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Esteve F, Rieu T, Lehn JM. Key structural features to favour imines over hydrates in water: pyridoxal phosphate as a muse. Chem Sci 2024; 15:10408-10415. [PMID: 38994419 PMCID: PMC11234862 DOI: 10.1039/d4sc02206h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
Imination reactions in water represent a challenge not only because of the high propensity of imines to be hydrolysed but also as a result of the competing hydrate formation through H2O addition to the aldehyde. In the present work we report a successful approach that allows for favouring imitation reactions while silencing hydrate formation. Such remarkable reactivity and selectivity can be attained by fine-tuning the electronic and steric structural features of the ortho-substituents of the carbonyl groups. It resulted from studying the structure-reactivity relationships in a series of condensation reactions between different amines and aldehydes, comparing the results to the ones obtained in the presence of the biologically-relevant pyridoxal phosphate (PLP). The key role of negatively-charged and sterically-crowding units (i.e., sulfonate groups) in disfavouring hydrate formation was corroborated by DFT and steric-hindrance calculations. Furthermore, the best-performing aldehyde leads to higher imine yields, selectivity and stability than those of PLP itself, allowing for the inhibition of a PLP-dependent enzyme (transaminase) through dynamic aldimine exchange. These results will increase the applicability of imine-based dynamic covalent chemistry (DCvC) under physiological conditions and will pave the way for the design of new carbonyl derivatives that might be used in the dynamic modification of biomolecules.
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Affiliation(s)
- Ferran Esteve
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
| | - Tanguy Rieu
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
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2
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Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
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3
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Wei L, Liu L, Gong W. Structure of mycobacterial ergothioneine-biosynthesis C-S lyase EgtE. J Biol Chem 2024; 300:105539. [PMID: 38072054 PMCID: PMC10805701 DOI: 10.1016/j.jbc.2023.105539] [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: 03/29/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 01/02/2024] Open
Abstract
L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5'-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present the crystallographic structure of the ergothioneine-biosynthesis C-S lyase EgtE from Mycobacterium smegmatis (MsEgtE) represents the first published structure of ergothioneine-biosynthesis C-S lyases in bacteria and shows the effects of active site residues on the enzymatic reaction. The MsEgtE and the previously reported ergothioneine-biosynthesis C-S lyase Egt2 from Neurospora crassa (NcEgt2) fold similarly. However, discrepancies arise in terms of substrate recognition, as observed through sequence and structure comparison of MsEgtE and NcEgt2. The structural-based sequence alignment of the ergothioneine-biosynthesis C-S lyase from fungi and bacteria shows clear distinctions among the recognized substrate residues, but Arg348 is critical and an extremely conserved residue for substrate recognition. The α14 helix is exclusively found in the bacteria EgtE, which represent the most significant difference between bacteria EgtE and fungi Egt2, possibly resulting from the convergent evolution of bacteria and fungi.
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Affiliation(s)
- Lili Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Weimin Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
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4
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Abstract
ConspectusOne of the fundamental goals of chemists is to develop highly efficient methods for producing optically active compounds, given their wide range of applications in chemistry, pharmaceutical industry, chemical biology, and material science. Biomimetic asymmetric catalysis, which imitates the structures and functions of enzymes, has emerged as an extremely attractive strategy for producing chiral compounds. This field has drawn tremendous research interest and has led to various protocols for constructing complex molecular scaffolds. The Vitamin B6 family, including pyridoxal, pyridoxamine, pyridoxine, and the corresponding phosphorylated derivatives, serves as the cofactors to catalyze more than 200 enzymatic functions, accounting for ∼4% of all enzyme activities. Although significant progress has been made in simulating the biological roles of vitamin B6 during the past several decades, its extraordinary catalytic power has not yet been successfully applied into asymmetric synthesis. In recent years, our group has been devoted to developing vitamin B6-based biomimetic asymmetric catalysis using chiral pyridoxals/pyridoxamines as catalysts. We are particularly interested in mimicking the processes of enzymatic transamination and biological aldol reaction of glycine, respectively, developing asymmetric biomimetic transamination and carbonyl catalysis enabled α-C-H transformation of primary amines. Using a chiral α,α-diarylprolinol-derived pyridoxal as the catalyst, we reported the first chiral pyridoxal catalyzed asymmetric transamination of α-keto acids in 2015. A significant breakthrough in biomimetic transamination was achieved by using an axially chiral biaryl pyridoxamine catalyst that bears a lateral amine side arm. The amine side arm acts as an intramolecular base, accelerating the transamination and proving highly effective for transamination of α-keto acids and α-keto amides. In addition, we discovered the catalytic power of chiral pyridoxals as carbonyl catalysts for asymmetric biomimetic Mannich/aldol reactions of glycinates. These chiral pyridoxals also enabled more α-C-H conversions of glycinates, such as asymmetric 1,4-addition toward α,β-unsaturated esters and asymmetric α-allylation with Morita-Baylis-Hillman acetates. Moreover, carbonyl catalysis can be further applied to highly challenging primary amines with inert α-C-H bonds, such as propargylamines and benzylamines, which represents a powerful strategy for direct asymmetric α-C-H functionalization of various primary amines without protection of the NH2 group. These biomimetic/bioinspired transformations provide efficient new protocols for the synthesis of chiral amines. Herein, we summarize our recent efforts on the development of the vitamin B6-based biomimetic asymmetric catalysis.
