1
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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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2
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Maciel L, Ferraz MVF, Oliveira AA, Lins RD, dos Anjos J, Guido RVC, Soares TA. Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses. ACS BIO & MED CHEM AU 2023; 3:211-222. [PMID: 37101811 PMCID: PMC10125267 DOI: 10.1021/acsbiomedchemau.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 04/28/2023]
Abstract
Arboviral infections such as Zika, chikungunya, dengue, and yellow fever pose significant health problems globally. The population at risk is expanding with the geographical distribution of the main transmission vector of these viruses, the Aedes aegypti mosquito. The global spreading of this mosquito is driven by human migration, urbanization, climate change, and the ecological plasticity of the species. Currently, there are no specific treatments for Aedes-borne infections. One strategy to combat different mosquito-borne arboviruses is to design molecules that can specifically inhibit a critical host protein. We obtained the crystal structure of 3-hydroxykynurenine transaminase (AeHKT) from A. aegypti, an essential detoxification enzyme of the tryptophan metabolism pathway. Since AeHKT is found exclusively in mosquitoes, it provides the ideal molecular target for the development of inhibitors. Therefore, we determined and compared the free binding energy of the inhibitors 4-(2-aminophenyl)-4-oxobutyric acid (4OB) and sodium 4-(3-phenyl-1,2,4-oxadiazol-5-yl)butanoate (OXA) to AeHKT and AgHKT from Anopheles gambiae, the only crystal structure of this enzyme previously known. The cocrystallized inhibitor 4OB binds to AgHKT with K i of 300 μM. We showed that OXA binds to both AeHKT and AgHKT enzymes with binding energies 2-fold more favorable than the crystallographic inhibitor 4OB and displayed a 2-fold greater residence time τ upon binding to AeHKT than 4OB. These findings indicate that the 1,2,4-oxadiazole derivatives are inhibitors of the HKT enzyme not only from A. aegypti but also from A. gambiae.
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Affiliation(s)
- Larissa
G. Maciel
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
| | - Matheus V. F. Ferraz
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
- Aggeu
Magalhães Institute, Oswaldo Cruz
Foundation, 50740-465 Recife, Brazil
| | - Andrew A. Oliveira
- São
Carlos Institute of Physics, University
of São Paulo, 13563-120 São Carlos, Brazil
| | - Roberto D. Lins
- Aggeu
Magalhães Institute, Oswaldo Cruz
Foundation, 50740-465 Recife, Brazil
| | - Janaína
V. dos Anjos
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
| | - Rafael V. C. Guido
- São
Carlos Institute of Physics, University
of São Paulo, 13563-120 São Carlos, Brazil
| | - Thereza A. Soares
- Department
of Chemistry, University of São Paulo, 055508-090 Ribeirão
Preto, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
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3
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Grottelli S, Annunziato G, Pampalone G, Pieroni M, Dindo M, Ferlenghi F, Costantino G, Cellini B. Identification of Human Alanine-Glyoxylate Aminotransferase Ligands as Pharmacological Chaperones for Variants Associated with Primary Hyperoxaluria Type 1. J Med Chem 2022; 65:9718-9734. [PMID: 35830169 PMCID: PMC9340776 DOI: 10.1021/acs.jmedchem.2c00142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Primary hyperoxaluria type I (PH1) is a rare kidney disease
due
to the deficit of alanine:glyoxylate aminotransferase (AGT), a pyridoxal-5′-phosphate-dependent
enzyme responsible for liver glyoxylate detoxification, which in turn
prevents oxalate formation and precipitation as kidney stones. Many
PH1-associated missense mutations cause AGT misfolding. Therefore,
the use of pharmacological chaperones (PCs), small molecules that
promote correct folding, represents a useful therapeutic option. To
identify ligands acting as PCs for AGT, we first performed a small
screening of commercially available compounds. We tested each molecule
by a dual approach aimed at defining the inhibition potency on purified
proteins and the chaperone activity in cells expressing a misfolded
variant associated with PH1. We then performed a chemical optimization
campaign and tested the resulting synthetic molecules using the same
approach. Overall, the results allowed us to identify a promising
hit compound for AGT and draw conclusions about the requirements for
optimal PC activity.
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Affiliation(s)
- Silvia Grottelli
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Giannamaria Annunziato
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Gioena Pampalone
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Marco Pieroni
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Francesca Ferlenghi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Gabriele Costantino
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
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4
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Dindo M, Pascarelli S, Chiasserini D, Grottelli S, Costantini C, Uechi G, Giardina G, Laurino P, Cellini B. Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase. Protein Sci 2022; 31:e4303. [PMID: 35481644 PMCID: PMC8996469 DOI: 10.1002/pro.4303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 01/24/2023]
Abstract
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT-Ma) and a minor polymorphic form (AGT-Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT-Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT-Mi. An in-depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT-Ma and AGT-Mi. Finally, co-immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein-protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well-defined fitness window, thus expanding the adaptability potential of the protein.
