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Pina AF, Sousa SF, Cerqueira NMFSA. The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study. Chembiochem 2021; 23:e202100555. [PMID: 34762772 DOI: 10.1002/cbic.202100555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.
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Affiliation(s)
- André F Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Nuno M F S A Cerqueira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
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2
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Leisico F, V Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trincão J, Romão MJ, de Lencastre H, Santos-Silva T. First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD. Sci Rep 2018; 8:5313. [PMID: 29593310 PMCID: PMC5871853 DOI: 10.1038/s41598-018-22986-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/27/2018] [Indexed: 12/05/2022] Open
Abstract
Gram-positive bacteria homeostasis and antibiotic resistance mechanisms are dependent on the intricate architecture of the cell wall, where amidated peptidoglycan plays an important role. The amidation reaction is carried out by the bi-enzymatic complex MurT-GatD, for which biochemical and structural information is very scarce. In this work, we report the first crystal structure of the glutamine amidotransferase member of this complex, GatD from Staphylococcus aureus, at 1.85 Å resolution. A glutamine molecule is found close to the active site funnel, hydrogen-bonded to the conserved R128. In vitro functional studies using 1H-NMR spectroscopy showed that S. aureus MurT-GatD complex has glutaminase activity even in the absence of lipid II, the MurT substrate. In addition, we produced R128A, C94A and H189A mutants, which were totally inactive for glutamine deamidation, revealing their essential role in substrate sequestration and catalytic reaction. GatD from S. aureus and other pathogenic bacteria share high identity to enzymes involved in cobalamin biosynthesis, which can be grouped in a new sub-family of glutamine amidotransferases. Given the ubiquitous presence of GatD, these results provide significant insights into the molecular basis of the so far undisclosed amidation mechanism, contributing to the development of alternative therapeutics to fight infections.
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Affiliation(s)
- Francisco Leisico
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diana V Vieira
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Oxford Protein Production Facility, Research Complex at Harwell, Didcot, United Kingdom
| | - Teresa A Figueiredo
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal
| | - Micael Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita G Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Madalena Ludovice
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Maria João Romão
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal.
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA.
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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Bairagya HR, Bansal M. New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study. Proteins 2016; 84:360-73. [PMID: 26756917 DOI: 10.1002/prot.24983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/06/2015] [Accepted: 12/19/2015] [Indexed: 11/11/2022]
Abstract
Human Guanine Monophosphate Synthetase (hGMPS) converts XMP to GMP, and acts as a bifunctional enzyme with N-terminal "glutaminase" (GAT) and C-terminal "synthetase" domain. The enzyme is identified as a potential target for anti-cancer and immunosuppressive therapies. GAT domain of enzyme plays central role in metabolism, and contains conserved catalytic residues Cys104, His190, and Glu192. MD simulation studies on GAT domain suggest that position of oxyanion in unliganded conformation is occupied by one conserved water molecule (W1), which also stabilizes that pocket. This position is occupied by a negatively charged atom of the substrate or ligand in ligand bound crystal structures. In fact, MD simulation study of Ser75 to Val indicates that W1 conserved water molecule is stabilized by Ser75, while Thr152, and His190 also act as anchor residues to maintain appropriate architecture of oxyanion pocket through water mediated H-bond interactions. Possibly, four conserved water molecules stabilize oxyanion hole in unliganded state, but they vacate these positions when the enzyme (hGMPS)-substrate complex is formed. Thus this study not only reveals functionally important role of conserved water molecules in GAT domain, but also highlights essential role of other non-catalytic residues such as Ser75 and Thr152 in this enzymatic domain. The results from this computational study could be of interest to experimental community and provide a testable hypothesis for experimental validation. Conserved sites of water molecules near and at oxyanion hole highlight structural importance of water molecules and suggest a rethink of the conventional definition of chemical geometry of inhibitor binding site.
