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Takishita Y, Subramanian S, Souleimanov A, Smith DL. Interactive effects of Pseudomonas entomophila strain 23S and Clavibacter michiganensis subsp. michiganensis on proteome and anti-Cmm compound production. J Proteomics 2023; 289:105006. [PMID: 37717723 DOI: 10.1016/j.jprot.2023.105006] [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: 02/11/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, the interactions between pure cultures of P. entomophila 23S and Cmm were investigated. First, the population dynamics of each bacterium during the interaction was determined using the selective media. Second, the amount of anti-Cmm compound produced by P. entomophila 23S in the presence of Cmm was quantified using HPLC. Lastly, a label-free shotgun proteomics study of P. entomophila 23S, Cmm, and a co-culture was conducted to understand the effects of the interaction of each bacterium at the proteomic level. Compared with the pure culture grown, the total number of proteins decreased in the interaction for both bacteria. P. entomophila 23S secreted stress-related proteins, such as chaperonins, peptidases, ABC-transporters and elongation factors. The bacterium also produced more proteins related with purine, pyrimidine, carbon and nitrogen metabolisms in the presence of Cmm. The population enumeration study revealed that the Cmm population declined dramatically during the interaction, while the population of P. entomophila 23S maintained. The quantification of anti-Cmm compound indicated that P. entomophila 23S produced significantly higher amount of anti-Cmm compound when it was cultured with Cmm. Overall, the study suggested that P. entomophila 23S, although is cidal to Cmm, was also negatively affected by the presence of Cmm, while trying to adapt to the stress condition, and that such an environment favored increased production of the anti-Cmm compound by P. entomophila 23S. SIGNIFICANCE: Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, secreted proteome of pure cultures of P. entomophila 23S and Cmm, and also of a co-culture was first time identified. Furthermore, the study found that P. entomophila strain 23S produced significantly higher amount of anti-Cmm compound when the bacterium was grown together with Cmm. Co-culture enhancing anti-Cmm compound production by P. entomophila 23S is useful information, particularly from a commercial point of view of biocontrol application, and for scale-up of anti-Cmm compound production.
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Affiliation(s)
- Yoko Takishita
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Sowmyalakshmi Subramanian
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Alfred Souleimanov
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Donald L Smith
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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2
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McNeale D, Esquirol L, Okada S, Strampel S, Dashti N, Rehm B, Douglas T, Vickers C, Sainsbury F. Tunable In Vivo Colocalization of Enzymes within P22 Capsid-Based Nanoreactors. ACS APPLIED MATERIALS & INTERFACES 2023; 15:17705-17715. [PMID: 36995754 DOI: 10.1021/acsami.3c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Virus-like particles (VLPs) derived from bacteriophage P22 have been explored as biomimetic catalytic compartments. In vivo colocalization of enzymes within P22 VLPs uses sequential fusion to the scaffold protein, resulting in equimolar concentrations of enzyme monomers. However, control over enzyme stoichiometry, which has been shown to influence pathway flux, is key to realizing the full potential of P22 VLPs as artificial metabolons. We present a tunable strategy for stoichiometric control over in vivo co-encapsulation of P22 cargo proteins, verified for fluorescent protein cargo by Förster resonance energy transfer. This was then applied to a two-enzyme reaction cascade. l-homoalanine, an unnatural amino acid and chiral precursor to several drugs, can be synthesized from the readily available l-threonine by the sequential activity of threonine dehydratase and glutamate dehydrogenase. We found that the loading density of both enzymes influences their activity, with higher activity found at lower loading density implying an impact of molecular crowding on enzyme activity. Conversely, increasing overall loading density by increasing the amount of threonine dehydratase can increase activity from the rate-limiting glutamate dehydrogenase. This work demonstrates the in vivo colocalization of multiple heterologous cargo proteins in a P22-based nanoreactor and shows that controlled stoichiometry of individual enzymes in an enzymatic cascade is required for the optimal design of nanoscale biocatalytic compartments.