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Affiliation(s)
- Mirco Dindo
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Stefano Pascarelli
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | | | - Silvia Grottelli
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
| | | | - Gen‐Ichiro Uechi
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Giorgio Giardina
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Barbara Cellini
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
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5
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Hong KQ, Zhang J, Jin B, Chen T, Wang ZW. Development and characterization of a glycine biosensor system for fine-tuned metabolic regulation in Escherichia coli. Microb Cell Fact 2022; 21:56. [PMID: 35392910 PMCID: PMC8991567 DOI: 10.1186/s12934-022-01779-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background In vivo biosensors have a wide range of applications, ranging from the detection of metabolites to the regulation of metabolic networks, providing versatile tools for synthetic biology and metabolic engineering. However, in view of the vast array of metabolite molecules, the existing number and performance of biosensors is far from sufficient, limiting their potential applications in metabolic engineering. Therefore, we developed the synthetic glycine-ON and -OFF riboswitches for metabolic regulation and directed evolution of enzyme in Escherichia coli. Results The results showed that a synthetic glycine-OFF riboswitch (glyOFF6) and an increased-detection-range synthetic glycine-ON riboswitch (glyON14) were successfully screened from a library based on the Bacillus subtilis glycine riboswitch using fluorescence-activated cell sorting (FACS) and tetA-based dual genetic selection. The two synthetic glycine riboswitches were successfully used in tunable regulation of lactate synthesis, dynamic regulation of serine synthesis and directed evolution of alanine-glyoxylate aminotransferase in Escherichia coli, respectively. Mutants AGXT22 and AGXT26 of alanine-glyoxylate aminotransferase with an increase of 58% and 73% enzyme activity were obtained by using a high-throughput screening platform based on the synthetic glycine-OFF riboswitch, and successfully used to increase the 5-aminolevulinic acid yield of engineered Escherichia coli. Conclusions A synthetic glycine-OFF riboswitch and an increased-detection-range synthetic glycine-ON riboswitch were successfully designed and screened. The developed riboswitches showed broad application in tunable regulation, dynamic regulation and directed evolution of enzyme in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01779-4.
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Affiliation(s)
- Kun-Qiang Hong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jing Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Biao Jin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Zhi-Wen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China. .,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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6
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Spizzichino S, Pampalone G, Dindo M, Bruno A, Romani L, Cutruzzolà F, Zelante T, Pieroni M, Cellini B, Giardina G. Crystal structure of Aspergillus fumigatus AroH, an aromatic amino acid aminotransferase. Proteins 2021; 90:435-442. [PMID: 34495558 PMCID: PMC9290597 DOI: 10.1002/prot.26234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022]
Abstract
Aspergillus fumigatus is a saprophytic ubiquitous fungus whose spores can trigger reactions such as allergic bronchopulmonary aspergillosis or the fatal invasive pulmonary aspergillosis. To survive in the lungs, the fungus must adapt to a hypoxic and nutritionally restrictive environment, exploiting the limited availability of aromatic amino acids (AAAs) in the best possible way, as mammals do not synthesize them. A key enzyme for AAAs catabolism in A. fumigatus is AroH, a pyridoxal 5′‐phosphate‐dependent aromatic aminotransferase. AroH was recently shown to display a broad substrate specificity, accepting L‐kynurenine and α‐aminoadipate as amino donors besides AAAs. Given its pivotal role in the adaptability of the fungus to nutrient conditions, AroH represents a potential target for the development of innovative therapies against A. fumigatus‐related diseases. We have solved the crystal structure of Af‐AroH at 2.4 Å resolution and gained new insight into the dynamics of the enzyme's active site, which appears to be crucial for the design of inhibitors. The conformational plasticity of the active site pocket is probably linked to the wide substrate specificity of AroH.