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Affiliation(s)
- Xiao Xiao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Baoguo Zhao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 200234, P. R. China
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5
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de Dios SMR, Hass JL, Graham DL, Kumar N, Antony AE, Morton MD, Berkowitz DB. Information-Rich, Dual-Function 13C/ 2H-Isotopic Crosstalk NMR Assay for Human Serine Racemase (hSR) Provides a PLP-Enzyme "Partitioning Fingerprint" and Reveals Disparate Chemotypes for hSR Inhibition. J Am Chem Soc 2023; 145:3158-3174. [PMID: 36696670 PMCID: PMC11103274 DOI: 10.1021/jacs.2c12774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The first dual-function assay for human serine racemase (hSR), the only bona fide racemase in human biology, is reported. The hSR racemization function is essential for neuronal signaling, as the product, d-serine (d-Ser), is a potent N-methyl d-aspartate (NMDA) coagonist, important for learning and memory, with dysfunctional d-Ser-signaling being observed in some neuronal disorders. The second hSR function is β-elimination and gives pyruvate; this activity is elevated in colorectal cancer. This new NMR-based assay allows one to monitor both α-proton-exchange chemistry and β-elimination using only the native l-Ser substrate and hSR and is the most sensitive such assay. The assay judiciously employs segregated dual 13C-labeling and 13C/2H crosstalk, exploiting both the splitting and shielding effects of deuterium. The assay is deployed to screen a 1020-compound library and identifies an indolo-chroman-2,4-dione inhibitor family that displays allosteric site binding behavior (noncompetitive inhibition vs l-Ser substrate; competitive inhibition vs adenosine 5'-triphosphate (ATP)). This assay also reveals important mechanistic information for hSR; namely, that H/D exchange is ∼13-fold faster than racemization, implying that K56 protonates the carbanionic intermediate on the si-face much faster than does S84 on the re-face. Moreover, the 13C NMR peak pattern seen is suggestive of internal return, pointing to K56 as the likely enamine-protonating residue for β-elimination. The 13C/2H-isotopic crosstalk assay has also been applied to the enzyme tryptophan synthase and reveals a dramatically different partition ratio in this active site (β-replacement: si-face protonation ∼6:1 vs β-elimination: si-face protonation ∼1:3.6 for hSR), highlighting the value of this approach for fingerprinting the pyridoxal phosphate (PLP) enzyme mechanism.
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Affiliation(s)
| | | | | | - Nivesh Kumar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Aina E. Antony
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Martha D. Morton
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
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6
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Ngo HPT, Nguyen DQ, Park H, Park YS, Kwak K, Kim T, Lee JH, Cho KS, Kang LW. Conformational change of organic cofactor PLP is essential for catalysis in PLP-dependent enzymes. BMB Rep 2022; 55:439-446. [PMID: 36104257 PMCID: PMC9537024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 03/08/2024] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are ubiquitous, catalyzing various biochemical reactions of approximately 4% of all classified enzymatic activities. They transform amines and amino acids into important metabolites or signaling molecules and are important drug targets in many diseases. In the crystal structures of PLP-dependent enzymes, organic cofactor PLP showed diverse conformations depending on the catalytic step. The conformational change of PLP is essential in the catalytic mechanism. In the study, we review the sophisticated catalytic mechanism of PLP, especially in transaldimination reactions. Most drugs targeting PLP-dependent enzymes make a covalent bond to PLP with the transaldimination reaction. A detailed understanding of organic cofactor PLP will help develop a new drug against PLP-dependent enzymes. [BMB Reports 2022; 55(9): 439-446].
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Affiliation(s)
- Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Kiwoong Kwak
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Taejoon Kim
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Jang Ho Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
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7
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Pfanzelt M, Maher TE, Absmeier RM, Schwarz M, Sieber SA. Tailored Pyridoxal Probes Unravel Novel Cofactor-Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202117724. [PMID: 35199904 PMCID: PMC9321722 DOI: 10.1002/anie.202117724] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 01/21/2023]
Abstract
Unprecedented bacterial targets are urgently needed to overcome the resistance crisis. Herein we systematically mine pyridoxal phosphate‐dependent enzymes (PLP‐DEs) in bacteria to focus on a target class which is involved in crucial metabolic processes. For this, we tailored eight pyridoxal (PL) probes bearing modifications at various positions. Overall, the probes exceeded the performance of a previous generation and provided a detailed map of PLP‐DEs in clinically relevant pathogens including challenging Gram‐negative strains. Putative PLP‐DEs with unknown function were exemplarily characterized via in‐depth enzymatic assays. Finally, we screened a panel of PLP binders for antibiotic activity and unravelled the targets of hit molecules. Here, an uncharacterized enzyme, essential for bacterial growth, was assigned as PLP‐dependent cysteine desulfurase and confirmed to be inhibited by the marketed drug phenelzine. Our approach provides a basis for deciphering novel PLP‐DEs as essential antibiotic targets along with corresponding ways to decipher small molecule inhibitors.
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Affiliation(s)
- Martin Pfanzelt
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Thomas E Maher
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany.,Department of Chemistry, Molecular Sciences Research Hub, White City Campus and Institute of Chemical Biology, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Ramona M Absmeier
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Markus Schwarz
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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8
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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9
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Lechner H, Oberdorfer G. Derivatives of natural organocatalytic cofactors and artificial organocatalytic cofactors as catalysts in enzymes. Chembiochem 2022; 23:e202100599. [PMID: 35302276 PMCID: PMC9401024 DOI: 10.1002/cbic.202100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/14/2022] [Indexed: 11/11/2022]
Abstract
Catalytically active non-metal cofactors in enzymes carry out a variety of different reactions. The efforts to develop derivatives of natural occurring cofactors such as flavins or pyridoxal phosphate and the advances to design new, non-natural cofactors are reviewed here. We report the status quo for enzymes harboring organocatalysts as derivatives of natural cofactors or as artificial ones and their application in the asymmetric synthesis of various compounds.
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Affiliation(s)
- Horst Lechner
- Graz University of Technology: Technische Universitat Graz, Institute of Biochemistry, Petersgasse 12/2, 8010, Graz, AUSTRIA
| | - Gustav Oberdorfer
- Graz University of Technology: Technische Universitat Graz, Institute of Biochemistry, Petersgasse 12/2, 8010, Graz, AUSTRIA
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10
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Tailored Pyridoxal Probes Unravel Novel Cofactor‐Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Asymmetric biomimetic transamination of α-keto amides to peptides. Nat Commun 2021; 12:5174. [PMID: 34462436 PMCID: PMC8405696 DOI: 10.1038/s41467-021-25449-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
Peptides are important compounds with broad applications in many areas. Asymmetric transamination of α-keto amides can provide an efficient strategy to synthesize peptides, however, the process has not been well developed yet and still remains a great challenge in both enzymatic and catalytic chemistry. For biological transamination, the high activity is attributed to manifold structural and electronic factors of transaminases. Based on the concept of multiple imitation of transaminases, here we report N-quaternized axially chiral pyridoxamines 1 for enantioselective transamination of α-keto amides, to produce various peptides in good yields with excellent enantio- and diastereoselectivities. The reaction is especially attractive for the synthesis of peptides made of unnatural amino acids since it doesn’t need great efforts to make chiral unnatural amino acids before amide bond formation. Asymmetric transamination of α-keto amides could provide an efficient strategy to synthesise peptides, but has not been well developed yet. Here, the authors design chiral pyridoxamine catalyst and realize the asymmetric biomimetic transamination of α-keto amides, providing access to various peptides with excellent enantiopurities.
