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Pick A, Beer B, Hemmi R, Momma R, Schmid J, Miyamoto K, Sieber V. Identification and characterization of two new 5-keto-4-deoxy-D-Glucarate Dehydratases/Decarboxylases. BMC Biotechnol 2016; 16:80. [PMID: 27855668 PMCID: PMC5114784 DOI: 10.1186/s12896-016-0308-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/21/2016] [Indexed: 11/11/2022] Open
Abstract
Background Hexuronic acids such as D-galacturonic acid and D-glucuronic acid can be utilized via different pathways within the metabolism of microorganisms. One representative, the oxidative pathway, generates α-keto-glutarate as the direct link entering towards the citric acid cycle. The penultimate enzyme, keto-deoxy glucarate dehydratase/decarboxylase, catalyses the dehydration and decarboxylation of keto-deoxy glucarate to α-keto-glutarate semialdehyde. This enzymatic reaction can be tracked continuously by applying a pH-shift assay. Results Two new keto-deoxy glucarate dehydratases/decarboxylases (EC 4.2.1.41) from Comamonas testosteroni KF-1 and Polaromonas naphthalenivorans CJ2 were identified and expressed in an active form using Escherichia coli ArcticExpress(DE3). Subsequent characterization concerning Km, kcat and thermal stability was conducted in comparison with the known keto-deoxy glucarate dehydratase/decarboxylase from Acinetobacter baylyi ADP1. The kinetic constants determined for A. baylyi were Km 1.0 mM, kcat 4.5 s−1, for C. testosteroni Km 1.1 mM, kcat 3.1 s−1, and for P. naphthalenivorans Km 1.1 mM, kcat 1.7 s−1. The two new enzymes had a slightly lower catalytic activity (increased Km and a decreased kcat) but showed a higher thermal stability than that of A. baylyi. The developed pH-shift assay, using potassium phosphate and bromothymol blue as the pH indicator, enables a direct measurement. The use of crude extracts did not interfere with the assay and was tested for wild-type landscapes for all three enzymes. Conclusions By establishing a pH-shift assay, an easy measurement method for keto-deoxy glucarate dehydratase/decarboxylase could be developed. It can be used for measurements of the purified enzymes or using crude extracts. Therefore, it is especially suitable as the method of choice within an engineering approach for further optimization of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0308-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- André Pick
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Barbara Beer
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Risa Hemmi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Rena Momma
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Jochen Schmid
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Volker Sieber
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany.
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North RA, Kessans SA, Atkinson SC, Suzuki H, Watson AJA, Burgess BR, Angley LM, Hudson AO, Varsani A, Griffin MDW, Fairbanks AJ, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:306-12. [PMID: 23519810 PMCID: PMC3606580 DOI: 10.1107/s1744309113003060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/30/2013] [Indexed: 01/13/2023]
Abstract
The enzyme N-acetylneuraminate lyase (EC 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-D-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic DNA, and recombinant protein was expressed and purified from Escherichia coli BL21 (DE3). The enzyme crystallized in a number of crystal forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.70 Å resolution in space group P2₁. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights for the development of future antimicrobials.