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Affiliation(s)
- Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD 4102, Australia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
- CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
| | - Shoko Okada
- CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
| | - Shai Strampel
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
| | - Noor Dashti
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
| | - Bernd Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Indiana University, Bloomington, Indiana 47405, United States
| | - Claudia Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD 4102, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD 4000, Australia
- School of Biological and Environmental Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, QLD 4111, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD 4102, Australia
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Shortall K, Djeghader A, Magner E, Soulimane T. Insights into Aldehyde Dehydrogenase Enzymes: A Structural Perspective. Front Mol Biosci 2021; 8:659550. [PMID: 34055881 PMCID: PMC8160307 DOI: 10.3389/fmolb.2021.659550] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Aldehyde dehydrogenases engage in many cellular functions, however their dysfunction resulting in accumulation of their substrates can be cytotoxic. ALDHs are responsible for the NAD(P)-dependent oxidation of aldehydes to carboxylic acids, participating in detoxification, biosynthesis, antioxidant and regulatory functions. Severe diseases, including alcohol intolerance, cancer, cardiovascular and neurological diseases, were linked to dysfunctional ALDH enzymes, relating back to key enzyme structure. An in-depth understanding of the ALDH structure-function relationship and mechanism of action is key to the understanding of associated diseases. Principal structural features 1) cofactor binding domain, 2) active site and 3) oligomerization mechanism proved critical in maintaining ALDH normal activity. Emerging research based on the combination of structural, functional and biophysical studies of bacterial and eukaryotic ALDHs contributed to the appreciation of diversity within the superfamily. Herewith, we discuss these studies and provide our interpretation for a global understanding of ALDH structure and its purpose–including correct function and role in disease. Our analysis provides a synopsis of a common structure-function relationship to bridge the gap between the highly studied human ALDHs and lesser so prokaryotic models.
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Affiliation(s)
- Kim Shortall
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Edmond Magner
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
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Liu Y, Wang H, Li S, Zhang Y, Cheng X, Xiang W, Wang X. Engineering of primary metabolic pathways for titer improvement of milbemycins in Streptomyces bingchenggensis. Appl Microbiol Biotechnol 2021; 105:1875-1887. [PMID: 33564920 DOI: 10.1007/s00253-021-11164-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
Milbemycins are used commercially as insect repellents and acaricides; however, their high cost remains a significant challenge to commercial production. Hence, improving the titer of milbemycins for commercial application is an urgent priority. The present study aimed to effectively increase the titer of milbemycins using a combination of genome re-sequencing and metabolic engineering. First, 133 mutation sites were identified by genome re-sequencing in the mutagenized high-yielding strain BC04. Among them, three modifiable candidate genes (sbi_04868 encoding citrate synthase, sbi_06921 and sbi_06922 encoding alpha and beta subunits of acetyl-CoA carboxylase, and sbi_04683 encoding carbon uptake system gluconate transporter) related to primary metabolism were screened and identified. Next, the DNase-deactivated Cpf1-based integrative CRISPRi system was used in S. bingchenggensis to downregulate the transcription level of gene sbi_04868. Then, overexpression of the potential targets sbi_06921-06922 and sbi_04683 further facilitated milbemycin biosynthesis. Finally, those candidate genes were engineered to produce strains with combinatorial downregulation and overexpression, which resulted in the titer of milbemycin A3/A4 increased by 27.6% to 3164.5 mg/L. Our research not only identified three genes in S. bingchenggensis that are closely related to the production of milbemycins, but also offered an efficient engineering strategy to improve the titer of milbemycins using genome re-sequencing. KEY POINTS: • We compared the genomes of two strains with different titers of milbemycins. • We found three genes belonging to primary metabolism influence milbemycin production. • We improved titer of milbemycins by a combinatorial engineering of three targets.