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12
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Ooi T, Ohmatsu K, Kiyokawa M, Shirai Y, Nagato Y. Hybrid Catalysis of 8-Quinolinecarboxaldehyde and Brønsted Acid for Efficient Racemization of α-Amino Amides and Its Application in Chemoenzymatic Dynamic Kinetic Resolution. HETEROCYCLES 2021. [DOI: 10.3987/com-20-s(k)32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Hai Y, Chen M, Huang A, Tang Y. Biosynthesis of Mycotoxin Fusaric Acid and Application of a PLP-Dependent Enzyme for Chemoenzymatic Synthesis of Substituted l-Pipecolic Acids. J Am Chem Soc 2020; 142:19668-19677. [PMID: 33155797 PMCID: PMC8093010 DOI: 10.1021/jacs.0c09352] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fusaric acid (FA) is a well-known mycotoxin that plays an important role in plant pathology. The biosynthetic gene cluster for FA has been identified, but the biosynthetic pathway remains unclarified. Here, we elucidated the biosynthesis of FA, which features a two-enzyme catalytic cascade, a pyridoxal 5'-phosphate (PLP)-dependent enzyme (Fub7), and a flavin mononucleotide (FMN)-dependent oxidase (Fub9) in synthesizing the picolinic acid scaffold. FA biosynthesis also involves an off-line collaboration between a highly reducing polyketide synthase (HRPKS, Fub1) and a nonribosomal peptide synthetase (NRPS)-like carboxylic acid reductase (Fub8) in making an aliphatic α,β-unsaturated aldehyde. By harnessing the stereoselective C-C bond-forming activity of Fub7, we established a chemoenzymatic route for stereoconvergent synthesis of a series of 5-alkyl-, 5,5-dialkyl-, and 5,5,6-trialkyl-l-pipecolic acids of high diastereomeric ratio.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Arthur Huang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
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14
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Song W, Xu X, Gao C, Zhang Y, Wu J, Liu J, Chen X, Luo Q, Liu L. Open Gate of Corynebacterium glutamicum Threonine Deaminase for Efficient Synthesis of Bulky α-Keto Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01672] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Yuxuan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
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15
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Chen M, Liu CT, Tang Y. Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C-C Bond Formation. J Am Chem Soc 2020; 142:10506-10515. [PMID: 32434326 DOI: 10.1021/jacs.0c03535] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes can catalyze transformations of l-amino acids at α, β, and γ positions. These enzymes are frequently involved in the biosynthesis of nonproteinogenic amino acids as building blocks of natural products and are attractive biocatalysts. Here, we report the discovery of a two-step enzymatic synthesis of (2S,6S)-6-methyl pipecolate 1, from the biosynthetic pathway of citrinadin. The key enzyme CndF is PLP-dependent and catalyzes the synthesis of (S)-2-amino-6-oxoheptanoate 3 that is in equilibrium with the cyclic Schiff base. The second enzyme CndE is a stereoselective imine reductase that gives 1. Biochemical characterization of CndF showed this enzyme performs γ-elimination of O-acetyl-l-homoserine to generate the vinylglycine ketimine, which is subjected to nucleophilic attack by acetoacetate to form the new Cγ-Cδ bond in 3 and complete the γ-substitution reaction. CndF displays promiscuity toward different β-keto carboxylate and esters. With use of an Aspergillus strain expressing CndF and CndE, feeding various alkyl-β-keto esters led to the biosynthesis of 6-substituted l-pipecolates. The discovery of CndF expands the repertoire of reactions that can be catalyzed by PLP-dependent enzymes.
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Affiliation(s)
- Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chun-Ting Liu
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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16
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Mueser TC, Drago V, Kovalevsky A, Dajnowicz S. Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase. Methods Enzymol 2020; 634:333-359. [PMID: 32093839 DOI: 10.1016/bs.mie.2020.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.
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Affiliation(s)
- Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States.
| | - Victoria Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States; Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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17
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Bezsudnova EY, Popov VO, Boyko KM. Structural insight into the substrate specificity of PLP fold type IV transaminases. Appl Microbiol Biotechnol 2020; 104:2343-2357. [PMID: 31989227 DOI: 10.1007/s00253-020-10369-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/04/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023]
Abstract
Pyridoxal-5'-phosphate-dependent transaminases of fold type IV (class IV) are promising enzymes for (R)-selective amination of organic compounds. Transaminases of fold type IV exhibit either strict (R)-selectivity or (S)-selectivity that is implemented within geometrically similar active sites of different amino acid compositions. Based on substrate specificity, class IV comprises three large families of transaminases: (S)-selective branched-chain L-amino acid aminotransferases and (R)-selective D-amino acid aminotransferases and (R)-amine:pyruvate transaminases. In this review, we aim to analyze the substrate profiles and correlations between the substrate specificity and organization of the active site in transaminases from these structurally related families. New transaminases with an expanded substrate specificity are also discussed. An analysis of the structural features of substrate binding and comparisons of structural determinants of chiral discrimination between members of the class IV transaminases could be helpful in identifying new biocatalytically relevant enzymes as well as rational protein engineering.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.,Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, Moscow, Russian Federation, 123182
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071
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18
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Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J Struct Biol 2019; 208:137-151. [PMID: 31445086 DOI: 10.1016/j.jsb.2019.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023]
Abstract
Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5'-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7 Å resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.
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19
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Borchert AJ, Ernst DC, Downs DM. Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm. Trends Biochem Sci 2019; 44:849-860. [PMID: 31103411 PMCID: PMC6760865 DOI: 10.1016/j.tibs.2019.04.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/19/2023]
Abstract
Metabolic networks are webs of integrated reactions organized to maximize growth and replication while minimizing the detrimental impact that reactive metabolites can have on fitness. Enamines and imines, such as 2-aminoacrylate (2AA), are reactive metabolites produced as short-lived intermediates in a number of enzymatic processes. Left unchecked, the inherent reactivity of enamines and imines may perturb the metabolic network. Genetic and biochemical studies have outlined a role for the broadly conserved reactive intermediate deaminase (Rid) (YjgF/YER057c/UK114) protein family, in particular RidA, in catalyzing the hydrolysis of enamines and imines to their ketone product. Herein, we discuss new findings regarding the biological significance of enamine and imine production and outline the importance of RidA in controlling the accumulation of reactive metabolites.