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Affiliation(s)
| | - Gioena Pampalone
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Agostino Bruno
- Food and Drug Department, University of Parma, Parma, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome
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7
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Brewster JL, Pachl P, McKellar JLO, Selmer M, Squire CJ, Patrick WM. Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis. J Biol Chem 2021; 296:100797. [PMID: 34019879 PMCID: PMC8191291 DOI: 10.1016/j.jbc.2021.100797] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial methionine biosynthesis can take place by either the trans-sulfurylation route or direct sulfurylation. The enzymes responsible for trans-sulfurylation have been characterized extensively because they occur in model organisms such as Escherichia coli. However, direct sulfurylation is actually the predominant route for methionine biosynthesis across the phylogenetic tree. In this pathway, most bacteria use an O-acetylhomoserine aminocarboxypropyltransferase (MetY) to catalyze the formation of homocysteine from O-acetylhomoserine and bisulfide. Despite the widespread distribution of MetY, this pyridoxal 5'-phosphate-dependent enzyme remains comparatively understudied. To address this knowledge gap, we have characterized the MetY from Thermotoga maritima (TmMetY). At its optimal temperature of 70 °C, TmMetY has a turnover number (apparent kcat = 900 s-1) that is 10- to 700-fold higher than the three other MetY enzymes for which data are available. We also present crystal structures of TmMetY in the internal aldimine form and, fortuitously, with a β,γ-unsaturated ketimine reaction intermediate. This intermediate is identical to that found in the catalytic cycle of cystathionine γ-synthase (MetB), which is a homologous enzyme from the trans-sulfurylation pathway. By comparing the TmMetY and MetB structures, we have identified Arg270 as a critical determinant of specificity. It helps to wall off the active site of TmMetY, disfavoring the binding of the first MetB substrate, O-succinylhomoserine. It also ensures a strict specificity for bisulfide as the second substrate of MetY by occluding the larger MetB substrate, cysteine. Overall, this work illuminates the subtle structural mechanisms by which homologous pyridoxal 5'-phosphate-dependent enzymes can effect different catalytic, and therefore metabolic, outcomes.
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Affiliation(s)
- Jodi L Brewster
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Wayne M Patrick
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
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8
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Kim JE, Choi S, Balamurugan M, Jang JH, Nam KT. Electrochemical C–N Bond Formation for Sustainable Amine Synthesis. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2020.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1. Biochem J 2020; 476:3751-3768. [PMID: 31794008 DOI: 10.1042/bcj20190507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Peroxisomal alanine:glyoxylate aminotransferase (AGT) is responsible for glyoxylate detoxification in human liver and utilizes pyridoxal 5'-phosphate (PLP) as coenzyme. The deficit of AGT leads to Primary Hyperoxaluria Type I (PH1), a rare disease characterized by calcium oxalate stones deposition in the urinary tract as a consequence of glyoxylate accumulation. Most missense mutations cause AGT misfolding, as in the case of the G41R, which induces aggregation and proteolytic degradation. We have investigated the interaction of wild-type AGT and the pathogenic G41R variant with d-cycloserine (DCS, commercialized as Seromycin), a natural product used as a second-line treatment of multidrug-resistant tuberculosis, and its synthetic enantiomer l-cycloserine (LCS). In contrast with evidences previously reported on other PLP-enzymes, both ligands are AGT reversible inhibitors showing inhibition constants in the micromolar range. While LCS undergoes half-transamination generating a ketimine intermediate and behaves as a classical competitive inhibitor, DCS displays a time-dependent binding mainly generating an oxime intermediate. Using a mammalian cellular model, we found that DCS, but not LCS, is able to promote the correct folding of the G41R variant, as revealed by its increased specific activity and expression as a soluble protein. This effect also translates into an increased glyoxylate detoxification ability of cells expressing the variant upon treatment with DCS. Overall, our findings establish that DCS could play a role as pharmacological chaperone, thus suggesting a new line of intervention against PH1 based on a drug repositioning approach. To a widest extent, this strategy could be applied to other disease-causing mutations leading to AGT misfolding.
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10
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Liepman AH, Vijayalakshmi J, Peisach D, Hulsebus B, Olsen LJ, Saper MA. Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1229. [PMID: 31681359 PMCID: PMC6797613 DOI: 10.3389/fpls.2019.01229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/04/2019] [Indexed: 05/14/2023]
Abstract
Photorespiration is an energetically costly metabolic pathway for the recycling of phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) to phosphoglycerate. Arabidopsis alanine:glyoxylate aminotransferase 1 (AGT1) is a peroxisomal aminotransferase with a central role in photorespiration. This enzyme catalyzes various aminotransferase reactions, including serine:glyoxylate, alanine:glyoxylate, and asparagine:glyoxylate transaminations. To better understand structural features that govern the specificity of this enzyme, its crystal structures in the native form (2.2-Å resolution) and in the presence of l-serine (2.1-Å resolution) were solved. The structures confirm that this enzyme is dimeric, in agreement with studies of the active enzyme in solution. In the crystal, another dimer related by noncrystallographic symmetry makes close interactions to form a tetramer mediated in part by an extra carboxyl-terminal helix conserved in plant homologs of AGT1. Pyridoxal 5'-phosphate (PLP) is bound at the active site but is not held in place by covalent interactions. Residues Tyr35' and Arg36', entering the active site from the other subunits in the dimer, mediate interactions between AGT and l-serine when used as a substrate. In comparison, AGT1 from humans and AGT1 from Anabaena lack these two residues and instead position a tyrosine ring into the binding site, which accounts for their preference for l-alanine instead of l-serine. The structure also rationalizes the phenotype of the sat mutant, Pro251 to Leu, which likely affects the dimer interface near the catalytic site. This structural model of AGT1 provides valuable new information about this protein that may enable improvements to the efficiency of photorespiration.