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Affiliation(s)
- Hridoy R Bairagya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LPS, Riccardi G, Cole ST, Pasca MR. Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG. ACTA ACUST UNITED AC 2015; 22:917-27. [PMID: 26097035 PMCID: PMC4521081 DOI: 10.1016/j.chembiol.2015.05.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/25/2015] [Accepted: 05/30/2015] [Indexed: 11/06/2022]
Abstract
To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). Mutants resistant to both compounds harbored mutations in ethA (rv3854c), the gene encoding the monooxygenase EthA, and/or in pyrG (rv1699) coding for the CTP synthetase, PyrG. Biochemical investigations demonstrated that EthA is responsible for the activation of the compounds, and by mass spectrometry we identified the active metabolite of 7947882, which directly inhibits PyrG activity. Metabolomic studies revealed that pharmacological inhibition of PyrG strongly perturbs DNA and RNA biosynthesis, and other metabolic processes requiring nucleotides. Finally, the crystal structure of PyrG was solved, paving the way for rational drug design with this newly validated drug target. Two compounds activated by EthA kill M. tuberculosis through PyrG inhibition EthA metabolite is active against PyrG and M. tuberculosis growth Definition of the mechanism of activation and validation of PyrG as a new drug target
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Affiliation(s)
- Giorgia Mori
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marta Esposito
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Giulia Degiacomi
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA
| | | | - Leonardo B Marino
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK; Faculty of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Araraquara, São Paulo 14801-902, Brazil
| | - Ivana Centárová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Zuzana Svetlíková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Jaroslav Blaško
- Institute of Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovak Republic
| | - Elena Kazakova
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Alexander Lepioshkin
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Giuseppe Zanoni
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Alessio Porta
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Alain R Baulard
- Institut Pasteur de Lille, Center for Infection and Immunity, 59019 Lille, France
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland.
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy.
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Loong AM, Chng YR, Chew SF, Wong WP, Ip YK. Molecular characterization and mRNA expression of carbamoyl phosphate synthetase III in the liver of the African lungfish, Protopterus annectens, during aestivation or exposure to ammonia. J Comp Physiol B 2011; 182:367-79. [PMID: 22038021 DOI: 10.1007/s00360-011-0626-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 09/27/2011] [Accepted: 10/04/2011] [Indexed: 01/01/2023]
Abstract
This study aimed to obtain the full sequence of carbamoyl phosphate synthetase III (cps III) from, and to determine the mRNA expression of cps III in, the liver of P. annectens during aestivation in air, hypoxia or mud, or exposure to environmental ammonia (100 mmol l(-1) NH(4)Cl). The complete coding cDNA sequence of cps III from the liver of P. annectens consisted of 4530 bp, which coded for 1,510 amino acids with an estimated molecular mass of 166.1 kDa. The Cps III of P. annectens consisted of a mitochondrial targeting sequence of 44 amino acid residues, a GAT domain spanning from tyrosine 45 to isoleucine 414, and a methylglyoxal synthase-like domain spanning from valine 433 to arginine 1513. Two cysteine residues (cysteine 1337 and cysteine 1347) that are characteristic of N-acetylglutamate dependency were also present. The critical Cys-His-Glu catalytic triad (cysteine 301, histidine 385 and glutamate 387) together with methionine 302 and glutamine 305 affirmed that P. annectens expressed Cps III and not Cps I. A comparison of the translated amino acid sequence of Cps III from P. annectens with CPS sequences from other animals revealed that it shared the highest similarity with elasmobranch Cps III. A phylogenetic analysis indicates that P. annectens CPS III could have evolved from Cps III of elasmobranchs. Indeed, Cps III from P. annectens used mainly glutamine as the substrate, and its activity decreased significantly when glutamine and ammonia were included together in the assay system. There were significant increases (9- to 12-fold) in the mRNA expression of cps III in the liver of fish during the induction phase (days 3 and 6) of aestivation in air. Aestivation in hypoxia or in mud had a delayed effect on the increase in the mRNA expression of cps III, which extended beyond the induction phase of aestivation, reiterating the importance of differentiating effects that are intrinsic to aestivation from those intrinsic to hypoxia. Furthermore, results from this study confirmed that environmental ammonia exposure led to a significant increase in the mRNA expression of cps III in the liver of P. annectens, alluding to the important functional role of urea not only as a product of ammonia detoxification but also as a putative internal cue for aestivation.
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Affiliation(s)
- A M Loong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, 117543, Republic of Singapore
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