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Dunham NP, Winston MS, Ray R, Eberle CM, Newman JA, Gao Q, Cao Y, Barrientos RC, Ji Y, Reibarkh MY, Silverman SM. Transaminase-Catalyzed Synthesis of β-Branched Noncanonical Amino Acids Driven by a Lysine Amine Donor. J Am Chem Soc 2024; 146:16306-16313. [PMID: 38804633 DOI: 10.1021/jacs.4c05175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transaminases are choice biocatalysts for the synthesis of chiral primary amines, including amino acids bearing contiguous stereocenters. In this study, we employ lysine as a "smart" amine donor in transaminase-catalyzed dynamic kinetic resolution reactions to access β-branched noncanonical arylalanines. Our mechanistic investigation demonstrates that, upon transamination, the lysine-derived ketone byproduct readily cyclizes to a six-membered imine, driving the equilibrium in the desired direction and thus alleviating the need to load superstoichiometric quantities of the amine donor or deploy a multienzyme cascade. Lysine also shows good overall compatibility with a panel of wild-type transaminases, a promising hint of its application as a smart donor more broadly. Indeed, by this approach, we furnished a broad scope of β-branched arylalanines, including some bearing hitherto intractable cyclopropyl and isopropyl substituents, with high yields and excellent selectivities.
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Affiliation(s)
- Noah P Dunham
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ritwika Ray
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Claire M Eberle
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Justin A Newman
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Qi Gao
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yang Cao
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rodell C Barrientos
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yining Ji
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Steven M Silverman
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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2
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Sao Emani C, Reiling N. The efflux pumps Rv1877 and Rv0191 play differential roles in the protection of Mycobacterium tuberculosis against chemical stress. Front Microbiol 2024; 15:1359188. [PMID: 38516013 PMCID: PMC10956863 DOI: 10.3389/fmicb.2024.1359188] [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: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Background It was previously shown that GlnA3sc enabled Streptomyces coelicolor to survive in excess polyamines. However, subsequent studies revealed that Rv1878, the corresponding Mycobacterium tuberculosis (M.tb) ortholog, was not essential for the detoxification of spermine (Spm), in M.tb. On the other hand, the multi-drug efflux pump Rv1877 was previously shown to enable export of a wide range of compounds, while Rv0191 was shown to be more specific to chloramphenicol. Rationale Therefore, we first wanted to determine if detoxification of Spm by efflux can be achieved by any efflux pump, or if that was dependent upon the function of the pump. Next, since Rv1878 was found not to be essential for the detoxification of Spm, we sought to follow-up on the investigation of the physiological role of Rv1878 along with Rv1877 and Rv0191. Approach To evaluate the specificity of efflux pumps in the mycobacterial tolerance to Spm, we generated unmarked ∆rv1877 and ∆rv0191 M.tb mutants and evaluated their susceptibility to Spm. To follow up on the investigation of any other physiological roles they may have, we characterized them along with the ∆rv1878 M.tb mutant. Results The ∆rv1877 mutant was sensitive to Spm stress, while the ∆rv0191 mutant was not. On the other hand, the ∆rv1878 mutant grew better than the wild-type during iron starvation yet was sensitive to cell wall stress. The proteins Rv1877 and Rv1878 seemed to play physiological roles during hypoxia and acidic stress. Lastly, the ∆rv0191 mutant was the only mutant that was sensitive to oxidative stress. Conclusion The multidrug MFS-type efflux pump Rv1877 is required for Spm detoxification, as opposed to Rv0191 which seems to play a more specific role. Moreover, Rv1878 seems to play a role in the regulation of iron homeostasis and the reconstitution of the cell wall of M.tb. On the other hand, the sensitivity of the ∆rv0191 mutant to oxidative stress, suggests that Rv0191 may be responsible for the transport of low molecular weight thiols.