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Affiliation(s)
- Andrew J Borchert
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Dustin C Ernst
- Current address: Center for Circadian Biology, University of California, San Diego, San Diego, CA 92161, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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20
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Moschitto MJ, Doubleday PF, Catlin DS, Kelleher NL, Liu D, Silverman RB. Mechanism of Inactivation of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid. J Am Chem Soc 2019; 141:10711-10721. [PMID: 31251613 DOI: 10.1021/jacs.9b03254] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The inhibition of ornithine aminotransferase (OAT), a pyridoxal 5'-phosphate-dependent enzyme, has been implicated as a treatment for hepatocellular carcinoma (HCC), the most common form of liver cancer, for which there is no effective treatment. From a previous evaluation of our aminotransferase inhibitors, (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride (1) was found to be a selective and potent inactivator of human OAT (hOAT), which inhibited the growth of HCC in athymic mice implanted with human-derived HCC, even at a dose of 0.1 mg/kg. Currently, investigational new drug (IND)-enabling studies with 1 are underway. The inactivation mechanism of 1, however, has proved to be elusive. Here we propose three possible mechanisms, based on mechanisms of known aminotransferase inactivators: Michael addition, enamine addition, and fluoride ion elimination followed by conjugate addition. On the basis of crystallography and intact protein mass spectrometry, it was determined that 1 inactivates hOAT through fluoride ion elimination to an activated 1,1'-difluoroolefin, followed by conjugate addition and hydrolysis. This result was confirmed with additional studies, including the detection of the cofactor structure by mass spectrometry and through the identification of turnover metabolites. On the basis of this inactivation mechanism and to provide further evidence for the mechanism, analogues of 1 (19, 20) were designed, synthesized, and demonstrated to have the predicted selective inactivation mechanism. These analogues highlight the importance of the trifluoromethyl group and provide a basis for future inactivator design.
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Affiliation(s)
| | | | - Daniel S Catlin
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | | | - Dali Liu
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
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21
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Graham DL, Beio ML, Nelson DL, Berkowitz DB. Human Serine Racemase: Key Residues/Active Site Motifs and Their Relation to Enzyme Function. Front Mol Biosci 2019; 6:8. [PMID: 30918891 PMCID: PMC6424897 DOI: 10.3389/fmolb.2019.00008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/12/2019] [Indexed: 01/06/2023] Open
Abstract
Serine racemase (SR) is the first racemase enzyme to be identified in human biology and converts L-serine to D-serine, an important neuronal signaling molecule that serves as a co-agonist of the NMDA (N-methyl-D-aspartate) receptor. This overview describes key molecular features of the enzyme, focusing on the side chains and binding motifs that control PLP (pyridoxal phosphate) cofactor binding as well as activity modulation through the binding of both divalent cations and ATP, the latter showing allosteric modulation. Discussed are catalytically important residues in the active site including K56 and S84—the si- and re-face bases, respectively,—and R135, a residue that appears to play a critical role in the binding of both negatively charged alternative substrates and inhibitors. The interesting bifurcated mechanism followed by this enzyme whereby substrate L-serine can be channeled either into D-serine (racemization pathway) or into pyruvate (β-elimination pathway) is discussed extensively, as are studies that focus on a key loop region (the so-called “triple serine loop”), the modification of which can be used to invert the normal in vitro preference of this enzyme for the latter pathway over the former. The possible cross-talk between the PLP enzymes hSR and hCBS (human cystathionine β-synthase) is discussed, as the former produces D-serine and the latter produces H2S, both of which stimulate the NMDAR and both of which have been implicated in neuronal infarction pursuant to ischemic stroke. Efforts to gain a more complete mechanistic understanding of these PLP enzymes are expected to provide valuable insights for the development of specific small molecule modulators of these enzymes as tools to study their roles in neuronal signaling and in modulation of NMDAR function.
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Affiliation(s)
- Danielle L Graham
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Matthew L Beio
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - David L Nelson
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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22
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Raboni S, Marchetti M, Faggiano S, Campanini B, Bruno S, Marchesani F, Margiotta M, Mozzarelli A. The Energy Landscape of Human Serine Racemase. Front Mol Biosci 2019; 5:112. [PMID: 30687716 PMCID: PMC6333871 DOI: 10.3389/fmolb.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022] Open
Abstract
Human serine racemase is a pyridoxal 5′-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available. The comparison of structures of serine racemase co-crystallized with or without ligands indicates the presence of at least one open and one closed conformation, suggesting that conformational flexibility plays a relevant role in enzyme regulation. ATP, Mg2+, Ca2+, anions, NADH and protein interactors, as well as the post-translational modifications nitrosylation and phosphorylation, finely tune the racemase and dehydratase activities and their relative reaction rates. Further information on serine racemase structure and dynamics resulted from the search for inhibitors with potential therapeutic applications. The cumulative knowledge on human serine racemase allowed obtaining insights into its conformational landscape and into the mechanisms of cross-talk between the effector binding sites and the active site.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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23
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Ni J, Xu G, Dai W, Zhao YL, Ni Y. Hyperconjugation promoted by hydrogen bonding between His98/His241 and a carboxyl group contributes to tyrosine decarboxylase catalysis. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01290g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article first demonstrates the utility of the σ → π* hyperconjugation by His98 and His241 in pyridoxal 5′-phosphate-dependent tyrosine decarboxylase.
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Affiliation(s)
- Jie Ni
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Wei Dai
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- MOE-LSB and MOE-LSC
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
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24
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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25
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Hoegl A, Nodwell MB, Kirsch VC, Bach NC, Pfanzelt M, Stahl M, Schneider S, Sieber SA. Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. Nat Chem 2018; 10:1234-1245. [PMID: 30297752 PMCID: PMC6252082 DOI: 10.1038/s41557-018-0144-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/03/2018] [Indexed: 02/01/2023]
Abstract
Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. We synthesized pyridoxal analogues modified at the 2'-position, which are taken up by cells and metabolized in situ. These pyridoxal analogues are phosphorylated to functional cofactor surrogates by cellular pyridoxal kinases and bind to PLP-DEs via an aldimine bond which can be rendered irreversible by NaBH4 reduction. Conjugation to a reporter tag enables the subsequent identification of PLP-DEs using quantitative, label-free mass spectrometry. Using these probes we accessed a significant portion of the Staphylococcus aureus PLP-DE proteome (73%) and annotate uncharacterized proteins as novel PLP-DEs. We also show that this approach can be used to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine.
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Affiliation(s)
- Annabelle Hoegl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthew B Nodwell
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Volker C Kirsch
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Nina C Bach
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Martin Pfanzelt
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany.