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Affiliation(s)
- Yuqing Liu
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Haiyan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xu Cheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Xiangjing Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
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Liu Y, Munteanu CR, Kong Z, Ran T, Sahagún-Ruiz A, He Z, Zhou C, Tan Z. Identification of coenzyme-binding proteins with machine learning algorithms. Comput Biol Chem 2019; 79:185-192. [PMID: 30851647 DOI: 10.1016/j.compbiolchem.2019.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/11/2018] [Accepted: 01/25/2019] [Indexed: 01/12/2023]
Abstract
The coenzyme-binding proteins play a vital role in the cellular metabolism processes, such as fatty acid biosynthesis, enzyme and gene regulation, lipid synthesis, particular vesicular traffic, and β-oxidation donation of acyl-CoA esters. Based on the theory of Star Graph Topological Indices (SGTIs) of protein primary sequences, we proposed a method to develop a first classification model for predicting protein with coenzyme-binding properties. To simulate the properties of coenzyme-binding proteins, we created a dataset containing 2897 proteins, among 456 proteins functioned as coenzyme-binding activity. The SGTIs of peptide sequence were calculated with Sequence to Star Network (S2SNet) application. We used the SGTIs as inputs to several classification techniques with a machine learning software - Weka. A Random Forest classifier based on 3 features of the embedded and non-embedded graphs was identified as the best predictive model for coenzyme-binding proteins. This model developed was with the true positive (TP) rate of 91.7%, false positive (FP) rate of 7.6%, and Area Under the Receiver Operating Characteristic Curve (AUROC) of 0.971. The prediction of new coenzyme-binding activity proteins using this model could be useful for further drug development or enzyme metabolism researches.
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Affiliation(s)
- Yong Liu
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, Hunan, 410128, PR China
| | - Cristian R Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain; Biomedical Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), A Coruña, 15006, Spain
| | - Zhiwei Kong
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tao Ran
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - Alfredo Sahagún-Ruiz
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Animal Science, National Autonomous University of Mexico, Universidad 3000, Copilco Coyoacán, CP 04510, México D.F., Mexico
| | - Zhixiong He
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, Hunan, 410128, PR China.
| | - Chuanshe Zhou
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, Hunan, 410128, PR China
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China; Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, Hunan, 410128, PR China
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6
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Prakash P, Punekar NS, Bhaumik P. Structural basis for the catalytic mechanism and α-ketoglutarate cooperativity of glutamate dehydrogenase. J Biol Chem 2018. [PMID: 29540480 DOI: 10.1074/jbc.ra117.000149] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP+-dependent allosteric enzyme that is forward-inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (α-ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (α-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously reported. The AnGDH hexamers having subunits with different conformations indicated that its α-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp-154 and Gly-153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning α-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.
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Affiliation(s)
- Prem Prakash
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Narayan S Punekar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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7
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Tomita T, Yin L, Nakamura S, Kosono S, Kuzuyama T, Nishiyama M. Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum. FEBS Lett 2017; 591:1611-1622. [PMID: 28486765 DOI: 10.1002/1873-3468.12667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 11/06/2022]
Abstract
The NADP+ -dependent glutamate dehydrogenase from Corynebacterium glutamicum (CgGDH) is considered to be one of the key enzymes in the industrial fermentation of glutamate due to its high glutamate-producing activity. We determined the crystal structure of CgGDH complexed with NADP+ and 2-iminoglutarate. Among six subunits of hexameric CgGDH-binding NADP+ , only four subunits bind 2-iminoglutarate in a closed form, while the other two are in an open form. In the closed form, 2-iminoglutarate is bound to the substrate-binding site with the 2-imino group stacked by the nicotinamide ring of the coenzyme, suggesting a prehydride transfer state in a hypothesized reaction scheme with the imino intermediate. We also conducted MD simulations and provide insights into the extreme preference for the glutamate-producing reaction of CgGDH. DATABASE The atomic coordinate and structure factors have been deposited in the RCSB PDB database under the accession number 5GUD.
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Affiliation(s)
- Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Lulu Yin
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Shugo Nakamura
- Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Japan
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8
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Chen H, Zhu Z, Huang R, Zhang YHP. Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP + to NAD + with Its Application to Biobatteries. Sci Rep 2016; 6:36311. [PMID: 27805055 PMCID: PMC5090862 DOI: 10.1038/srep36311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/13/2016] [Indexed: 01/30/2023] Open
Abstract
Engineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP+ to NAD+. Through amino acid-sequence alignment of NADP+- and NAD+-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP+ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 104-fold reversal of the coenzyme selectivity from NADP+ to NAD+. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm−2 and 0.255 mA cm−2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm−2. This study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries.