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Affiliation(s)
- Carine Sao Emani
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
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3
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Wei L, Liu L, Gong W. Structure of mycobacterial ergothioneine-biosynthesis C-S lyase EgtE. J Biol Chem 2024; 300:105539. [PMID: 38072054 PMCID: PMC10805701 DOI: 10.1016/j.jbc.2023.105539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 01/02/2024] Open
Abstract
L-ergothioneine is widely distributed among various microbes to regulate their physiology and pathogenicity within complex environments. One of the key steps in the ergothioneine-biosynthesis pathway, the C-S bond cleavage reaction, uses the pyridoxal 5'-phosphate dependent C-S lyase to produce the final product L-ergothioneine. Here, we present the crystallographic structure of the ergothioneine-biosynthesis C-S lyase EgtE from Mycobacterium smegmatis (MsEgtE) represents the first published structure of ergothioneine-biosynthesis C-S lyases in bacteria and shows the effects of active site residues on the enzymatic reaction. The MsEgtE and the previously reported ergothioneine-biosynthesis C-S lyase Egt2 from Neurospora crassa (NcEgt2) fold similarly. However, discrepancies arise in terms of substrate recognition, as observed through sequence and structure comparison of MsEgtE and NcEgt2. The structural-based sequence alignment of the ergothioneine-biosynthesis C-S lyase from fungi and bacteria shows clear distinctions among the recognized substrate residues, but Arg348 is critical and an extremely conserved residue for substrate recognition. The α14 helix is exclusively found in the bacteria EgtE, which represent the most significant difference between bacteria EgtE and fungi Egt2, possibly resulting from the convergent evolution of bacteria and fungi.
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Affiliation(s)
- Lili Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Weimin Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
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4
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Ki D, Hong H, Kim IK, Kim KJ. Crystal Structure and Functional Characterization of Acetylornithine Aminotransferase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37230944 DOI: 10.1021/acs.jafc.3c00659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The amino acids l-arginine and l-ornithine are widely used in animal feed and as health supplements and pharmaceutical compounds. In arginine biosynthesis, acetylornithine aminotransferase (AcOAT) uses pyridoxal-5'-phosphate (PLP) as a cofactor for amino group transfer. Here, we determined the crystal structures of the apo and PLP complex forms of AcOAT from Corynebacterium glutamicum (CgAcOAT). Our structural observations revealed that CgAcOAT undergoes an order-to-disorder conformational change upon binding with PLP. Additionally, we observed that unlike other AcOATs, CgAcOAT exists as a tetramer. Subsequently, we identified the key residues involved in PLP and substrate binding based on structural analysis and site-directed mutagenesis. This study might provide structural insights on CgAcOAT, which can be utilized for the development of improved l-arginine production enzymes.
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Affiliation(s)
- Dongwoo Ki
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hwaseok Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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5
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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Bangalore PK, Pedapati RK, Pranathi AN, Batchu UR, Misra S, Estharala M, Sriram D, Kantevari S. Aryl-n-hexanamide linked enaminones of usnic acid as promising antimicrobial agents. Mol Divers 2022; 27:811-836. [PMID: 35608808 DOI: 10.1007/s11030-022-10456-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
Lichen secondary metabolites are well explored medicinal agents with diverse pharmacological properties. One of the important antibiotic lichen secondary metabolites is usnic acid. Its diverse medicinal profiles prompted us to explore it as a potential antitubercular molecule. Towards this direction, continuing our efforts on the discovery and development of new analogs with potent antitubercular properties we designed, synthesized, and evaluated a set of 37 usnic acid enaminone-coupled aryl-n-hexanamides (3-39). The study yielded a 3,4-dimethoxyphenyl compound (13, 5.3 µM) as the most active anti-TB molecule. The docking studies were performed on 7 different enzymes to better understand the binding modes, where it was observed that compound 13 bound strongly with glucose dehydrogenase (Gscore: - 9.03). Further antibacterial investigations revealed compound 2 with potent inhibition on Salmonella typhi and Bacillus subtilis (MIC 3 µM) and MIC values of 7 and 14 µM on Streptococcus mutans and Escherichia coli respectively. Compound 19 (3-F-5-CF3-phenyl) displayed encouraging antibacterial profiles against E. coli, S. typhi and S. mutans with MIC values of 10 µM respectively. Interestingly, compound 20 (2,6-difluorophenyl) also displayed good antibacterial activity against E. coli with an MIC value of 6 µM. These encouraging pharmacological results will help for better designing and developing usnic acid-based semi-synthetic derivatives as potential antimicrobial agents. A set of 37 new usnic acid enaminone-coupled aryl-n-hexanamides were synthesized and evaluated as potential antimicrobial agents. Compound 13 was identified as the most active antitubercular molecule. 13 was further docked against 7 different enzymes of tuberculosis. The molecule displayed maximum binding energy with the enzyme Glucose dehydrogenase (Gscore: - 9.03), indicating that these hexanamides possibly act by inhibiting the glucose metabolic pathway of the bacterium. Surprisingly, the intermediate hexanoic acid 2 was identified as potent antibacterial agent, acting on both gram-positive and gram-negative bacterial strains (3-14 μM). The active compounds may be subjected to structural iterations to develop further leads.
