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Saez-Jimenez V, Maršić ŽS, Lambrughi M, Shin JH, van Havere R, Papaleo E, Olsson L, Mapelli V. Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction. PLoS One 2020; 15:e0233467. [PMID: 32437404 PMCID: PMC7241714 DOI: 10.1371/journal.pone.0233467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jae Ho Shin
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Robin van Havere
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Lambrughi M, Sanader Maršić Ž, Saez-Jimenez V, Mapelli V, Olsson L, Papaleo E. Conformational gating in ammonia lyases. Biochim Biophys Acta Gen Subj 2020; 1864:129605. [PMID: 32222547 DOI: 10.1016/j.bbagen.2020.129605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Ammonia lyases are enzymes of industrial and biomedical interest. Knowledge of structure-dynamics-function relationship in ammonia lyases is instrumental for exploiting the potential of these enzymes in industrial or biomedical applications. METHODS We investigated the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. At this scope, we used microsecond all-atom molecular dynamics simulations, analyzed with dimensionality reduction techniques, as well as in terms of contact networks and correlated motions. RESULTS We identify two regulatory elements in the MAL structure, i.e., the β5-α2 loop and the helix-hairpin-loop subdomain. These regulatory elements undergo conformational changes switching from 'occluded' to 'open' states. The rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the catalytic site, making the active site more accessible to the substrate when they are in an open state. CONCLUSIONS Our work pinpoints a sequential mechanism, in which the helix-hairpin-loop subdomain of MAL needs to break a subset of intramolecular interactions first to favor the displacement of the β5-α2 loop. The coupled conformational changes of these two elements contribute to modulate the accessibility of the catalytic site. GENERAL SIGNIFICANCE Similar molecular mechanisms can have broad relevance in other ammonia lyases with similar regulatory loops. Our results also imply that it is important to account for protein dynamics in the design of variants of ammonia lyases for industrial and biomedical applications.
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Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark.
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Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017; 71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Scott R. Miller
- Division of Biological SciencesThe University of Montana Missoula Montana 59812
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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de Villiers M, Puthan Veetil V, Raj H, de Villiers J, Poelarends GJ. Catalytic mechanisms and biocatalytic applications of aspartate and methylaspartate ammonia lyases. ACS Chem Biol 2012; 7:1618-28. [PMID: 22834890 DOI: 10.1021/cb3002792] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ammonia lyases catalyze the formation of α,β-unsaturated bonds by the elimination of ammonia from their substrates. This conceptually straightforward reaction has been the emphasis of many studies, with the main focus on the catalytic mechanism of these enzymes and/or the use of these enzymes as catalysts for the synthesis of enantiomerically pure α-amino acids. In this Review aspartate ammonia lyase and 3-methylaspartate ammonia lyase, which represent two different enzyme superfamilies, are discussed in detail. In the past few years, the three-dimensional structures of these lyases in complex with their natural substrates have revealed the details of two elegant catalytic strategies. These strategies exploit similar deamination mechanisms that involve general-base catalyzed formation of an enzyme-stabilized enolate anion (aci-carboxylate) intermediate. Recent progress in the engineering and application of these enzymes to prepare enantiopure l-aspartic acid derivatives, which are highly valuable as tools for biological research and as chiral building blocks for pharmaceuticals and food additives, is also discussed.
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Affiliation(s)
- Marianne de Villiers
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Vinod Puthan Veetil
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Hans Raj
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Jandré de Villiers
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
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Raj H, Puthan Veetil V, Szymanski W, Dekker FJ, Quax WJ, Feringa BL, Janssen DB, Poelarends GJ. Characterization of a thermostable methylaspartate ammonia lyase from Carboxydothermus hydrogenoformans. Appl Microbiol Biotechnol 2011; 94:385-97. [PMID: 22005738 PMCID: PMC3310078 DOI: 10.1007/s00253-011-3615-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/30/2011] [Accepted: 09/28/2011] [Indexed: 01/05/2023]
Abstract
Methylaspartate ammonia lyase (MAL; EC 4.3.1.2) catalyzes the reversible addition of ammonia to mesaconate to give (2S,3S)-3-methylaspartate and (2S,3R)-3-methylaspartate as products. MAL is of considerable biocatalytic interest because of its potential use for the asymmetric synthesis of substituted aspartic acids, which are important building blocks for synthetic enzymes, peptides, chemicals, and pharmaceuticals. Here, we have cloned the gene encoding MAL from the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. The enzyme (named Ch-MAL) was overproduced in Escherichia coli and purified to homogeneity by immobilized metal affinity chromatography. Ch-MAL is a dimer in solution, consisting of two identical subunits (∼49 kDa each), and requires Mg2+ and K+ ions for maximum activity. The optimum pH and temperature for the deamination of (2S,3S)-3-methylaspartic acid are 9.0 and 70°C (kcat = 78 s−1 and Km = 16 mM). Heat inactivation assays showed that Ch-MAL is stable at 50°C for >4 h, which is the highest thermal stability observed among known MALs. Ch-MAL accepts fumarate, mesaconate, ethylfumarate, and propylfumarate as substrates in the ammonia addition reaction. The enzyme also processes methylamine, ethylamine, hydrazine, hydroxylamine, and methoxylamine as nucleophiles that can replace ammonia in the addition to mesaconate, resulting in the corresponding N-substituted methylaspartic acids with excellent diastereomeric excess (>98% de). This newly identified thermostable MAL appears to be a potentially attractive biocatalyst for the stereoselective synthesis of aspartic acid derivatives on large (industrial) scale.