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Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA
| | - Zhiguang Zhu
- Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, VA 24060, USA.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA
| | - Yi-Heng Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA.,Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, VA 24060, USA.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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9
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Oliveira T, Sharkey MA, Engel PC, Khan AR. Crystal structure of a chimaeric bacterial glutamate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2016; 72:462-6. [PMID: 27303899 PMCID: PMC4909246 DOI: 10.1107/s2053230x16007305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/02/2016] [Indexed: 11/10/2022] Open
Abstract
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)(+) as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD(+) versus NADP(+), but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase from Clostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia coli enzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP(+) cofactor from the parent E. coli domain II, although there are subtle differences in catalytic activity.
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Affiliation(s)
- Tânia Oliveira
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
| | - Michael A. Sharkey
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul C. Engel
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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10
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Zhu L, Xu X, Wang L, Dong H, Yu B. The D-Lactate Dehydrogenase from Sporolactobacillus inulinus Also Possessing Reversible Deamination Activity. PLoS One 2015; 10:e0139066. [PMID: 26398356 PMCID: PMC4580590 DOI: 10.1371/journal.pone.0139066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/07/2015] [Indexed: 11/18/2022] Open
Abstract
Hydroxyacid dehydrogenases are responsible for the conversion of 2-keto acids to 2-hydroxyacids and have a wide range of biotechnological applications. In this study, a D-lactate dehydrogenase (D-LDH) from a Sporolactobacillus inulinus strain was experimentally verified to have both the D-LDH and glutamate dehydrogenase (GDH) activities (reversible deamination). The catalytic mechanism was demonstrated by identification of key residues from the crystal structure analysis and site-directed mutagenesis. The Arg234 and Gly79 residues of this enzyme play a significant role in both D-LDH and GDH activities. His295 and Phe298 in DLDH744 were identified to be key residues for lactate dehydrogenase (LDH) activity only whereas Tyr101 is a unique residue that is critical for GDH activity. Characterization of the biochemical properties contributes to understanding of the catalytic mechanism of this novel D-lactate dehydrogenase enzyme.
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Affiliation(s)
- Lingfeng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoling Xu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Limin Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Hui Dong
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, PR China
- * E-mail: (BY) (HD)
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- * E-mail: (BY) (HD)
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NADP+-Preferring D-Lactate Dehydrogenase from Sporolactobacillus inulinus. Appl Environ Microbiol 2015; 81:6294-301. [PMID: 26150461 DOI: 10.1128/aem.01871-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/28/2015] [Indexed: 11/20/2022] Open
Abstract
Hydroxy acid dehydrogenases, including l- and d-lactate dehydrogenases (L-LDH and D-LDH), are responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids and extensively used in a wide range of biotechnological applications. A common feature of LDHs is their high specificity for NAD(+) as a cofactor. An LDH that could effectively use NADPH as a coenzyme could be an alternative enzymatic system for regeneration of the oxidized, phosphorylated cofactor. In this study, a d-lactate dehydrogenase from a Sporolactobacillus inulinus strain was found to use both NADH and NADPH with high efficiencies and with a preference for NADPH as its coenzyme, which is different from the coenzyme utilization of all previously reported LDHs. The biochemical properties of the D-LDH enzyme were determined by X-ray crystal structural characterization and in vivo and in vitro enzymatic activity analyses. The residue Asn(174) was demonstrated to be critical for NADPH utilization. Characterization of the biochemical properties of this enzyme will contribute to understanding of the catalytic mechanism and provide referential information for shifting the coenzyme utilization specificity of 2-hydroxyacid dehydrogenases.
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12
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Son HF, Kim IK, Kim KJ. Structural insights into domain movement and cofactor specificity of glutamate dehydrogenase from Corynebacterium glutamicum. Biochem Biophys Res Commun 2015; 459:387-92. [PMID: 25727019 DOI: 10.1016/j.bbrc.2015.02.109] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
Glutamate dehydrogenase (GDH) is an enzyme involved in the synthesis of amino acids by converting glutamate to α-ketoglutarate, and vice versa. To investigate the molecular mechanism of GDH, we determined a crystal structure of the Corynebacterium glutamicum-derived GDH (CgGDH) in complex with its NADP cofactor and α-ketoglutarate substrate. CgGDH functions as a hexamer, and each CgGDH monomer comprises 2 separate domains; a Rossmann fold cofactor-binding domain and a substrate-binding domain. The structural comparison between the apo- and cofactor/substrate-binding forms revealed that the CgGDH enzyme undergoes a domain movement during catalysis. In the apo-form, CgGDH exists as an open state, and upon binding of the substrate and cofactor the protein undergoes a conformation change to a closed state. Our structural study also revealed that CgGDH has cofactor specificity for NADP, but not NAD, and this was confirmed by GDH activity measurements. Residues involved in the stabilization of the NADP cofactor and the α-ketoglutarate substrate were identified, and their roles in substrate/cofactor binding were confirmed by site-directed mutagenesis experiments.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Il-Kwon Kim
- Paik Kwang Industrial Company Ltd., 57 Oehang-4 Gil, Gunsan, Jellabuk-do 573-879, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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13
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Peng B, Su YB, Li H, Han Y, Guo C, Tian YM, Peng XX. Exogenous alanine and/or glucose plus kanamycin kills antibiotic-resistant bacteria. Cell Metab 2015; 21:249-262. [PMID: 25651179 DOI: 10.1016/j.cmet.2015.01.008] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/02/2014] [Accepted: 01/13/2015] [Indexed: 01/18/2023]
Abstract
Multidrug-resistant bacteria are an increasingly serious threat to human and animal health. However, novel drugs that can manage infections by multidrug-resistant bacteria have proved elusive. Here we show that glucose and alanine abundances are greatly suppressed in kanamycin-resistant Edwardsiella tarda by GC-MS-based metabolomics. Exogenous alanine or glucose restores susceptibility of multidrug-resistant E. tarda to killing by kanamycin, demonstrating an approach to killing multidrug-resistant bacteria. The mechanism underlying this approach is that exogenous glucose or alanine promotes the TCA cycle by substrate activation, which in turn increases production of NADH and proton motive force and stimulates uptake of antibiotic. Similar results are obtained with other Gram-negative bacteria (Vibrio parahaemolyticus, Klebsiella pneumoniae, Pseudomonas aeruginosa) and Gram-positive bacterium (Staphylococcus aureus), and the results are also reproduced in a mouse model for urinary tract infection. This study establishes a functional metabolomics-based strategy to manage infection by antibiotic-resistant bacteria.
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Affiliation(s)
- Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8197, USA
| | - Yu-Bin Su
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yi Han
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Chang Guo
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yao-Mei Tian
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Xuan-Xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Biocontrol, School of Life Sciences, MOE Key Lab Aquat Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
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14
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Prakash P, Walvekar AS, Punekar NS, Bhaumik P. Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase from Aspergillus niger. Acta Crystallogr F Struct Biol Commun 2014; 70:1508-12. [PMID: 25372818 PMCID: PMC4231853 DOI: 10.1107/s2053230x14021499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
Glutamate dehydrogenase (GDH) catalyzes the NAD-dependent or NADP-dependent oxidative deamination of L-glutamate to 2-oxoglutarate and ammonia. This important reversible reaction establishes the link between carbon and nitrogen metabolism. In this study, Aspergillus niger NADP-GDH (AnGDH) has been overexpressed and purified. Purified AnGDH, with a high specific activity of 631.1 units per milligram of protein, was crystallized and the crystal diffracted to 2.9 Å resolution using a home X-ray source. Preliminary analysis of the X-ray diffraction data showed that the crystal belonged to space group R32, with unit-cell parameters a=b=173.8, c=241.5 Å, α=β=90, γ=120°. The crystals exhibited an unusually high solvent content (83.0%) and had only one molecule in the asymmetric unit. Initial phases were obtained by molecular replacement, and model building and structure refinement of AnGDH are in progress.