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Affiliation(s)
- Pavan Kumar Bangalore
- Fluoro and Agrochemicals Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India. .,Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14850, USA.
| | - Ravi Kumar Pedapati
- Fluoro and Agrochemicals Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Abburi Naga Pranathi
- Fluoro and Agrochemicals Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Uma Rajeswari Batchu
- Applied Biology Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
| | - Sunil Misra
- Applied Biology Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India
| | - Madhurekha Estharala
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India
| | - Dharmarajan Sriram
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India
| | - Srinivas Kantevari
- Fluoro and Agrochemicals Division, CSIR- Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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7
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Madugula SS, Nagamani S, Jamir E, Priyadarsinee L, Sastry GN. Drug repositioning for anti-tuberculosis drugs: an in silico polypharmacology approach. Mol Divers 2021; 26:1675-1695. [PMID: 34468898 DOI: 10.1007/s11030-021-10296-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/10/2021] [Indexed: 01/20/2023]
Abstract
Development of potential antitubercular molecules is a challenging task due to the rapidly emerging drug-resistant strains of Mycobacterium tuberculosis (M.tb). Structure-based approaches hold greater benefit in identifying compounds/drugs with desired polypharmacological profiles. These methods can be employed based on the knowledge of protein binding sites to identify the complementary ligands. In this study, polypharmacology guided computational drug repurposing approach was applied to identify potential antitubercular drugs. 20 important druggable protein targets in M.tb were considered from the target library of Molecular Property Diagnostic Suite-Tuberculosis (MPDSTB- http://mpds.neist.res.in:8084 ) for virtual screening. FDA approved drugs were collected, preprocessed and docked in the active sites of the 20 M.tb targets. The top 300 drug molecules from each target (20 × 300) were filtered-in and subsequently screened for possible antitubercular and antimycobacterial activity using PASS tool. Using this approach, 34 drugs with predicted antitubercular and anti-mycobacterial activity were identified along with good binding affinity against multiple M.tb targets. Interestingly, 21 out of the 34 identified drugs are antibiotics while 4 drug molecules (nitrofural, stavudine, quinine and quinidine) are non-antibiotics showing promising predicted antitubercular activity. Most of these molecules have the similar privileged antimycobacterial drugs scaffold. Further drug likeness properties were calculated to get deeper insights to M.tb lead molecules. Interestingly, it was also observed that the drugs identified from the study are under different stages of drug discovery (i.e., in vitro, clinical trials) for the effective treatment of various diseases including cancer, degenerative diseases, dengue virus infection, tuberculosis, etc. Krasavin et al., 2017 synthesized nitrofuran analogues with appreciable MICs (22-23 µM) against M.tb H37Rv. These experiments further add to the credibility of the drugs identified in this study (TB).
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Affiliation(s)
- Sita Sirisha Madugula
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - Esther Jamir
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - G Narahari Sastry
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India.
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8
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Hillier HT, Altermark B, Leiros I. The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway. FEBS J 2020; 287:4641-4658. [PMID: 32112674 DOI: 10.1111/febs.15265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023]
Abstract
l-2,4-diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω-position of substrates, and is the intial and rate-limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)-2-methyl-1,4,5,6-tetrahydro-4-pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases remain poorly characterized. Herein, we present the crystal structure of EctB (2.45 Å), a DABA aminotransferase from Chromohalobacter salexigens DSM 3043, a well-studied organism with respect to osmoadaptation by ectoine biosynthesis. We investigate the enzyme's oligomeric state to show that EctB from C. salexigens is a tetramer of two functional dimers, and suggest conserved recognition sites for dimerization that also includes the characteristic gating loop that helps shape the active site of the neighboring monomer. Although ω-transaminases are known to have two binding pockets to accommodate for their dual substrate specificity, we herein provide the first description of two binding pockets in the active site that may account for the catalytic character of DABA aminotransferases. Furthermore, our biochemical data reveal that the EctB enzyme from C. salexigens is a thermostable, halotolerant enzyme with a broad pH tolerance which may be linked to its tetrameric state. Put together, this study creates a solid foundation for a deeper structural understanding of DABA aminotransferases and opening up for future downstream studies of EctB's catalytic character and its redesign as a better catalyst for ectoine biosynthesis. In summary, we believe that the EctB enzyme from C. salexigens can serve as a benchmark enzyme for characterization of DABA aminotransferases. DATABASE: Structural data are available in PDB database under the accession number 6RL5.