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26
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Harrison PJ, Dunn T, Campopiano DJ. Sphingolipid biosynthesis in man and microbes. Nat Prod Rep 2018; 35:921-954. [PMID: 29863195 PMCID: PMC6148460 DOI: 10.1039/c8np00019k] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/20/2022]
Abstract
A new review covering up to 2018 Sphingolipids are essential molecules that, despite their long history, are still stimulating interest today. The reasons for this are that, as well as playing structural roles within cell membranes, they have also been shown to perform a myriad of cell signalling functions vital to the correct function of eukaryotic and prokaryotic organisms. Indeed, sphingolipid disregulation that alters the tightly-controlled balance of these key lipids has been closely linked to a number of diseases such as diabetes, asthma and various neuropathologies. Sphingolipid biogenesis, metabolism and regulation is mediated by a large number of enzymes, proteins and second messengers. There appears to be a core pathway common to all sphingolipid-producing organisms but recent studies have begun to dissect out important, species-specific differences. Many of these have only recently been discovered and in most cases the molecular and biochemical details are only beginning to emerge. Where there is a direct link from classic biochemistry to clinical symptoms, a number a drug companies have undertaken a medicinal chemistry campaign to try to deliver a therapeutic intervention to alleviate a number of diseases. Where appropriate, we highlight targets where natural products have been exploited as useful tools. Taking all these aspects into account this review covers the structural, mechanistic and regulatory features of sphingolipid biosynthetic and metabolic enzymes.
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Affiliation(s)
- Peter J. Harrison
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
| | - Teresa M. Dunn
- Department of Biochemistry and Molecular Biology
, Uniformed Services University
,
Bethesda
, Maryland
20814
, USA
| | - Dominic J. Campopiano
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
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27
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Wen W, Chen L, Luo MJ, Zhang Y, Chen YC, Ouyang Q, Guo QX. Chiral Aldehyde Catalysis for the Catalytic Asymmetric Activation of Glycine Esters. J Am Chem Soc 2018; 140:9774-9780. [PMID: 29995401 DOI: 10.1021/jacs.8b06676] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral aldehyde catalysis is uniquely suitable for the direct asymmetric α-functionalization of N-unprotected amino acids, because aldehydes can reversibly form imines. However, there have been few successful reports of these transformations. In fact, only chiral aldehyde catalyzed aldol reactions of amino acids and alkylation of 2-amino malonates have been reported with good chiral induction. Here, we report a novel type of chiral aldehyde catalyst based on face control of the enolate intermediates. The resulting chiral aldehyde is the first efficient nonpyridoxal-dependent catalyst that can promote the direct asymmetric α-functionalization of N-unprotected glycine esters. Possible transition states and the proton transfer process were investigated by density functional theory calculations.
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Affiliation(s)
- Wei Wen
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Lei Chen
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Ming-Jing Luo
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Yan Zhang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Ying-Chun Chen
- College of Pharmacy , Third Military Medical University , Chongqing 400038 , China
| | - Qin Ouyang
- College of Pharmacy , Third Military Medical University , Chongqing 400038 , China
| | - Qi-Xiang Guo
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
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28
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Müller N. Iminiumsalz-Strukturen bei der durch Pyridoxalphosphat (Vitamin B6) katalysierten Bildung von Aromastoffen und Fehlaromen im Wein. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2018. [DOI: 10.1515/znb-2018-0038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Enzymes that use pyridoxal phosphate (PLP, Vitamin B6) as cofactor constitute a ubiquitous class of biocatalysts. A variety of PLP-dependant enzymes mainly involved in biochemical pathways concerning amino acid metabolism are found in all forms of life. These enzymes also play an important role in wine production, as well in grape growing as in enological processes. The formation of pleasant aroma compounds often runs with participation of pyridoxal-dependant enzymes. But these are also brought into context with the formation of off-odors, especially from sulfur compounds (i.e. sulfur containing amino acids cysteine, methionine). The versatility of PLP-dependant bioreactions arises from its ability to covalently bind the substrate and then to function as an electrophilic catalyst, thereby stabilizing different types of carbanionic reaction intermediates, containing iminium salt structures. This article summarizes the influence of PLP on sensorically important aroma compounds in wine growing and wine processing.
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29
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Liu F, Jiao C, Bi C, Xu Q, Chen P, Heuberger AL, Krishnan HB. Metabolomics Approach To Understand Mechanisms of β-N-Oxalyl-l-α,β-diaminopropionic Acid (β-ODAP) Biosynthesis in Grass Pea (Lathyrus sativus L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10206-10213. [PMID: 29112818 DOI: 10.1021/acs.jafc.7b04037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A study was performed to identify metabolic processes associated with β-ODAP synthesis in grass pea using a metabolomics approach. GC-MS metabolomics was performed on seedlings at 2, 6, and 25 days after sowing. A total of 141 metabolites were detected among the three time points representing much of grass pea primary metabolism, including amino acids, carbohydrates, purines, and others. Principal component analysis revealed unique metabolite profiles of grass pea tissues among the three time points. Fold change, hierarchical clustering, and orthogonal projections to latent structures-discriminant analyses, and biochemical pathway ontologies were used to characterize covariance of metabolites with β-ODAP content. The data indicates that alanine and nitrogen metabolism, cysteine and sulfur metabolism, and purine, pyrimidine, and pyridine metabolism were associated with β-ODAP metabolism. Our results reveal the metabolite profiles in grass pea development and provide insights into mechanisms of β-ODAP accumulation and degradation.
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Affiliation(s)
- Fengjuan Liu
- College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Chengjin Jiao
- College of Bioengineering and Biotechnology, Tianshui Normal University , Tianshui, Gansu 741000, China
| | - Chunxiao Bi
- College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Peng Chen
- College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-Agricultural Research Service, University of Missouri , Columbia, Missouri 65211, United States
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30
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Makins C, Whitelaw DA, McGregor M, Petit A, Mothersole RG, Prosser KE, Wolthers KR. Optimal electrostatic interactions between substrate and protein are essential for radical chemistry in ornithine 4,5-aminomutase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1077-1084. [DOI: 10.1016/j.bbapap.2017.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 11/17/2022]
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31
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Sato D, Shiba T, Karaki T, Yamagata W, Nozaki T, Nakazawa T, Harada S. X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase. Sci Rep 2017; 7:4874. [PMID: 28687762 PMCID: PMC5501846 DOI: 10.1038/s41598-017-05032-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/19/2017] [Indexed: 11/30/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine γ-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the γ-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4′=Nα–Cα moiety in an intermediate PLP-methionine imine to C4′–Nα=Cα in pyridoxamine 5′-phosphate (PMP)-α,β-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent γ-elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4′–Nα=Cα–Cβ=Cγ structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing α-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.
