology, and ¶Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan
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12
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Yan R, Vuong TV, Wang W, Master ER. Action of a GH115 α-glucuronidase from Amphibacillus xylanus at alkaline condition promotes release of 4-O-methylglucopyranosyluronic acid from glucuronoxylan and arabinoglucuronoxylan. Enzyme Microb Technol 2017. [PMID: 28648176 DOI: 10.1016/j.enzmictec.2017.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glucuronic acid and/or 4-O-methyl-glucuronic acid (GlcA/MeGlcA) are substituents of the main xylans present in hardwoods, conifers, and many cereal grains. α-Glucuronidases from glycoside hydrolase family GH115 can target GlcA/MeGlcA from both internally and terminally substituted regions of xylans. The current study describes the first GH115 α-glucuronidase, AxyAgu115A, from the alkaliphilic organism Amphilbacillus xylanus. AxyAgu115A was active in a wide pH range, and demonstrated better performance in alkaline condition compared to other characterized GH115 α-glucuronidases, which generally show optimal activity in acidic conditions. Specifically, its relative activity between pH 5.0 and pH 8.5 was above 80%, and was 35% of maximum at pH 10.5; although the enzyme lost 30% and 80% relative residual activity after 24-h pre-incubation at pH 9 and pH 10, respectively. AxyAgu115A was also similarly active towards glucuronoxylan as well as comparatively complex xylans such as spruce arabinoglucurunoxylan. Accommodation of complex xylans was supported by docking analyses that predicted accessibility of AxyAgu115A to branched xylo-oligosaccharides. MeGlcA release by AxyAgu115A from each xylan sample was increased by up to 30% by performing the reaction at pH 11.0 rather than pH 4.0, revealing applied benefits of AxyAgu115A for xylan recovery and processing.
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Affiliation(s)
- Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
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13
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Hernández K, Gómez A, Joglar J, Bujons J, Parella T, Clapés P. 2-Keto-3-Deoxy-l-Rhamnonate Aldolase (YfaU) as Catalyst in Aldol Additions of Pyruvate to Amino Aldehyde Derivatives. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700360] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Karel Hernández
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ariadna Gómez
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jesús Joglar
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear; Facultat de Ciències; Universitat Autònoma de Barcelona; 08193 Cerdanyola del Vallès Barcelona Spain
| | - Pere Clapés
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
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14
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Mazurkewich S, Seah SYK. Investigation into the Mode of Phosphate Activation in the 4-Hydroxy-4-Methyl-2-Oxoglutarate/4-Carboxy-4-Hydroxy-2-Oxoadipate Aldolase from Pseudomonas putida F1. PLoS One 2016; 11:e0164556. [PMID: 27741265 PMCID: PMC5065237 DOI: 10.1371/journal.pone.0164556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/03/2016] [Indexed: 11/18/2022] Open
Abstract
The 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolase is the last enzyme of both the gallate and protocatechuate 4,5-cleavage pathways which links aromatic catabolism to central cellular metabolism. The enzyme is a class II, divalent metal dependent, aldolase which is activated in the presence of inorganic phosphate (Pi), increasing its turnover rate >10-fold. This phosphate activation is unique for a class II aldolase. The aldolase pyruvate methyl proton exchange rate, a probe of the general acid half reaction, was increased 300-fold in the presence of 1 mM Pi and the rate enhancement followed saturation kinetics giving rise to a KM of 397 ± 30 μM. Docking studies revealed a potential Pi binding site close to, or overlapping with, the proposed general acid water site. Putative Pi binding residues were substituted by site-directed mutagenesis which resulted in reductions of Pi activation. Significantly, the active site residue Arg-123, known to be critical for the catalytic mechanism of the enzyme, was also implicated in supporting Pi mediated activation.
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Affiliation(s)
- Scott Mazurkewich
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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15
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Mazurkewich S, Brott AS, Kimber MS, Seah SYK. Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440. J Biol Chem 2016; 291:7669-86. [PMID: 26867578 PMCID: PMC4817193 DOI: 10.1074/jbc.m115.682054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 02/03/2016] [Indexed: 11/06/2022] Open
Abstract
The bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of ligno-biomass. The gallate degradation pathway ofPseudomonas putidaKT2440 requires a 4-carboxy-2-hydroxymuconate (CHM) hydratase (GalB), which has a 12% sequence identity to a previously identified CHM hydratase (LigJ) fromSphingomonassp. SYK-6. The structure of GalB was determined and found to be a member of the PIG-LN-acetylglucosamine deacetylase family; GalB is structurally distinct from the amidohydrolase fold of LigJ. LigJ has the same stereospecificity as GalB, providing an example of convergent evolution for catalytic conversion of a common metabolite in bacterial aromatic degradation pathways. Purified GalB contains a bound Zn(2+)cofactor; however the enzyme is capable of using Fe(2+)and Co(2+)with similar efficiency. The general base aspartate in the PIG-L deacetylases is an alanine in GalB; replacement of the alanine with aspartate decreased the GalB catalytic efficiency for CHM by 9.5 × 10(4)-fold, and the variant enzyme did not have any detectable hydrolase activity. Kinetic analyses and pH dependence studies of the wild type and variant enzymes suggested roles for Glu-48 and His-164 in the catalytic mechanism. A comparison with the PIG-L deacetylases led to a proposed mechanism for GalB wherein Glu-48 positions and activates the metal-ligated water for the hydration reaction and His-164 acts as a catalytic acid.