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Affiliation(s)
- Heidi Therese Hillier
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
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Voss M, Xiang C, Esque J, Nobili A, Menke MJ, André I, Höhne M, Bornscheuer UT. Creation of ( R)-Amine Transaminase Activity within an α-Amino Acid Transaminase Scaffold. ACS Chem Biol 2020; 15:416-424. [PMID: 31990173 DOI: 10.1021/acschembio.9b00888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The enzymatic transamination of ketones into (R)-amines represents an important route for accessing a range of pharmaceuticals or building blocks. Although many publications have dealt with enzyme discovery, protein engineering, and the application of (R)-selective amine transaminases [(R)-ATA] in biocatalysis, little is known about the actual in vivo role and how these enzymes have evolved from the ubiquitous α-amino acid transaminases (α-AATs). Here, we show the successful introduction of an (R)-transaminase activity in an α-amino acid aminotransferase with one to six amino acid substitutions in the enzyme's active site. Bioinformatic analysis combined with computational redesign of the d-amino acid aminotransferase (DATA) led to the identification of a sextuple variant having a specific activity of 326 milliunits mg-1 in the conversion of (R)-phenylethylamine and pyruvate to acetophenone and d-alanine. This value is similar to those of natural (R)-ATAs, which typically are in the range of 250 milliunits mg-1. These results demonstrate that (R)-ATAs can evolve from α-AAT as shown here for the DATA scaffold.
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Affiliation(s)
- Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Chao Xiang
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Jérémy Esque
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Alberto Nobili
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Marian J. Menke
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
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10
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Kwon S, Park HH. Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement. Comput Struct Biotechnol J 2019; 17:1031-1039. [PMID: 31452855 PMCID: PMC6698932 DOI: 10.1016/j.csbj.2019.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022] Open
Abstract
Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5′-phosphate (PLP) as a cofactor. TAs are categorized according to the amino group position of the donor substrate and respective TAs recognize their own specific substrates. Over the past decade, a number of TA structures have been determined by X-ray crystallography. On the basis of the structural information, the detailed mechanism of substrate recognition by TAs has also been elucidated. In this review, fold type I TAs are addressed intensively. Comparative studies on structural differences between the apo and holo forms of fold type I TAs have demonstrated that regions containing the active site exhibit structural plasticity in the apo form, facilitating PLP insertion into the active site. In addition, given that TAs recognize two different kinds of substrates, they possess dual substrate specificity. It is known that spatial rearrangements of active site residues occur upon binding of the substrates. Intriguingly, positively charged residues are predominantly distributed at the active site cavity. The electric field generated by such charge distributions may attract negatively charged molecules, such as PLP and amino group acceptors, into the active site. Indeed, TAs show remarkable dynamics in diverse aspects. In this review, we describe the comprehensive working mechanism of fold type I TAs, with a focus on conformational changes.
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Affiliation(s)
| | - Hyun Ho Park
- Corresponding author at: College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea.
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11
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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12
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Venugopala KN, Chandrashekharappa S, Pillay M, Bhandary S, Kandeel M, Mahomoodally FM, Morsy MA, Chopra D, Aldhubiab BE, Attimarad M, Alwassil OI, Harsha S, Mlisana K, Odhav B. Synthesis and Structural Elucidation of Novel Benzothiazole Derivatives as Anti-tubercular Agents: In-silico Screening for Possible Target Identification. Med Chem 2019; 15:311-326. [PMID: 29968540 DOI: 10.2174/1573406414666180703121815] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/14/2018] [Accepted: 06/13/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Benzothiazole derivatives are known for anti-TB properties. Based on the known anti-TB benzothiazole pharmacophore, in the present study, we described the synthesis, structural elucidation, and anti-tubercular screening of a series of novel benzothiazole (BNTZ) derivatives (BNTZ 1-7 and BNTZ 8-13). OBJECTIVE The study aims to carry out the development of benzothiazole based anti-TB compounds. METHODS Title compounds are synthesized by microwave method and purified by column chromatography. Characterization of the compounds is achieved by FT-IR, NMR (1H and 13C), LCMS and elemental analysis. Screening of test compounds for anti-TB activity is achieved by Resazurin Microplate Assay (REMA) Plate method. RESULTS It was noted that the BNTZ compound with an isoquinoline nucleus (BNTZ 9) exhibited remarkable anti-tubercular activity at 8 µg/mL against both the susceptible strain H37Rv and the multi-drug resistant tuberculosis strains of Mycobacterium tuberculosis. On the other hand, the BNTZ compound with a naphthalene nucleus (BNTZ 2) revealed anti-tubercular activity at 6 µg/mL and 11 µg/mL against both the susceptible strain H37Rv and the multi-drug resistant tuberculosis strains of M. tuberculosis, respectively. One of the selected BNTZ derivatives BNTZ 13 was used for single crystal X-ray studies. CONCLUSION To identify the appropriate target for potent BNTZ compounds from the series, molecular modeling studies revealed the multiple strong binding of several BNTZs with mycobacterium lysine-ɛ-aminotransferase and decaprenyl-phosphoryl-β-D-ribose 2'-oxidase. The interaction is derived by forming favorable hydrogen bonds and stacking interactions. This new class of BNTZ compounds gave promising anti-tubercular actions in the low micromolar range, and can be further optimized on a structural basis to develop promising, novel, BNTZ pharmacophore-based anti-tubercular drugs.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Sandeep Chandrashekharappa
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, TIFR, GKVK, Bellary Road, Bangalore 560 065, India
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | - Subhrajyoti Bhandary
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Mahmoud Kandeel
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
| | - Fawzi M Mahomoodally
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia.,Department of Pharmacology, Faculty of Medicine, Minia University, 61511 El-Minia, Egypt
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Osama I Alwassil
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia.,Department of Pharmaceutical Sciences, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, 3163, P.O. Box 3660, Riyadh, 11481, Saudi Arabia
| | - Sree Harsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
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13
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Dey A, Shree S, Pandey SK, Tripathi RP, Ramachandran R. Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene: DNA BINDING AND IDENTIFICATION OF SMALL MOLECULE INHIBITORS. J Biol Chem 2016; 291:11967-80. [PMID: 27006398 DOI: 10.1074/jbc.m115.700484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 11/06/2022] Open
Abstract
Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30-60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target.
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Affiliation(s)
- Abhishek Dey
- From the Molecular and Structural Biology Division and
| | - Sonal Shree
- From the Molecular and Structural Biology Division and
| | - Sarvesh Kumar Pandey
- the Medicinal and Process Chemistry Division, Council of Scientific and Industrial Research-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Rama Pati Tripathi
- the Medicinal and Process Chemistry Division, Council of Scientific and Industrial Research-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
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14
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Seo JH, Kim EM, Chae A, Kim BG. Lysine ε-aminotransferases: kinetic constants, substrate specificities, and the variation in active site residues. Enzyme Microb Technol 2016; 84:11-6. [PMID: 26827769 DOI: 10.1016/j.enzmictec.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 11/29/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
L-Lysine ε-aminotransferase (lysAT) is an important enzyme in tailoring the terminal amino group of L-lysine or L-ornithine and can be directed to the synthesis of various value-added chemicals such as adipic acid. Three lysATs, lysAT from Saccharopolyspora erythraea NRRL 2338 (lysAT_Sery), lysAT from Nocardia farcinica IFM 10152, and lysAT from Rhodococcus jostii RHA1, were cloned, and their kinetic values and substrate specificities were investigated. In the reaction using 5mM L-lysine and 10mM α-ketoglutarate, lysAT_Sery from S. erythraea NRRL 2338 showed 72% higher specific activity than lysAT from Nocardia farcinica IFM 10152 and 42% higher specific activity than lysAT from R. jostii RHA1. More interesting result was that lysAT Sery, exhibiting the highest activity among three lysATs, did not show any activity to L-ornithine. The alignment of 146 lysAT sequences from RefSeq database was searched by the EC number of lysAT to compare the active site residues among the lysAT sequences. The sequence alignment showed that only two residues, corresponding to Ala129 and Asn328 of lysAT from Mycobacterium tuberculosis H37Rv (lysAT_Mtub), showed variations among the active site residues. All the active site residues except those two residues were completely conserved throughout 145 lysAT sequences. lysAT from S. erythraea NRRL 2338 has A129T and N328S variations (residue numbers are those of the crystal structure of lysAT_Mtub). The structural analysis by the homology model indicate that Thr126 by A129T variation in lysAT_Sery is appeared to interact more tightly with the phosphate group of PLP than alanine (the distance between Thr126 and the phosphate group of PLP was 2.92Å). In addition, Ser328 is located at the substrate recognition site of active site and, therefore, N328S variation may be connected to the substrate specificity of lysAT.