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Affiliation(s)
- Dan Sato
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomoo Shiba
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tsuyoshi Karaki
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Wataru Yamagata
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women's University, Nara, 630-8506, Japan
| | - Shigeharu Harada
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan.
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32
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PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. Proc Natl Acad Sci U S A 2017; 114:3891-3896. [PMID: 28348215 DOI: 10.1073/pnas.1703019114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.
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33
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Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC. Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5'-phosphate in aspartate aminotransferase. J Biol Chem 2017; 292:5970-5980. [PMID: 28232482 DOI: 10.1074/jbc.m116.774588] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a fundamental, multifunctional enzyme cofactor used to catalyze a wide variety of chemical reactions involved in amino acid metabolism. PLP-dependent enzymes optimize specific chemical reactions by modulating the electronic states of PLP through distinct active site environments. In aspartate aminotransferase (AAT), an extended hydrogen bond network is coupled to the pyridinyl nitrogen of the PLP, influencing the electrophilicity of the cofactor. This network, which involves residues Asp-222, His-143, Thr-139, His-189, and structural waters, is located at the edge of PLP opposite the reactive Schiff base. We demonstrate that this hydrogen bond network directly influences the protonation state of the pyridine nitrogen of PLP, which affects the rates of catalysis. We analyzed perturbations caused by single- and double-mutant variants using steady-state kinetics, high resolution X-ray crystallography, and quantum chemical calculations. Protonation of the pyridinyl nitrogen to form a pyridinium cation induces electronic delocalization in the PLP, which correlates with the enhancement in catalytic rate in AAT. Thus, PLP activation is controlled by the proximity of the pyridinyl nitrogen to the hydrogen bond microenvironment. Quantum chemical calculations indicate that Asp-222, which is directly coupled to the pyridinyl nitrogen, increases the pKa of the pyridine nitrogen and stabilizes the pyridinium cation. His-143 and His-189 also increase the pKa of the pyridine nitrogen but, more significantly, influence the position of the proton that resides between Asp-222 and the pyridinyl nitrogen. These findings indicate that the second shell residues directly enhance the rate of catalysis in AAT.
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Affiliation(s)
- Steven Dajnowicz
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606.,the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Jerry M Parks
- the University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Xiche Hu
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Korie Gesler
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Andrey Y Kovalevsky
- the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Timothy C Mueser
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606,
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34
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Pilicer SL, Bakhshi PR, Bentley KW, Wolf C. Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate. J Am Chem Soc 2017; 139:1758-1761. [PMID: 28128945 DOI: 10.1021/jacs.6b12056] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.
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Affiliation(s)
- Samantha L Pilicer
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Pegah R Bakhshi
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Keith W Bentley
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Christian Wolf
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
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35
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Caulkins BG, Young RP, Kudla RA, Yang C, Bittbauer T, Bastin B, Hilario E, Fan L, Marsella MJ, Dunn MF, Mueller LJ. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity. J Am Chem Soc 2016; 138:15214-15226. [PMID: 27779384 PMCID: PMC5129030 DOI: 10.1021/jacs.6b08937] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Indexed: 12/22/2022]
Abstract
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.
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Affiliation(s)
- Bethany G. Caulkins
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Robert P. Young
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Ryan A. Kudla
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Chen Yang
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Thomas
J. Bittbauer
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Baback Bastin
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Li Fan
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael J. Marsella
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Leonard J. Mueller
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
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36
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Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalysts 2016; 6. [PMID: 27885336 PMCID: PMC5119520 DOI: 10.3390/catal6060082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.
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37
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Gökcan H, Monard G, Sungur Konuklar FA. Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes. Proteins 2016; 84:875-91. [PMID: 26800298 DOI: 10.1002/prot.24991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 11/08/2022]
Abstract
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is γ-aminobutyric acid aminotransferase (GABA-AT) which is responsible for the degradation of the neurotransmitter GABA. Its inhibition or inactivation can be used to prevent the reduction of GABA concentration in brain which is the source of several neurological disorders. As a test case for PLP dependent enzymes, we have performed molecular dynamics simulations of GABA-AT to reveal the roles of the protein residues and its cofactor. Three different states have been considered: the apoenzyme, the holoenzyme, and the inactive state obtained after the suicide inhibition by vigabatrin. Different protonation states have also been considered for PLP and two key active site residues: Asp298 and His190. Together, 24 independent molecular dynamics trajectories have been simulated for a cumulative total of 2.88 µs. Our results indicate that, unlike in aqueous solution, the PLP pyridine moiety is protonated in GABA-AT. This is a consequence of a pKa shift triggered by a strong charge-charge interaction with an ionic "diad" formed by Asp298 and His190 that would help the activation of the first half-reaction of the catalytic mechanism in GABA-AT: the conversion of PLP to free pyridoxamine phosphate (PMP). In addition, our MD simulations exhibit additional strong hydrogen bond networks between the protein and PLP: the phosphate group is held in place by the donation of at least three hydrogen bonds while the carbonyl oxygen of the pyridine ring interacts with Gln301; Phe181 forms a π-π stacking interaction with the pyridine ring and works as a gate keeper with the assistance of Val300. All these interactions are hypothesized to help maintain free PMP in place inside the protein active site to facilitate the second half-reaction in GABA-AT: the regeneration of PLP-bound GABA-AT (i.e., the holoenzyme). Proteins 2016; 84:875-891. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hatice Gökcan
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
| | - Gerald Monard
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France
| | - F Aylin Sungur Konuklar
- Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
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38
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Seo JH, Kim EM, Chae A, Kim BG. Lysine ε-aminotransferases: kinetic constants, substrate specificities, and the variation in active site residues. Enzyme Microb Technol 2016; 84:11-6. [PMID: 26827769 DOI: 10.1016/j.enzmictec.2015.12.001] [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: 06/08/2015] [Revised: 11/29/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
L-Lysine ε-aminotransferase (lysAT) is an important enzyme in tailoring the terminal amino group of L-lysine or L-ornithine and can be directed to the synthesis of various value-added chemicals such as adipic acid. Three lysATs, lysAT from Saccharopolyspora erythraea NRRL 2338 (lysAT_Sery), lysAT from Nocardia farcinica IFM 10152, and lysAT from Rhodococcus jostii RHA1, were cloned, and their kinetic values and substrate specificities were investigated. In the reaction using 5mM L-lysine and 10mM α-ketoglutarate, lysAT_Sery from S. erythraea NRRL 2338 showed 72% higher specific activity than lysAT from Nocardia farcinica IFM 10152 and 42% higher specific activity than lysAT from R. jostii RHA1. More interesting result was that lysAT Sery, exhibiting the highest activity among three lysATs, did not show any activity to L-ornithine. The alignment of 146 lysAT sequences from RefSeq database was searched by the EC number of lysAT to compare the active site residues among the lysAT sequences. The sequence alignment showed that only two residues, corresponding to Ala129 and Asn328 of lysAT from Mycobacterium tuberculosis H37Rv (lysAT_Mtub), showed variations among the active site residues. All the active site residues except those two residues were completely conserved throughout 145 lysAT sequences. lysAT from S. erythraea NRRL 2338 has A129T and N328S variations (residue numbers are those of the crystal structure of lysAT_Mtub). The structural analysis by the homology model indicate that Thr126 by A129T variation in lysAT_Sery is appeared to interact more tightly with the phosphate group of PLP than alanine (the distance between Thr126 and the phosphate group of PLP was 2.92Å). In addition, Ser328 is located at the substrate recognition site of active site and, therefore, N328S variation may be connected to the substrate specificity of lysAT.
