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Piskol F, Lukat P, Kaufhold L, Heger A, Blankenfeldt W, Jahn D, Moser J. Biochemical and structural elucidation of the L-carnitine degradation pathway of the human pathogen Acinetobacter baumannii. Front Microbiol 2024; 15:1446595. [PMID: 39206375 PMCID: PMC11353897 DOI: 10.3389/fmicb.2024.1446595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic human pathogen which can use host-derived L-carnitine as sole carbon and energy source. Recently, an L-carnitine transporter (Aci1347) and a specific monooxygense (CntA/CntB) for the intracellular cleavage of L-carnitine have been characterized. Subsequent conversion of the resulting malic semialdehyde into the central metabolite L-malate was hypothesized. Alternatively, L-carnitine degradation via D-malate with subsequent oxidation into pyruvate was proposed. Here we describe the in vitro and in vivo reconstitution of the entire pathway, starting from the as yet uncharacterized gene products of the carnitine degradation gene operon. Using recombinantly purified enzymes, enantiomer-specific formation of D-malate by the NAD(P)+-dependent malic semialdehyde dehydrogenase (MSA-DH) is demonstrated. The solved X-ray crystal structure of tetrameric MSA-DH reveals the key catalytic residues Cys290 and Glu256, accessible through opposing substrate and cofactor funnels. Specific substrate binding is enabled by Arg166, Arg284 and Ser447 while dual cofactor specificity for NAD+ and NADP+ is mediated by Asn184. The subsequent conversion of the unusual D-malate reaction product by an uncharacterized NAD+-dependent malate dehydrogenase (MDH) is shown. Tetrameric MDH is a β-decarboxylating dehydrogenase that synthesizes pyruvate. MDH experiments with alternative substrates showed a high degree of substrate specificity. Finally, the entire A. baumannni pathway was heterologously reconstituted, allowing E. coli to grow on L-carnitine as a carbon and energy source. Overall, the metabolic conversion of L-carnitine via malic semialdehyde and D-malate into pyruvate, CO2 and trimethylamine was demonstrated. Trimethylamine is also an important gut microbiota-dependent metabolite that is associated with an increased risk of cardiovascular disease. The pathway reconstitution experiments allowed us to assess the TMA forming capacity of gut microbes which is related to human cardiovascular health.
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Affiliation(s)
- Fabian Piskol
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Peer Lukat
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Laurin Kaufhold
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Alexander Heger
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Biochemistry, Biotechnology and Bioinformatic, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jürgen Moser
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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2
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Xie C, Li ZM, Bai F, Hu Z, Zhang W, Li Z. Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142. PLoS One 2020; 15:e0239372. [PMID: 32966327 PMCID: PMC7510979 DOI: 10.1371/journal.pone.0239372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/06/2020] [Indexed: 11/26/2022] Open
Abstract
As a ubiquitous enzyme, succinic semialdehyde dehydrogenase contributes significantly in many pathways including the tricarboxylic acid cycle and other metabolic processes such as detoxifying the accumulated succinic semialdehyde and surviving in nutrient-limiting conditions. Here the cce4228 gene encoding succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142 was cloned and the homogenous recombinant cce4228 protein was obtained by Ni-NTA affinity chromatography. Biochemical characterization revealed that cce4228 protein displayed optimal activity at presence of metal ions in basic condition. Although the binding affinity of cce4228 protein with NAD+ was about 50-fold lower than that of cce4228 with NADP+, the catalytic efficiency of cce4228 protein towards succinic semialdehyde with saturated concentration of NADP+ is same as that with saturated concentration of NAD+ as its cofactors. Meanwhile, the catalytic activity of cce4228 was competitively inhibited by succinic semialdehyde substrate. Kinetic and structural analysis demonstrated that the conserved Cys262 and Glu228 residues were crucial for the catalytic activity of cce4228 protein and the Ser157 and Lys154 residues were determinants of cofactor preference.