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Affiliation(s)
- Hans Raj
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, Groningen, The Netherlands
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Asano Y, Kato Y, Levy C, Baker P, Rice D. Structure and Function of Amino Acid Ammonia-lyases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420410001703496] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Levy CW, Buckley PA, Sedelnikova S, Kato Y, Asano Y, Rice DW, Baker PJ. Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase. Structure 2002; 10:105-13. [PMID: 11796115 DOI: 10.1016/s0969-2126(01)00696-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Methylaspartate ammonia lyase (MAL) catalyzes the magnesium-dependent reversible alpha,beta-elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to mesaconic acid. The 1.3 A MAD crystal structure of the dimeric Citrobacter amalonaticus MAL shows that each subunit comprises two domains, one of which adopts the classical TIM barrel fold, with the active site at the C-terminal end of the barrel. Despite very low sequence similarity, the structure of MAL is closely related to those of representative members of the enolase superfamily, indicating that the mechanism of MAL involves the initial abstraction of a proton alpha to the 3-carboxyl of (2S,3S)-3-methylasparic acid to yield an enolic intermediate. This analysis resolves the conflict that had linked MAL to the histidine and phenylalanine ammonia lyase family of enzymes.
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Affiliation(s)
- C W Levy
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
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Bearne SL, White RL, MacDonnell JE, Bahrami S, Grønlund J. Purification and characterization of beta-methylaspartase from Fusobacterium varium. Mol Cell Biochem 2001; 221:117-26. [PMID: 11506174 DOI: 10.1023/a:1010938111292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Beta-methylaspartase (EC 4.3.1.2) was purified 20-fold in 35% yield from Fusobacterium varium, an obligate anaerobe. The purification steps included heat treatment, fractional precipitation with ammonium sulfate and ethanol, gel filtration, and ion exchange chromatography on DEAE-Sepharose. The enzyme is dimeric, consisting of two identical 46 kDa subunits, and requires Mg2+ (Km = 0.27+/-0.01 mM) and K+ (Km = 3.3+/-0.8 mM) for maximum activity. Beta-methylaspartase-catalyzed addition of ammonia to mesaconate yielded two diastereomeric amino acids, identified by HPLC as (2S,3S)-3-methylaspartate (major product) and (2S,3R)-3-methylaspartate (minor product). Optimal activity for the deamination of (2S,3S)-3-methylaspartate (Km = 0.51+/-0.04 mM) was observed at pH 9.7. The N-terminal protein sequence (30 residues) of the F. varium enzyme is 83% identical to the corresponding sequence of the clostridial enzyme.
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Affiliation(s)
- S L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Gani D, Archer CH, Botting NP, Pollard JR. The 3-methylaspartase reaction probed using 2H- and 15N-isotope effects for three substrates: a flip from a concerted to a carbocationic amino-enzyme elimination mechanism upon changing the C-3 stereochemistry in the substrate from R to S. Bioorg Med Chem 1999; 7:977-90. [PMID: 10400349 DOI: 10.1016/s0968-0896(99)00043-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mechanisms of the elimination of ammonia from (2S,3S)-3-methylaspartic acid, (2S)-aspartic acid and (2S,3R)-3-methylaspartic acid, catalysed by the enzyme L-threo-3-methylaspartase ammonia-lyase (EC 4.3.1.2) have been probed using 15N-isotope effects. The 15N-isotope effects for V/K for both (2S,3S)-3-methylaspartic acid and aspartic acid are 1.0246 +/- 0.0013 and 1.0390 +/- 0.0031, respectively. The natural substrate, (2S,3S)-3-methylaspartic acid, is eliminated in a concerted fashion such that the C(beta)-H and C(alpha)-N bonds are cleaved in the same transition state. (2S)-Aspartic acid appears to follow the same mechanistic pathway, but deprotonation of the conjugate acid of the base for C-3 is kinetically important and influences the extent of 15N-fractionation. (2S,3R)-3-Methylaspartic acid is deaminated via a stepwise carbocationic mechanism. Here we elaborate on the proposed model for the mechanism of methylaspartase and propose that a change in stereochemistry of the substrate induces a change in the mechanism of ammonia elimination.
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Affiliation(s)
- D Gani
- School of Chemistry and Centre for Biomolecular Sciences, The University of St. Andrews, Scotland, UK
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