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Affiliation(s)
- Joo-Hyun Seo
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Eun-Mi Kim
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ahram Chae
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea.
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39
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Choi KY. Non-enzymatic PLP-dependent oxidative deamination of amino acids induces higher alcohol synthesis. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0434-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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40
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Fuchs M, Farnberger JE, Kroutil W. The Industrial Age of Biocatalytic Transamination. European J Org Chem 2015; 2015:6965-6982. [PMID: 26726292 PMCID: PMC4690199 DOI: 10.1002/ejoc.201500852] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 12/25/2022]
Abstract
During the last decade the use of ω-transaminases has been identified as a very powerful method for the preparation of optically pure amines from the corresponding ketones. Their immense potential for the preparation of chiral amines, together with their ease of use in combination with existing biocatalytic methods, have made these biocatalysts a competitor to any chemical methodology for (asymmetric) amination. An increasing number of examples, especially from industry, shows that this biocatalytic technology outmaneuvers existing chemical processes by its simple and flexible nature. In the last few years numerous publications and patents on synthetic routes, mainly to pharmaceuticals, involving ω-transaminases have been published. The review gives an overview of the application of ω-transaminases in organic synthesis with a focus on active pharmaceutical ingredients (APIs) and the developments during the last few years.
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Affiliation(s)
- Michael Fuchs
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz NAWI Graz Heinrichstrasse 28, 8010 Graz, Austria E-mail: http://biocatalysis.uni-graz.at
| | - Judith E Farnberger
- Austrian Centre of Industrial Biotechnology (acib), c/o University of Graz Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz NAWI Graz Heinrichstrasse 28, 8010 Graz, Austria E-mail: http://biocatalysis.uni-graz.at
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41
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Huang YMM, You W, Caulkins BG, Dunn MF, Mueller LJ, Chang CEA. Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sci 2015; 25:166-83. [PMID: 26013176 DOI: 10.1002/pro.2709] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Abstract
The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to investigate pKa values can provide general guidance for assigning proton locations, only static pictures of the chemical species are available. To obtain the overall protein dynamics for the interpretation of detailed enzyme catalysis in this study, guided by information from solid-state NMR, we performed molecular dynamics (MD) simulations for the PLP-dependent enzyme tryptophan synthase (TRPS), whose catalytic mechanism features multiple quasi-stable intermediates. The primary objective of this work is to elucidate how the position of a single proton on the reacting substrate affects local and global protein dynamics during the catalytic cycle. In general, proteins create a chemical environment and an ensemble of conformational motions to recognize different substrates with different protonations. The study of these interactions in TRPS shows that functional groups on the reacting substrate, such as the phosphoryl group, pyridine nitrogen, phenolic oxygen and carboxyl group, of each PLP-bound intermediate play a crucial role in constructing an appropriate molecular interface with TRPS. In particular, the protonation states of the ionizable groups on the PLP cofactor may enhance or weaken the attractions between the enzyme and substrate. In addition, remodulation of the charge distribution for the intermediates may help generate a suitable environment for chemical reactions. The results of our study enhance knowledge of protonation states for several PLP intermediates and help to elucidate their effects on protein dynamics in the function of TRPS and other PLP-dependent enzymes.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Wanli You
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, California, 92521
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, California, 92521
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42
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Milano T, Di Salvo ML, Angelaccio S, Pascarella S. Conserved water molecules in bacterial serine hydroxymethyltransferases. Protein Eng Des Sel 2015; 28:415-26. [DOI: 10.1093/protein/gzv026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/17/2015] [Indexed: 12/27/2022] Open
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43
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Huang YMM, Kang M, Chang CEA. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J Mol Recognit 2015; 27:537-48. [PMID: 25042708 DOI: 10.1002/jmr.2377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/05/2022]
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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Steffen-Munsberg F, Vickers C, Kohls H, Land H, Mallin H, Nobili A, Skalden L, van den Bergh T, Joosten HJ, Berglund P, Höhne M, Bornscheuer UT. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv 2015; 33:566-604. [PMID: 25575689 DOI: 10.1016/j.biotechadv.2014.12.012] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/25/2023]
Abstract
In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
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Affiliation(s)
- Fabian Steffen-Munsberg
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Clare Vickers
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hannes Kohls
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrik Land
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Hendrik Mallin
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Alberto Nobili
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Lilly Skalden
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Per Berglund
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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Nitoker N, Major DT. Understanding the Reaction Mechanism and Intermediate Stabilization in Mammalian Serine Racemase Using Multiscale Quantum-Classical Simulations. Biochemistry 2014; 54:516-27. [DOI: 10.1021/bi500984m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Neta Nitoker
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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46
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Okuda K, Kato S, Ito T, Shiraki S, Kawase Y, Goto M, Kawashima S, Hemmi H, Fukada H, Yoshimura T. Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator. Mol Microbiol 2014; 95:245-57. [PMID: 25388514 DOI: 10.1111/mmi.12861] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2014] [Indexed: 11/30/2022]
Abstract
MocR/GabR family proteins are widely distributed prokaryotic transcriptional regulators containing pyridoxal 5'-phosphate (PLP), a coenzyme form of vitamin B6. The Bacillus subtilis GabR, probably the most extensively studied MocR/GabR family protein, consists of an N-terminal DNA-binding domain and a PLP-binding C-terminal domain that has a structure homologous to aminotransferases. GabR suppresses transcription of gabR and activates transcription of gabT and gabD, which encode γ-aminobutyrate (GΑΒΑ) aminotransferase and succinate semialdehyde dehydrogenase, respectively, in the presence of PLP and GABA. In this study, we examined the mechanism underlying GabR-mediated gabTD transcription with spectroscopic, crystallographic and thermodynamic studies, focusing on the function of the aminotransferase domain. Spectroscopic studies revealed that GABA forms an external aldimine with the PLP in the aminotransferase domain. Isothermal calorimetry demonstrated that two GabR molecules bind to the 51-bp DNA fragment that contains the GabR-binding region. GABA minimally affected ΔG(binding) upon binding of GabR to the DNA fragment but greatly affected the contributions of ΔH and ΔS to ΔG(binding). GABA forms an external aldimine with PLP and causes a conformational change in the aminotransferase domain, and this change likely rearranges GabR binding to the promoter and thus activates gabTD transcription.