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Affiliation(s)
- Aaron H. Liepman
- Biology Department, Eastern Michigan University, Ypsilanti, MI, United States
| | - J. Vijayalakshmi
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Peisach
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Brian Hulsebus
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
| | - Laura J. Olsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Mark A. Saper
- Department of Biological Chemistry and LSA Biophysics Program, University of Michigan, Ann Arbor, MI, United States
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11
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Montioli R, Paiardini A, Giardina G, Zanzoni S, Cutruzzola F, Cellini B, Borri Voltattorni C. R180T variant of δ-ornithine aminotransferase associated with gyrate atrophy: biochemical, computational, X-ray and NMR studies provide insight into its catalytic features. FEBS J 2019; 286:2787-2798. [PMID: 30957963 DOI: 10.1111/febs.14843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 04/05/2019] [Indexed: 02/01/2023]
Abstract
Among the over 50 gyrate atrophy-causing mutations of ornithine δ-aminotransferase (OAT), the R180T involves an active site residue located at the dimer interface, which in the crystal structure of OAT complexed with 5-fluoromethylornithine engages a salt bridge with the α-carboxylate of the substrate analogue. Starting from the previous finding that no transaminase activity was detected in CHO-K1 cells expressing the R180T variant, here we try to shed light at the protein level on the structural and/or functional defects of the R180T variant. To this aim, the variant has been cloned, expressed, purified and characterized by a combination of biochemical and structural studies. Although the R180T variant shares a similar overall conformation with the wild-type, its crystal structure solved at 1.8 Ǻ reveals slight structural alterations at the active site and at the dimeric interface. These changes are consistent with the spectroscopic and kinetic results, indicating that the variant, as compared with the wild-type OAT, shows (a) an increased Km value for l-ornithine (l-Orn), (b) an altered pyridoxal 5'-phosphate binding mode and affinity and (c) an increased thermostability. In addition, the R180T mutant exhibits a remarkable loss of catalytic activity and is endowed with the ability to catalyse not only the δ-transamination but also, albeit to a lesser extent, the α-transamination of l-Orn. Overall, these data indicate that the slight structural changes caused by the R180T mutation, preventing a proper collocation of l-Orn at the active site of OAT, are responsible for the notable reduction of the catalytic efficiency. ENZYMES: Ornithine aminotransferase EC 2.6.1.13. DATABASES: 6HX7.pdb.
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Affiliation(s)
- Riccardo Montioli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Serena Zanzoni
- Centro Piattaforme Tecnologiche, University of Verona, Italy
| | - Francesca Cutruzzola
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Italy
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Giardina G, Paone A, Tramonti A, Lucchi R, Marani M, Magnifico MC, Bouzidi A, Pontecorvi V, Guiducci G, Zamparelli C, Rinaldo S, Paiardini A, Contestabile R, Cutruzzolà F. The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells. FEBS J 2018; 285:3238-3253. [PMID: 30035852 DOI: 10.1111/febs.14610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/04/2018] [Accepted: 07/20/2018] [Indexed: 12/20/2022]
Abstract
Cancer cells reprogramme one-carbon metabolism (OCM) to sustain growth and proliferation. Depending on cell demands, serine hydroxymethyltransferase (SHMT) dynamically changes the fluxes of OCM by reversibly converting serine and tetrahydrofolate (THF) into 5,10-methylene-THF and glycine. SHMT is a tetrameric enzyme that mainly exists in three isoforms; two localize in the cytosol (SHMT1/SHMT2α) and one (SHMT2) in the mitochondria. Both the cytosolic isoforms can also translocate to the nucleus to sustain de novo thymidylate synthesis and support cell proliferation. Finally, the expression levels of the different isoforms are regulated to a certain extent by a yet unknown crosstalk mechanism. We have designed and fully characterized a set of three SHMT1 mutants, which uncouple the oligomeric state of the enzyme from its catalytic activity. We have then investigated the effects of the mutations on SHMT1 nuclear localization, cell viability and crosstalk in lung cancer cells (A549; H1299). Our data reveal that in these cell lines de novo thymidylate synthesis requires SHMT1 to be active, regardless of its oligomeric state. We have also confirmed that the crosstalk between the cytosolic and mitochondrial SHMT actually takes place and regulates the expression of the two isoforms. Apparently, the crosstalk mechanism is independent from the oligomeric state and the catalytic activity of SHMT1. DATABASE Structural data are available in the PDB under the accession number 6FL5.
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Affiliation(s)
- Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Marina Marani
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | | | - Amani Bouzidi
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | | | - Giulia Guiducci
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | | | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Italy
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