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Affiliation(s)
- Congcong Xie
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhi-Min Li
- College of Science, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Fumei Bai
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ziwei Hu
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wei Zhang
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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3
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Phonbuppha J, Maenpuen S, Munkajohnpong P, Chaiyen P, Tinikul R. Selective determination of the catalytic cysteine pK a of two-cysteine succinic semialdehyde dehydrogenase from Acinetobacter baumannii using burst kinetics and enzyme adduct formation. FEBS J 2018; 285:2504-2519. [PMID: 29734522 DOI: 10.1111/febs.14497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/27/2018] [Accepted: 04/30/2018] [Indexed: 11/27/2022]
Abstract
Succinic semialdehyde dehydrogenase (SSADH) from Acinetobacter baumannii (Ab) catalyzes the oxidation of succinic semialdehyde (SSA). This enzyme has two conserved cysteines (Cys289 and Cys291) and preferentially uses NADP+ over NAD+ as a hydride acceptor. Steady-state kinetic analysis showed that AbSSADH has the highest catalytic turnover (137 s-1 ) and can tolerate SSA inhibition the most (< 500 μm) among all SSADHs reported. Alanine substitutions of the two conserved cysteines indicated that Cys291Ala has ~ 65% activity compared with the wild-type enzyme while Cys289Ala is inactive, suggesting that Cys289 is the active residue participating in catalysis. Pre-steady-state kinetics showed for the first time burst kinetics for NADPH formation in SSADH, indicating that the rate-limiting step is associated with steps that occur after the hydride transfer. As the magnitude of burst kinetics represents the amount of NADPH formed during the first turnover, it is directly dependent on the amount of the deprotonated form of cysteine. The pKa of Cys289 was calculated from a plot of the burst magnitude vs pH as 7.4 ± 0.2. The Cys289 pKa was also measured based on the ability of AbSSADH to form an NADP-cysteine adduct, which can be detected by the increase of absorbance at ~ 330 nm as 7.9 ± 0.2. The lowering of the catalytic cysteine pKa by 0.6-1 unit renders the catalytic thiol more nucleophilic, which facilitates AbSSADH catalysis under physiological conditions. The methods established herein can specifically measure the active site cysteine pKa without interference from other cysteines. These techniques may be useful for studying ionization state of other cysteine-containing aldehyde dehydrogenases. ENZYME Succinic semialdehyde dehydrogenase, EC1.2.1.24.
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Affiliation(s)
- Jittima Phonbuppha
- Department of Biomolecular Science and Engineering, School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pobthum Munkajohnpong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- Department of Biomolecular Science and Engineering, School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Mahidol University, Nakhonsawan, Thailand
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4
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Wang X, Lai C, Lei G, Wang F, Long H, Wu X, Chen J, Huo G, Li Z. Kinetic characterization and structural modeling of an NADP +-dependent succinic semialdehyde dehydrogenase from Anabaena sp. PCC7120. Int J Biol Macromol 2017; 108:615-624. [PMID: 29242124 DOI: 10.1016/j.ijbiomac.2017.12.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022]
Abstract
Succinic semialdehyde dehydrogenases (SSADH) of cyanobacteria played a pivotal role in completing the cyanobacterial tricarboxylic acid cycle. The structural information of cofactor preference and catalysis for SSADH from cyanobacteria is currently available. However, the detailed kinetics of SSADH from cyanobacteria were not characterized yet. In this study, an all3556 gene encoding SSADH from Anabaena sp. PCC7120 (ApSSADH) was amplified and the recombinant ApSSADH was purified homogenously. Kinetic analysis showed that ApSSADH was an NADP+-dependent SSADH, which utilized NADP+ and succinic semialdehyde (SSA) as its preferred substrates and the activity of ApSSADH was inhibited by its substrate of SSA. At the same time, the Ser157 residue was found to function as the determinant of cofactor preference. Further study demonstrated that activity and substrate inhibition of ApSSADH would be greatly reduced by the mutation of the residues at the active site. Bioinformatic analysis indicated that those residues were highly conserved throughout the SSADHs. To our knowledge this is the first report exploring the detailed kinetics of SSADH from cyanobacteria.
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Affiliation(s)
- Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Chongde Lai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China
| | - Guofeng Lei
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Haozhi Long
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jinyin Chen
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China
| | - Guanghua Huo
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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5
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Kopečná M, Vigouroux A, Vilím J, Končitíková R, Briozzo P, Hájková E, Jašková L, von Schwartzenberg K, Šebela M, Moréra S, Kopečný D. The ALDH21 gene found in lower plants and some vascular plants codes for a NADP + -dependent succinic semialdehyde dehydrogenase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:229-243. [PMID: 28749584 DOI: 10.1111/tpj.13648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP+ -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD+ is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP+ binding induces a conformational change of the loop carrying Arg-228, which seals the NADP+ in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.