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Affiliation(s)
- Keita Okuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-chou, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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Peña-Soler E, Fernandez FJ, López-Estepa M, Garces F, Richardson AJ, Quintana JF, Rudd KE, Coll M, Vega MC. Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli. PLoS One 2014; 9:e102139. [PMID: 25014014 PMCID: PMC4094517 DOI: 10.1371/journal.pone.0102139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
In order to maintain proper cellular function, the metabolism of the bacterial microbiota presents several mechanisms oriented to keep a correctly balanced amino acid pool. Central components of these mechanisms are enzymes with alanine transaminase activity, pyridoxal 5′-phosphate-dependent enzymes that interconvert alanine and pyruvate, thereby allowing the precise control of alanine and glutamate concentrations, two of the most abundant amino acids in the cellular amino acid pool. Here we report the 2.11-Å crystal structure of full-length AlaA from the model organism Escherichia coli, a major bacterial alanine aminotransferase, and compare its overall structure and active site composition with detailed atomic models of two other bacterial enzymes capable of catalyzing this reaction in vivo, AlaC and valine-pyruvate aminotransferase (AvtA). Apart from a narrow entry channel to the active site, a feature of this new crystal structure is the role of an active site loop that closes in upon binding of substrate-mimicking molecules, and which has only been previously reported in a plant enzyme. Comparison of the available structures indicates that beyond superficial differences, alanine aminotransferases of diverse phylogenetic origins share a universal reaction mechanism that depends on an array of highly conserved amino acid residues and is similarly regulated by various unrelated motifs. Despite this unifying mechanism and regulation, growth competition experiments demonstrate that AlaA, AlaC and AvtA are not freely exchangeable in vivo, suggesting that their functional repertoire is not completely redundant thus providing an explanation for their independent evolutionary conservation.
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Affiliation(s)
- Esther Peña-Soler
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Francisco J. Fernandez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Miguel López-Estepa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew J. Richardson
- University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Juan F. Quintana
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
| | - Kenneth E. Rudd
- University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Madrid, Spain
- * E-mail:
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48
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Ito T, Matsuoka M, Koga K, Hemmi H, Yoshimura T. Reaction mechanism of Zn2+-dependent d-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate. J Biochem 2014; 156:173-80. [PMID: 24881047 DOI: 10.1093/jb/mvu035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
d-Serine dehydratase from Saccharomyces cerevisiae (Dsd1p) is a pyridoxal 5'-phosphate (PLP)- and Zn(2+)-dependent enzyme that catalyzes the dehydration of d-serine to yield pyruvate and ammonia. Dsd1p uses the Tyr residue (Y203) to interact with the pyridine nitrogen of PLP, which is a unique feature of PLP enzymes. To investigate the role of Y203 in catalysis, a series of Y203 mutants was constructed and studied. Mutant enzymes possessing a non-polar or a basic residue instead of Y203 (Y203F, A, S and R) exhibited substantial levels of catalytic activity, and among these, the Y203F mutant had the least impact on catalytic activity. The Y203D exhibited a 10(5)-fold decrease in enzyme activity, and unlike wild-type enzyme, the mutant enzyme favoured the Cα reprotonation before hydroxyl group protonation. Our data show that the Y203 does not participate in the protonation of the pyridine nitrogen (N1) of PLP, and Dsd1p uses the cofactor in an N1-unprotonated state. The unprotonated N1 promotes elimination of the leaving group and evades Cα reprotonation before hydroxyl group protonation.
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Affiliation(s)
- Tomokazu Ito
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Mai Matsuoka
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kazushi Koga
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Hisashi Hemmi
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Tohru Yoshimura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan
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49
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Maity AN, Chen YH, Ke SC. Large-scale domain motions and pyridoxal-5'-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases. Int J Mol Sci 2014; 15:3064-87. [PMID: 24562332 PMCID: PMC3958899 DOI: 10.3390/ijms15023064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/25/2013] [Accepted: 01/22/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine 5,6-aminomutase (5,6-LAM) and ornithine 4,5-aminomutase (4,5-OAM) are two of the rare enzymes that use assistance of two vitamins as cofactors. These enzymes employ radical generating capability of coenzyme B12 (5'-deoxyadenosylcobalamin, dAdoCbl) and ability of pyridoxal-5'-phosphate (PLP, vitamin B6) to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. In spite of all the similarities, these enzymes differ in substrate specificities. 4,5-OAM is highly specific for D-ornithine as a substrate while 5,6-LAM can accept D-lysine and L-β-lysine. This review focuses on recent computational, spectroscopic and structural studies of these enzymes and their implications on the related enzymes. Additionally, we also discuss the potential biosynthetic application of 5,6-LAM.
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Affiliation(s)
| | - Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
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50
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Beattie AE, Clarke DJ, Wadsworth JM, Lowther J, Sin HL, Campopiano DJ. Reconstitution of the pyridoxal 5'-phosphate (PLP) dependent enzyme serine palmitoyltransferase (SPT) with pyridoxal reveals a crucial role for the phosphate during catalysis. Chem Commun (Camb) 2014; 49:7058-60. [PMID: 23814788 DOI: 10.1039/c3cc43001d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pyridoxal 5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) is required for de novo sphingolipid biosynthesis. A previous study revealed a novel and unexpected interaction between the hydroxyl group of the l-serine substrate and the 5'-phosphate group of PLP. By using pyridoxal (PL), the dephosphorylated analogue of vitamin B6, we show here that this interaction is important for substrate specificity and optimal catalytic efficiency.
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Affiliation(s)
- Ashley E Beattie
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ, Scotland, UK
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