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Affiliation(s)
- Prem Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Adhish S. Walvekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Narayan S. Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo. mBio 2013; 4:e00881-13. [PMID: 24255125 PMCID: PMC3870243 DOI: 10.1128/mbio.00881-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
UNLABELLED Nitrogen regulation in Escherichia coli is a model system for gene regulation in bacteria. Growth on glutamine as a sole nitrogen source is assumed to be nitrogen limiting, inferred from slow growth and strong NtrB/NtrC-dependent gene activation. However, we show that under these conditions, the intracellular glutamine concentration is not limiting but 5.6-fold higher than in ammonium-replete conditions; in addition, α-ketoglutarate concentrations are elevated. We address this glutamine paradox from a systems perspective. We show that the dominant role of NtrC is to regulate glnA transcription and its own expression, indicating that the glutamine paradox is not due to NtrC-independent gene regulation. The absolute intracellular NtrC and GS concentrations reveal molecular control parameters, where NtrC-specific activities were highest in nitrogen-starved cells, while under glutamine growth, NtrC showed intermediate specific activity. We propose an in vivo model in which α-ketoglutarate can derepress nitrogen regulation despite nitrogen sufficiency. IMPORTANCE Nitrogen is the most important nutrient for cell growth after carbon, and its metabolism is coordinated at the metabolic, transcriptional, and protein levels. We show that growth on glutamine as a sole nitrogen source, commonly assumed to be nitrogen limiting and used as such as a model system for nitrogen limitation, is in fact nitrogen replete. Our integrative quantitative analysis of key molecules involved in nitrogen assimilation and regulation reveal that glutamine is not necessarily the dominant molecule signaling nitrogen sufficiency and that α-ketoglutarate may play a more important role in signaling nitrogen status. NtrB/NtrC integrates α-ketoglutarate and glutamine signaling--sensed by the UTase (glnD) and PII (glnB), respectively--and regulates the nitrogen response through self-regulated expression and phosphorylation-dependent activation of the nitrogen (ntr) regulon. Our findings support α-ketoglutarate acting as a global regulatory metabolite.
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Engel PC. Glutamate dehydrogenases: the why and how of coenzyme specificity. Neurochem Res 2013; 39:426-32. [PMID: 23761034 DOI: 10.1007/s11064-013-1089-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 05/23/2013] [Accepted: 05/25/2013] [Indexed: 11/28/2022]
Abstract
NAD(+) and NADP(+), chemically similar and with almost identical standard oxidation-reduction potentials, nevertheless have distinct roles, NAD(+) serving catabolism and ATP generation whereas NADPH is the biosynthetic reductant. Separating these roles requires strict specificity for one or the other coenzyme for most dehydrogenases. In many organisms this holds also for glutamate dehydrogenases (GDH), NAD(+)-dependent for glutamate oxidation, NADP(+)-dependent for fixing ammonia. In higher animals, however, GDH has dual specificity. It has been suggested that GDH in mitochondria reacts only with NADP(H), the NAD(+) reaction being an in vitro artefact. However, contrary evidence suggests mitochondrial GDH not only reacts with NAD(+) but maintains equilibrium using the same pool as accessed by β-hydroxybutyrate dehydrogenase. Another complication is the presence of an energy-linked dehydrogenase driving NADP(+) reduction by NADH, maintaining the coenzyme pools at different oxidation-reduction potentials. Its coexistence with GDH makes possible a futile cycle, control of which is not yet properly explained. Structural studies show NAD(+)-dependent, NADP(+)-dependent and dual-specificity GDHs are closely related and a few site-directed mutations can reverse specificity. Specificity for NAD(+) or for NADP(+) has probably emerged repeatedly during evolution, using different structural solutions on different occasions. In various GDHs the P7 position in the coenzyme-binding domain plays a key role. However, whereas in other dehydrogenases an acidic P7 residue usually hydrogen bonds to the 2'- and 3'-hydroxyls, dictating NAD(+) specificity, among GDHs, depending on detailed conformation of surrounding residues, an acidic P7 may permit binding of NAD(+) only, NADP(+) only, or in higher animals both.
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Affiliation(s)
- Paul C Engel
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland,
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