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Affiliation(s)
- Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Andrew J. A. Watson
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Benjamin R. Burgess
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Lauren M. Angley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Arvind Varsani
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Antony J. Fairbanks
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
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Aghaie A, Lechaplais C, Sirven P, Tricot S, Besnard-Gonnet M, Muselet D, de Berardinis V, Kreimeyer A, Gyapay G, Salanoubat M, Perret A. New insights into the alternative D-glucarate degradation pathway. J Biol Chem 2008; 283:15638-46. [PMID: 18364348 DOI: 10.1074/jbc.m800487200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the D-glucarate degradation pathway is well characterized in Escherichia coli, genetic and biochemical information concerning the alternative pathway proposed in Pseudomonas species and Bacillus subtilis remains incomplete. Acinetobacter baylyi ADP1 is a Gram-negative soil bacterium possessing the alternative pathway and able to grow using D-glucarate as the only carbon source. Based on the annotation of its sequenced genome (1), we have constructed a complete collection of singlegene deletion mutants (2). High throughput profiling for growth on a minimal medium containing D-glucarate as the only carbon source for approximately 2450 mutants led to the identification of the genes involved in D-glucarate degradation. Protein purification after recombinant production in E. coli allowed us to reconstitute the enzymatic pathway in vitro. We describe here the kinetic characterization of D-glucarate dehydratase, d-5-keto-4-deoxyglucarate dehydratase, and of cooperative alpha-ketoglutarate semialdehyde dehydrogenase. Transcription and expression analyses of the genes involved in D-glucarate metabolism within a single organism made it possible to access information regarding the regulation of this pathway for the first time.
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Affiliation(s)
- Asadollah Aghaie
- CNRS-UMR 8030, Genoscope-Commissariat à l'Energie Atomique, 2 Rue Gaston Crémieux, Evry 91057, France
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Babbitt PC, Gerlt JA. New functions from old scaffolds: how nature reengineers enzymes for new functions. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:1-28. [PMID: 11050931 DOI: 10.1016/s0065-3233(01)55001-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- P C Babbitt
- Department of Biopharmaceutical Sciences, University of California, San Francisco 94143, USA
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Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM. Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase. J Mol Biol 1997; 266:381-99. [PMID: 9047371 DOI: 10.1006/jmbi.1996.0769] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.
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Affiliation(s)
- M C Lawrence
- Biomolecular Research Institute, Parkville, Victoria, Australia
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Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA. The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 1996; 35:16489-501. [PMID: 8987982 DOI: 10.1021/bi9616413] [Citation(s) in RCA: 252] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have discovered a superfamily of enzymes related by their ability to catalyze the abstraction of the alpha-proton of a carboxylic acid to form an enolic intermediate. Although each reaction catalyzed by these enzymes is initiated by this common step, their overall reactions (including racemization, beta-elimination of water, beta-elimination of ammonia, and cycloisomerization) as well as the stereochemical consequences (syn vs anti) of the beta-elimination reactions are diverse. Analysis of sequence and structural similarities among these proteins suggests that all of their chemical reactions are mediated by a common active site architecture modified through evolution to allow the enolic intermediates to partition to different products in their respective active sites via different overall mechanisms. All of these enzymes retain the ability to catalyze the thermodynamically difficult step of proton abstraction. These homologous proteins, designated the "enolase superfamily", include enolase as well as more metabolically specialized enzymes: mandelate racemase, galactonate dehydratase, glucarate dehydratase, muconate-lactonizing enzymes, N-acylamino acid racemase, beta-methylaspartate ammonia-lyase, and o-succinylbenzoate synthase. Comparative analysis of structure-function relationships within the superfamily suggests that carboxyphosphonoenolpyruvate synthase, another member of the superfamily, does not catalyze the reaction proposed in the literature but catalyzes an enolase-like reaction instead. The established and deduced structure-function relationships in the superfamily allow the prediction that other apparent members of the family for which no catalytic functions have yet been assigned will also perform chemistry involving abstraction of the alpha-protons of carboxylic acids.