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Affiliation(s)
- Joo-Hyun Seo
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Eun-Mi Kim
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ahram Chae
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering and Institute of Bioengineering, Seoul National University, Seoul 151-742, Republic of Korea.
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15
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Duan X, Li Y, Du Q, Huang Q, Guo S, Xu M, Lin Y, Liu Z, Xie J. Mycobacterium Lysine ε-aminotransferase is a novel alarmone metabolism related persister gene via dysregulating the intracellular amino acid level. Sci Rep 2016; 6:19695. [PMID: 26806099 PMCID: PMC4726150 DOI: 10.1038/srep19695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
Bacterial persisters, usually slow-growing, non-replicating cells highly tolerant to antibiotics, play a crucial role contributing to the recalcitrance of chronic infections and treatment failure. Understanding the molecular mechanism of persister cells formation and maintenance would obviously inspire the discovery of new antibiotics. The significant upregulation of Mycobacterium tuberculosis Rv3290c, a highly conserved mycobacterial lysine ε-aminotransferase (LAT) during hypoxia persistent model, suggested a role of LAT in persistence. To test this, a lat deleted Mycobacterium smegmatis was constructed. The expression of transcriptional regulator leucine-responsive regulatory protein (LrpA) and the amino acids abundance in M. smegmatis lat deletion mutants were lowered. Thus, the persistence capacity of the deletion mutant was impaired upon norfloxacin exposure under nutrient starvation. In summary, our study firstly reported the involvement of mycobacterium LAT in persister formation, and possibly through altering the intracellular amino acid metabolism balance.
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Affiliation(s)
- Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
| | - Yunsong Li
- Department of thoracic surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Qinglin Du
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
| | - Qinqin Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
| | - Siyao Guo
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China.,Hanhong College, Southwest University. Chongqing 400715, China
| | - Mengmeng Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
| | - Yanping Lin
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
| | - Zhidong Liu
- Department of thoracic surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, key laboratory of Eco-environment three gorges reservoir, Ministry of Education, School of Life Sciences, Southwest University. Chongqing 400715, China
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16
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Parthiban BD, Saxena S, Chandran M, Jonnalagadda PS, Yadav R, Srilakshmi RR, Perumal Y, Dharmarajan S. Design and Development ofMycobacterium tuberculosisLysineɛ-Aminotransferase Inhibitors for Latent Tuberculosis Infection. Chem Biol Drug Des 2015; 87:265-74. [DOI: 10.1111/cbdd.12655] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 08/13/2015] [Accepted: 08/27/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Brindha Devi Parthiban
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Shalini Saxena
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Manoj Chandran
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Padma Sridevi Jonnalagadda
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Renu Yadav
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Rudraraju Reshma Srilakshmi
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Yogeeswari Perumal
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Sriram Dharmarajan
- Centre for Infectious Disease Research; Department of Pharmacy; Birla Institute of Technology & Science-Pilani; Hyderabad Campus Hyderabad 500078 India
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17
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Tripathi SM, Agarwal A, Ramachandran R. Mutational analysis of Mycobacterium tuberculosis lysine ɛ-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes. Biochem Biophys Res Commun 2015; 463:154-60. [DOI: 10.1016/j.bbrc.2015.05.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/12/2015] [Indexed: 11/24/2022]
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18
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Schiroli D, Peracchi A. A subfamily of PLP-dependent enzymes specialized in handling terminal amines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1200-11. [PMID: 25770684 DOI: 10.1016/j.bbapap.2015.02.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 01/04/2023]
Abstract
The present review focuses on a subfamily of pyridoxal phosphate (PLP)-dependent enzymes, belonging to the broader fold-type I structural group and whose archetypes can be considered ornithine δ-transaminase and γ-aminobutyrate transaminase. These proteins were originally christened "subgroup-II aminotransferases" (AT-II) but are very often referred to as "class-III aminotransferases". As names suggest, the subgroup includes mainly transaminases, with just a few interesting exceptions. However, at variance with most other PLP-dependent enzymes, catalysts in this subfamily seem specialized at utilizing substrates whose amino function is not adjacent to a carboxylate group. AT-II enzymes are widespread in biology and play mostly catabolic roles. Furthermore, today several transaminases in this group are being used as bioorganic tools for the asymmetric synthesis of chiral amines. We present an overview of the biochemical and structural features of these enzymes, illustrating how they are distinctive and how they compare with those of the other fold-type I enzymes. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Davide Schiroli
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy
| | - Alessio Peracchi
- Department of Life Sciences, Laboratory of Biochemistry, Molecular Biology and Bioinformatics, University of Parma, 43124 Parma, Italy.