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Affiliation(s)
- Scott Mazurkewich
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ashley S Brott
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Stephen Y K Seah
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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16
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Jutila AA, Zignego DL, Hwang BK, Hilmer JK, Hamerly T, Minor CA, Walk ST, June RK. Candidate mediators of chondrocyte mechanotransduction via targeted and untargeted metabolomic measurements. Arch Biochem Biophys 2014; 545:116-23. [PMID: 24440608 DOI: 10.1016/j.abb.2014.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/10/2014] [Accepted: 01/11/2014] [Indexed: 11/30/2022]
Abstract
Chondrocyte mechanotransduction is the process by which cartilage cells transduce mechanical loads into biochemical and biological signals. Previous studies have identified several pathways by which chondrocytes transduce mechanical loads, yet a general understanding of which signals are activated and in what order remains elusive. This study was performed to identify candidate mediators of chondrocyte mechanotransduction using SW1353 chondrocytes embedded in physiologically stiff agarose. Dynamic compression was applied to cell-seeded constructs for 0-30min, followed immediately by whole-cell metabolite extraction. Metabolites were detected via LC-MS, and compounds of interest were identified via database searches. We found several metabolites which were statistically different between the experimental groups, and we report the detection of 5 molecules which are not found in metabolite databases of known compounds indicating potential novel molecules. Targeted studies to quantify the response of central energy metabolites to compression found a transient increase in the ratio of NADP+ to NADPH and a continual decrease in the ratio of GDP to GTP, suggesting a flux of energy into the TCA cycle. These data are consistent with the remodeling of cytoskeletal components by mechanically induced signaling, and add substantial new data to a complex picture of how chondrocytes transduce mechanical loads.
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Affiliation(s)
- Aaron A Jutila
- Department of Mechanical and Industrial Engineering, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Donald L Zignego
- Department of Mechanical and Industrial Engineering, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Bradley K Hwang
- Department of Mechanical and Industrial Engineering, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Jonathan K Hilmer
- Department of Chemistry and Biochemistry, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Timothy Hamerly
- Department of Chemistry and Biochemistry, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Cody A Minor
- Department of Mechanical and Industrial Engineering, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Seth T Walk
- Department of Immunology and Microbiology, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States
| | - Ronald K June
- Department of Cell Biology and Neuroscience, Montana State University, PO Box 173800, Bozeman, MT 59717-3800, United States.
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17
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Mazurkewich S, Wang W, Seah SYK. Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases. Biochemistry 2014; 53:542-53. [PMID: 24359411 DOI: 10.1021/bi401486g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
4-Hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolases are class II (divalent metal ion dependent) pyruvate aldolases from the meta cleavage pathways of protocatechuate and gallate. The enzyme from Pseudomonas putida F1 is structurally similar to a group of proteins termed regulators of RNase E activity A (RraA) that bind to the regulatory domain of RNase E and inhibit the ribonuclease activity in certain bacteria. Analysis of homologous RraA-like proteins from varying species revealed that they share sequence conservation within the active site of HMG/CHA aldolase. In particular, the P. putida F1 HMG/CHA aldolase has a D-X20-R-D motif, whereas a G-X20-R-D-X2-E/D motif is observed in the structures of the RraA-like proteins from Thermus thermophilus HB8 (TtRraA) and Saccharomyces cerevisiae S288C (Yer010Cp) that may support metal binding. TtRraA and Yer010Cp were found to contain HMG aldolase and oxaloacetate decarboxylase activities. Similar to the P. putida F1 HMG/CHA aldolase, both TtRraA and Yer010Cp enzymes required divalent metal ions for activity and were competitively inhibited by oxalate, a pyruvate enolate analogue, suggesting a common mechanism among the enzymes. The RraA from Escherichia coli (EcRraA) lacked detectable C-C lyase activity. Upon restoration of the G-X20-R-D-X2-E/D motif, by site-specific mutagenesis, the EcRraA variant was able to catalyze oxaloacetate decarboxylation. Sequence analysis of RraA-like gene products found across all the domains of life revealed conservation of the metal binding motifs that can likely support a divalent metal ion-dependent enzyme reaction either in addition to or in place of the putative RraA function.