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Affiliation(s)
- P C Babbitt
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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7
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Palmer DRJ, Gerlt JA. Evolution of Enzymatic Activities: Multiple Pathways for Generating and Partitioning a Common Enolic Intermediate by Glucarate Dehydratase from Pseudomonas putida. J Am Chem Soc 1996. [DOI: 10.1021/ja962126v] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David R. J. Palmer
- Department of Biochemistry School of Chemical Sciences University of Illinois, Urbana, Illinois 61801
| | - John A. Gerlt
- Department of Biochemistry School of Chemical Sciences University of Illinois, Urbana, Illinois 61801
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8
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Donald A, Sibley D, Lyons D, Dahms A. D-Galactonate dehydrase. Purification and properties. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37776-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Jeffcoat R. Studies on glucarate catabolism: the oxodeoxyglucarate aldolase activity of glucarate hydro-lyase from Pseudomonas acidovorans. Biochem J 1974; 139:477-80. [PMID: 4447622 PMCID: PMC1166306 DOI: 10.1042/bj1390477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glucarate hydro-lyase was isolated and purified to near homogeneity from cells of Pseudomonas acidovorans grown on glucarate. By using gel filtration and ion-exchange chromatography, it was shown that the oxodeoxyglucarate aldolase activity observed in such extracts is associated with the glucarate hydro-lyase protein.
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12
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13
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Bender R, Gottschalk G. Purification and properties of D-gluconate dehydratase from Clostridium pasteurianum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 40:309-21. [PMID: 4772682 DOI: 10.1111/j.1432-1033.1973.tb03198.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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14
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Sharma BS, Blumenthal HJ. Catabolism of D-gluaric acid to alpha-ketoglutarate in Bacillus megaterium. J Bacteriol 1973; 116:1346-54. [PMID: 4148097 PMCID: PMC246494 DOI: 10.1128/jb.116.3.1346-1354.1973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Crude cell-free extracts of d-glucarate-grown cells of Bacillus megaterium converted d-glucarate to alpha-keto-beta-deoxy-d-glucarate (KDG). Charcoal-treated cell-free extracts or partially purified enzyme preparations converted KDG to an intermediate which was isolated and identified as 2,5-diketoadipate (DKA). This compound was synthesized, and the cell-free extracts of d-glucarate grown cells were found to catalyze the reduction of nicotinamide adenine dinucleotide (NAD) in its presence. In the absence of NAD, the same enzyme preparation catalyzed the decarboxylation of the DKA to alpha-ketoglutarate semialdehyde (KGS), whereas in the presence of NAD the KGS was subsequently oxidized to alpha-ketoglutarate by alpha-ketoglutarate semialdehyde dehydrogenase. Since galactarate-grown B. megaterium contains a galactarate dehydrase forming KDG, the complete pathway for the metabolism of d-glucarate or galactarate to alpha-ketoglutarate and CO(2) is now known in a gram-positive bacterium.
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15
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Jeffcoat R, Dagley S. Bacterial hydrolases and aldolases in evolution. NATURE: NEW BIOLOGY 1973; 241:186-7. [PMID: 4573270 DOI: 10.1038/newbio241186a0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Jeffcoat R. Chemical modification and kinetic studies on glucarate hydro-lyase from a species of Pseudomonas A. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 25:515-23. [PMID: 5043319 DOI: 10.1111/j.1432-1033.1972.tb01723.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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17
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Kersters K, Khan-Matsubara J, Nelen L, De Ley J. Purification and properties of D-gluconate dehydratase from Achromobacter. Antonie Van Leeuwenhoek 1971; 37:233-46. [PMID: 5314556 DOI: 10.1007/bf02218486] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Jeffcoat R, Hassall H, Dagley S. Purification and properties of D-4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating). Biochem J 1969; 115:977-83. [PMID: 4982840 PMCID: PMC1185240 DOI: 10.1042/bj1150977] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
1. An enzyme extracted from Pseudomonas acidovorans was purified and shown to catalyse the simultaneous dehydration and decarboxylation of d-4-deoxy-5-oxoglucarate. It is proposed to name the enzyme d-4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating), trivial name ;deoxyoxoglucarate dehydratase'. 2. No added cofactors were required, and the enzyme was inactivated when incubated with its substrate in the presence of sodium borohydride. Under these conditions the substrate and enzyme appeared to be bound covalently. 3. The action of the enzyme is readily explained if it is assumed that d-4-deoxy-5-oxoglucarate forms a Schiff base with a lysine residue in the enzyme.
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