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19
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Steffen-Munsberg F, Vickers C, Kohls H, Land H, Mallin H, Nobili A, Skalden L, van den Bergh T, Joosten HJ, Berglund P, Höhne M, Bornscheuer UT. Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. Biotechnol Adv 2015; 33:566-604. [PMID: 25575689 DOI: 10.1016/j.biotechadv.2014.12.012] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/25/2023]
Abstract
In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
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Affiliation(s)
- Fabian Steffen-Munsberg
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Clare Vickers
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hannes Kohls
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany; Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrik Land
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Hendrik Mallin
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Alberto Nobili
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Lilly Skalden
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Tom van den Bergh
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Per Berglund
- KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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20
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Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Crystallization and preliminary X-ray diffraction studies of the (R)-selective amine transaminase from Aspergillus fumigatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1415-7. [PMID: 24316843 PMCID: PMC3855733 DOI: 10.1107/s1744309113030923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/11/2013] [Indexed: 11/11/2022]
Abstract
The (R)-selective amine transaminase from Aspergillus fumigatus was expressed in Escherichia coli and purified to homogeneity. Bright yellow crystals appeared while storing the concentrated solution in the refrigerator and belonged to space group C222(1). X-ray diffraction data were collected to 1.27 Å resolution, as well as an anomalous data set to 1.84 Å resolution that was suitable for S-SAD phasing.
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Affiliation(s)
- Maren Thomsen
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Lilly Skalden
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Gottfried J. Palm
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Matthias Höhne
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
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21
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Rausch C, Lerchner A, Schiefner A, Skerra A. Crystal structure of the ω-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential. Proteins 2013; 81:774-87. [PMID: 23239223 DOI: 10.1002/prot.24233] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/12/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022]
Abstract
Apart from their crucial role in metabolism, pyridoxal 5'-phosphate (PLP)-dependent aminotransferases (ATs) constitute a class of enzymes with increasing application in industrial biotechnology. To provide better insight into the structure-function relationships of ATs with biotechnological potential we performed a fundamental bioinformatics analysis of 330 representative sequences of pro- and eukaryotic Class III ATs using a structure-guided approach. The calculated phylogenetic maximum likelihood tree revealed six distinct clades of which the first segregates with a very high bootstrap value of 92%. Most enzymes in this first clade have been functionally well characterized, whereas knowledge about the natural functions and substrates of enzymes in the other branches is sparse. Notably, in those clades 2-6 members of the peculiar class of ω-ATs prevail, many of which have proven useful for the preparation of chiral amines or artificial amino acids. One representative is the ω-AT from Paracoccus denitrificans (PD ω-AT) which catalyzes, for example, the transamination in a novel biocatalytic process for the production of L-homoalanine from L-threonine. To gain structural insight into this important enzyme, its X-ray analysis was carried out at a resolution of 2.6 Å, including the covalently bound PLP as well as 5-aminopentanoate as a putative amino donor substrate. On the basis of this crystal structure in conjunction with our phylogenetic analysis, we have identified a generic set of active site residues of ω-ATs that are associated with a strong preference for aromatic substrates, thus guiding the discovery of novel promising enzymes for the biotechnological production of corresponding chiral amines.
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Affiliation(s)
- Christian Rausch
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany
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Arora A, Chandra NR, Das A, Gopal B, Mande SC, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi AK, Vijayan M. Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts. Tuberculosis (Edinb) 2011; 91:456-68. [DOI: 10.1016/j.tube.2011.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 01/23/2023]
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Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry 2010; 49:6746-60. [PMID: 20565114 DOI: 10.1021/bi902097j] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analogue sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.