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Affiliation(s)
- Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - Jan Vilím
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRA-AgroParisTech, Université Paris-Saclay, Route de Saint-Cyr, F-78026, Versailles, France
| | - Eva Hájková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Lenka Jašková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | | | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
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6
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Crabo AG, Singh B, Nguyen T, Emami S, Gassner GT, Sazinsky MH. Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway. Arch Biochem Biophys 2017; 616:47-58. [PMID: 28153386 PMCID: PMC5318141 DOI: 10.1016/j.abb.2017.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 01/03/2017] [Accepted: 01/23/2017] [Indexed: 01/07/2023]
Abstract
Phenylacetaldehyde dehydrogenase catalyzes the NAD+-dependent oxidation of phenylactealdehyde to phenylacetic acid in the styrene catabolic and detoxification pathway of Pseudomonas putida (S12). Here we report the structure and mechanistic properties of the N-terminally histidine-tagged enzyme, NPADH. The 2.83 Å X-ray crystal structure is similar in fold to sheep liver cytosolic aldehyde dehydrogenase (ALDH1), but has unique set of intersubunit interactions and active site tunnel for substrate entrance. In solution, NPADH occurs as 227 kDa homotetramer. It follows a sequential reaction mechanism in which NAD+ serves as both the leading substrate and homotropic allosteric activator. In the absence of styrene monooxygenase reductase, which regenerates NAD+ from NADH in the first step of styrene catabolism, NPADH is inhibited by a ternary complex involving NADH, product, and phenylacetaldehyde, substrate. Each oligomerization domain of NPADH contains a six-residue insertion that extends this loop over the substrate entrance tunnel of a neighboring subunit, thereby obstructing the active site of the adjacent subunit. This feature could be an important factor in the homotropic activation and product inhibition mechanisms. Compared to ALDH1, the substrate channel of NPADH is narrower and lined with more aromatic residues, suggesting a means for enhancing substrate specificity.
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7
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Coitinho JB, Pereira MS, Costa DMA, Guimarães SL, Araújo SS, Hengge AC, Brandão TAS, Nagem RAP. Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation. Biochemistry 2016; 55:5453-63. [DOI: 10.1021/acs.biochem.6b00614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juliana B. Coitinho
- Departamento
de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mozart S. Pereira
- Departamento
de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Débora M. A. Costa
- Departamento
de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Samuel L. Guimarães
- Departamento
de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Simara S. Araújo
- Departamento
de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Tiago A. S. Brandão
- Departamento
de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ronaldo A. P. Nagem
- Departamento
de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
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Alternative Biotransformation of Retinal to Retinoic Acid or Retinol by an Aldehyde Dehydrogenase from Bacillus cereus. Appl Environ Microbiol 2016; 82:3940-3946. [PMID: 27107124 DOI: 10.1128/aem.00848-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A novel bacterial aldehyde dehydrogenase (ALDH) that converts retinal to retinoic acid was first identified in Bacillus cereus The amino acid sequence of ALDH from B. cereus (BcALDH) was more closely related to mammalian ALDHs than to bacterial ALDHs. This enzyme converted not only small aldehydes to carboxylic acids but also the large aldehyde all-trans-retinal to all-trans-retinoic acid with NAD(P)(+) We newly found that BcALDH and human ALDH (ALDH1A1) could reduce all-trans-retinal to all-trans-retinol with NADPH. The catalytic residues in BcALDH were Glu266 and Cys300, and the cofactor-binding residues were Glu194 and Glu457. The E266A and C300A variants showed no oxidation activity. The E194S and E457V variants showed 15- and 7.5-fold higher catalytic efficiency (kcat/Km) for the reduction of all-trans-retinal than the wild-type enzyme, respectively. The wild-type, E194S variant, and E457V variant enzymes with NAD(+) converted 400 μM all-trans-retinal to 210 μM all-trans-retinoic acid at the same amount for 240 min, while with NADPH, they converted 400 μM all-trans-retinal to 20, 90, and 40 μM all-trans-retinol, respectively. These results indicate that BcALDH and its variants are efficient biocatalysts not only in the conversion of retinal to retinoic acid but also in its conversion to retinol with a cofactor switch and that retinol production can be increased by the variant enzymes. Therefore, BcALDH is a novel bacterial enzyme for the alternative production of retinoic acid and retinol. IMPORTANCE Although mammalian ALDHs have catalyzed the conversion of retinal to retinoic acid with NAD(P)(+) as a cofactor, a bacterial ALDH involved in the conversion is first characterized. The biotransformation of all-trans-retinal to all-trans-retinoic acid by BcALDH and human ALDH was altered to the biotransformation to all-trans-retinol by a cofactor switch using NADPH. Moreover, the production of all-trans-retinal to all-trans-retinol was changed by mutations at positions 194 and 457 in BcALDH. The alternative biotransformation of retinoids was first performed in the present study. These results will contribute to the biotechnological production of retinoids, including retinoic acid and retinol.