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Affiliation(s)
- Scott Mazurkewich
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 5E9
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Simkhada D, Zhang H, Mori S, Williams H, Watanabe CMH. Activation of cryptic metabolite production through gene disruption: Dimethyl furan-2,4-dicarboxylate produced by Streptomyces sahachiroi. Beilstein J Org Chem 2013; 9:1768-73. [PMID: 24062841 PMCID: PMC3778384 DOI: 10.3762/bjoc.9.205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/09/2013] [Indexed: 01/23/2023] Open
Abstract
At least 65% of all small molecule drugs on the market today are natural products, however, re-isolation of previously identified and characterized compounds has become a serious impediment to the discovery of new bioactive natural products. Here, genetic knockout of an unusual non-ribosomal peptide synthetase (NRPS) C-PCP-C module, aziA2, is performed resulting in the accumulation of the secondary metabolite, dimethyl furan-2,4-dicarboxylate. The cryptic metabolite represents the first non-azinomycin related compound to be isolated and characterized from the soil bacterium, S. sahachiroi. The results from this study suggest that abolishing production of otherwise predominant natural products through genetic knockout may constitute a means to “activate” the production of novel secondary metabolites that would otherwise lay dormant within microbial genome sequences.
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Affiliation(s)
- Dinesh Simkhada
- Texas A&M University, Department of Chemistry, College Station, TX 77843, USA
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Carere J, McKenna SE, Kimber MS, Seah SYK. Characterization of an aldolase-dehydrogenase complex from the cholesterol degradation pathway of Mycobacterium tuberculosis. Biochemistry 2013; 52:3502-11. [PMID: 23614353 DOI: 10.1021/bi400351h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HsaF and HsaG are an aldolase and dehydrogenase from the cholesterol degradation pathway of Mycobacterium tuberculosis. HsaF could be heterologously expressed and purified as a soluble dimer, but the enzyme was inactive in the absence of HsaG. HsaF catalyzes the aldol cleavage of 4-hydroxy-2-oxoacids to produce pyruvate and an aldehyde. The enzyme requires divalent metals for activity, with a preference for Mn(2+). The Km values for 4-hydroxy-2-oxoacids were about 20-fold lower than observed for the aldolase homologue, BphI from the polychlorinated biphenyl degradation pathway. Acetaldehyde and propionaldehyde were channeled directly to the dehydrogenase, HsaG, without export to the bulk solvent where they were transformed to acyl-CoA in an NAD(+) and coenzyme A dependent reaction. HsaG is able to utilize aldehydes up to five carbons in length as substrates, with similar catalytic efficiencies. The HsaF-HsaG complex was crystallized and its structure was determined to a resolution of 1.93 Å. Substitution of serine 41 in HsaG with isoleucine or aspartate resulted in about 35-fold increase in Km for CoA but only 4-fold increase in Km dephospho-CoA, suggesting that this residue interacts with the 3'-ribose phosphate of CoA. A second protein annotated as a 4-hydroxy-2-oxopentanoic acid aldolase in M. tuberculosis (MhpE, Rv3469c) was expressed and purified, but was found to lack aldolase activity. Instead this enzyme was found to possess oxaloacetate decarboxylase activity, consistent with the conservation (with the 4-hydroxy-2-oxoacid aldolases) of residues involved in pyruvate enolate stabilization.
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Affiliation(s)
- Jason Carere
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
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20
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Coincon M, Wang W, Sygusch J, Seah SYK. Crystal structure of reaction intermediates in pyruvate class II aldolase: substrate cleavage, enolate stabilization, and substrate specificity. J Biol Chem 2012; 287:36208-21. [PMID: 22908224 PMCID: PMC3476288 DOI: 10.1074/jbc.m112.400705] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/16/2012] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8-2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3-C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg(70) assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg(70) stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.
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Affiliation(s)
- Mathieu Coincon
- From the Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Weijun Wang
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jurgen Sygusch
- From the Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Stephen Y. K. Seah
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Ni B, Zhang Y, Chen DW, Wang BJ, Liu SJ. Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria. Appl Microbiol Biotechnol 2012; 97:6031-41. [DOI: 10.1007/s00253-012-4402-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/25/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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22
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Baker P, Seah SYK. Rational Design of Stereoselectivity in the Class II Pyruvate Aldolase BphI. J Am Chem Soc 2011; 134:507-13. [DOI: 10.1021/ja208754r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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24
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Baker P, Carere J, Seah SYK. Probing the Molecular Basis of Substrate Specificity, Stereospecificity, and Catalysis in the Class II Pyruvate Aldolase, BphI. Biochemistry 2011; 50:3559-69. [DOI: 10.1021/bi101947g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jason Carere
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y. K. Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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