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Affiliation(s)
- Sanghamitra Dey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Shrivastava T, Dey A, Ramachandran R. Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c). J Mol Biol 2009; 392:1007-19. [DOI: 10.1016/j.jmb.2009.07.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/16/2009] [Accepted: 07/22/2009] [Indexed: 01/09/2023]
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Taneja B, Yadav J, Chakraborty TK, Brahmachari SK. An Indian effort towards affordable drugs: “Generic to designer drugs”. Biotechnol J 2009; 4:348-60. [DOI: 10.1002/biot.200900031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Identification of in vitro inhibitors of Mycobacterium tuberculosis Lysine ε-aminotransferase by pharmacophore mapping and three-dimensional flexible searches. Med Chem Res 2007. [DOI: 10.1007/s00044-007-9048-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shrivastava T, Ramachandran R. Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv. Nucleic Acids Res 2007; 35:7324-35. [PMID: 17962306 PMCID: PMC2175373 DOI: 10.1093/nar/gkm850] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Rv3291c gene from Mycobacterium tuberculosis codes for a transcriptional regulator belonging to the (leucine responsive regulatory protein/regulator of asparigine synthase C gene product) Lrp/AsnC-family. We have identified a novel effector-binding site from crystal structures of the apo protein, complexes with a variety of amino acid effectors, X-ray based ligand screening and qualitative fluorescence spectroscopy experiments. The new effector site is in addition to the structural characterization of another distinct site in the protein conserved in the related AsnC-family of regulators. The structures reveal that the ligand-binding loops of two crystallographically independent subunits adopt different conformations to generate two distinct effector-binding sites. A change in the conformation of the binding site loop 100–106 in the B subunit is apparently necessary for octameric association and also allows the loop to interact with a bound ligand in the newly identified effector-binding site. There are four sites of each kind in the octamer and the protein preferentially binds to aromatic amino acids. While amino acids like Phe, Tyr and Trp exhibit binding to only one site, His exhibits binding to both sites. Binding of Phe is accompanied by a conformational change of 3.7 Å in the 75–83 loop, which is advantageously positioned to control formation of higher oligomers. Taken together, the present studies suggest an elegant control mechanism for global transcription regulation involving binding of ligands to the two sites, individually or collectively.
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Affiliation(s)
- Tripti Shrivastava
- Molecular & Structural Biology Division, Central Drug Research Institute, P.O. Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow-226001, India
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Murphy DJ, Brown JR. Identification of gene targets against dormant phase Mycobacterium tuberculosis infections. BMC Infect Dis 2007; 7:84. [PMID: 17655757 PMCID: PMC1950094 DOI: 10.1186/1471-2334-7-84] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 07/26/2007] [Indexed: 12/30/2022] Open
Abstract
Background Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), infects approximately 2 billion people worldwide and is the leading cause of mortality due to infectious disease. Current TB therapy involves a regimen of four antibiotics taken over a six month period. Patient compliance, cost of drugs and increasing incidence of drug resistant M. tuberculosis strains have added urgency to the development of novel TB therapies. Eradication of TB is affected by the ability of the bacterium to survive up to decades in a dormant state primarily in hypoxic granulomas in the lung and to cause recurrent infections. Methods The availability of M. tuberculosis genome-wide DNA microarrays has lead to the publication of several gene expression studies under simulated dormancy conditions. However, no single model best replicates the conditions of human pathogenicity. In order to identify novel TB drug targets, we performed a meta-analysis of multiple published datasets from gene expression DNA microarray experiments that modeled infection leading to and including the dormant state, along with data from genome-wide insertional mutagenesis that examined gene essentiality. Results Based on the analysis of these data sets following normalization, several genome wide trends were identified and used to guide the selection of targets for therapeutic development. The trends included the significant up-regulation of genes controlled by devR, down-regulation of protein and ATP synthesis, and the adaptation of two-carbon metabolism to the hypoxic and nutrient limited environment of the granuloma. Promising targets for drug discovery were several regulatory elements (devR/devS, relA, mprAB), enzymes involved in redox balance and respiration, sulfur transport and fixation, pantothenate, isoprene, and NAD biosynthesis. The advantages and liabilities of each target are discussed in the context of enzymology, bacterial pathways, target tractability, and drug development. Conclusion Based on our bioinformatics analysis and additional discussion of in-depth biological rationale, several novel anti-TB targets have been proposed as potential opportunities to improve present therapeutic treatments for this disease.
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Affiliation(s)
- Dennis J Murphy
- Informatics, Molecular Discovery Research, GlaxoSmithKline, 1250 South Collegeville Road, UP1345, PO Box 5089, Collegeville, PA 19426-0989, USA
- Department of Biochemistry, UW2523, Cardiovascular and Urogenital CEDD, GlaxoSmithKline, 709 Swedeland Road, Box 1539, King of Prussia, PA 19406, USA
| | - James R Brown
- Informatics, Molecular Discovery Research, GlaxoSmithKline, 1250 South Collegeville Road, UP1345, PO Box 5089, Collegeville, PA 19426-0989, USA
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