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9
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SdhE-dependent formation of a functional Acetobacter pasteurianus succinate dehydrogenase in Gluconobacter oxydans—a first step toward a complete tricarboxylic acid cycle. Appl Microbiol Biotechnol 2015; 99:9147-60. [DOI: 10.1007/s00253-015-6972-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/17/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
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10
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Muñoz-Clares RA, González-Segura L, Riveros-Rosas H, Julián-Sánchez A. Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases. Chem Biol Interact 2015; 234:45-58. [DOI: 10.1016/j.cbi.2015.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/21/2014] [Accepted: 01/15/2015] [Indexed: 11/26/2022]
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11
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Liu L, Pan A, Spofford C, Zhou N, Alper HS. An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica. Metab Eng 2015; 29:36-45. [DOI: 10.1016/j.ymben.2015.02.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 12/29/2022]
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12
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González-Segura L, Riveros-Rosas H, Julián-Sánchez A, Muñoz-Clares RA. Residues that influence coenzyme preference in the aldehyde dehydrogenases. Chem Biol Interact 2015; 234:59-74. [PMID: 25601141 DOI: 10.1016/j.cbi.2014.12.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/12/2014] [Accepted: 12/31/2014] [Indexed: 11/25/2022]
Abstract
To find out the residues that influence the coenzyme preference of aldehyde dehydrogenases (ALDHs), we reviewed, analyzed and correlated data from their known crystal structures and amino-acid sequences with their published kinetic parameters for NAD(P)(+). We found that the conformation of the Rossmann-fold loops participating in binding the adenosine ribose is very conserved among ALDHs, so that coenzyme specificity is mainly determined by the nature of the residue at position 195 (human ALDH2 numbering). Enzymes with glutamate or proline at 195 prefer NAD(+) because the side-chains of these residues electrostatically and/or sterically repel the 2'-phosphate group of NADP(+). But contrary to the conformational rigidity of proline, the conformational flexibility of glutamate may allow NADP(+)-binding in some enzymes by moving the carboxyl group away from the 2'-phosphate group, which is possible if a small neutral residue is located at position 224, and favored if the residue at position 53 interacts with Glu195 in a NADP(+)-compatible conformation. Of the residues found at position 195, only glutamate interacts with the NAD(+)-adenosine ribose; glutamine and histidine cannot since their side-chain points are opposite to the ribose, probably because the absence of the electrostatic attraction by the conserved nearby Lys192, or its electrostatic repulsion, respectively. The shorter side-chains of other residues-aspartate, serine, threonine, alanine, valine, leucine, or isoleucine-are distant from the ribose but leave room for binding the 2'-phosphate group. Generally, enzymes having a residue different from Glu bind NAD(+) with less affinity, but they can also bind NADP(+) even sometimes with higher affinity than NAD(+), as do enzymes containing Thr/Ser/Gln195. Coenzyme preference is a variable feature within many ALDH families, consistent with being mainly dependent on a single residue that apparently has no other structural or functional roles, and therefore can easily be changed through evolution and selected in response to physiological needs.
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Affiliation(s)
- Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico.
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13
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Zhang J, Liu Y. A QM/MM study of the catalytic mechanism of succinic semialdehyde dehydrogenase from Synechococcus sp. PCC 7002 and Salmonella typhimurium. RSC Adv 2015. [DOI: 10.1039/c5ra21535h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The catalytic mechanism of succinic semialdehyde dehydrogenase (SSADH) has been studied using a combined quantum mechanics and molecular mechanics (QM/MM) approach.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
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14
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Meyer M, Schweiger P, Deppenmeier U. Succinic semialdehyde reductase Gox1801 from Gluconobacter oxydans in comparison to other succinic semialdehyde-reducing enzymes. Appl Microbiol Biotechnol 2014; 99:3929-39. [PMID: 25425279 DOI: 10.1007/s00253-014-6191-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 01/07/2023]
Abstract
Gluconobacter oxydans is an industrially important bacterium that possesses many uncharacterized oxidoreductases, which might be exploited for novel biotechnological applications. In this study, gene gox1801 was homologously overexpressed in G. oxydans and it was found that the relative expression of gox1801 was 13-fold higher than that in the control strain. Gox1801 was predicted to belong to the 3-hydroxyisobutyrate dehydrogenase-type proteins. The purified enzyme had a native molecular mass of 134 kDa and forms a homotetramer. Analysis of the enzymatic activity revealed that Gox1801 is a succinic semialdehyde reductase that used NADH and NADPH as electron donors. Lower activities were observed with glyoxal, methylglyoxal, and phenylglyoxal. The enzyme was compared to the succinic semialdehyde reductase GsSSAR from Geobacter sulfurreducens and the γ-hydroxybutyrate dehydrogenase YihU from Escherichia coli K-12. The comparison revealed that Gox1801 is the first enzyme from an aerobic bacterium reducing succinic semialdehyde with high catalytic efficiency. As a novel succinic semialdehyde reductase, Gox1801 has the potential to be used in the biotechnological production of γ-hydroxybutyrate.
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Affiliation(s)
- Maria Meyer
- Institute of Microbiology and Biotechnology, Meckenheimer Allee 168, 53115, Bonn, Germany
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15
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Jang EH, Ah Park S, Min Chi Y, Lee KS. Kinetic and structural characterization for cofactor preference of succinic semialdehyde dehydrogenase from Streptococcus pyogenes. Mol Cells 2014; 37:719-26. [PMID: 25256219 PMCID: PMC4213762 DOI: 10.14348/molcells.2014.0162] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/29/2014] [Accepted: 09/02/2014] [Indexed: 02/04/2023] Open
Abstract
The γ-Aminobutyric acid (GABA) that is found in prokaryotic and eukaryotic organisms has been used in various ways as a signaling molecule or a significant component generating metabolic energy under conditions of nutrient limitation or stress, through GABA catabolism. Succinic semialdehyde dehydrogenase (SSADH) catalyzes the oxidation of succinic semialdehyde to succinic acid in the final step of GABA catabolism. Here, we report the catalytic properties and two crystal structures of SSADH from Streptococcus pyogenes (SpSSADH) regarding its cofactor preference. Kinetic analysis showed that SpSSADH prefers NADP(+) over NAD(+) as a hydride acceptor. Moreover, the structures of SpSSADH were determined in an apo-form and in a binary complex with NADP(+) at 1.6 Å and 2.1 Å resolutions, respectively. Both structures of SpSSADH showed dimeric conformation, containing a single cysteine residue in the catalytic loop of each subunit. Further structural analysis and sequence comparison of SpSSADH with other SSADHs revealed that Ser158 and Tyr188 in SpSSADH participate in the stabilization of the 2'-phosphate group of adenine-side ribose in NADP(+). Our results provide structural insights into the cofactor preference of SpSSADH as the gram-positive bacterial SSADH.
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Affiliation(s)
- Eun Hyuk Jang
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713,
Korea
| | - Seong Ah Park
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 609-757,
Korea
| | - Young Min Chi
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713,
Korea
| | - Ki Seog Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 609-757,
Korea
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16
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Yin B, Cui D, Zhang L, Jiang S, Machida S, Yuan YA, Wei D. Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans. Proteins 2014; 82:2925-35. [PMID: 24825769 DOI: 10.1002/prot.24603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/26/2014] [Accepted: 04/29/2014] [Indexed: 11/07/2022]
Abstract
Gox2253 from Gluconobacter oxydans belongs to the short-chain dehydrogenases/reductases family, and catalyzes the reduction of heptanal, octanal, nonanal, and decanal with NADPH. To develop a robust working platform to engineer novel G. oxydans oxidoreductases with designed coenzyme preference, we adopted a structure based rational design strategy using computational predictions that considers the number of hydrogen bonds formed between enzyme and docked coenzyme. We report the crystal structure of Gox2253 at 2.6 Å resolution, ternary models of Gox2253 mutants in complex with NADH/short-chain aldehydes, and propose a structural mechanism of substrate selection. Molecular dynamics simulation shows that hydrogen bonds could form between 2'-hydroxyl group in the adenosine moiety of NADH and the side chain of Gox2253 mutant after arginine at position 42 is replaced with tyrosine or lysine. Consistent with the molecular dynamics prediction, Gox2253-R42Y/K mutants can use both NADH and NADPH as a coenzyme. Hence, the strategies here could provide a practical platform to engineer coenzyme selectivity for any given oxidoreductase and could serve as an additional consideration to engineer substrate-binding pockets.
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Affiliation(s)
- Bo Yin
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China; Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117543, Singapore
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