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Ballut L, Violot S, Kumar S, Aghajari N, Balaram H. GMP Synthetase: Allostery, Structure, and Function. Biomolecules 2023; 13:1379. [PMID: 37759779 PMCID: PMC10526850 DOI: 10.3390/biom13091379] [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: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Glutamine amidotransferases (GATs) catalyze the hydrolysis of glutamine and transfer the generated ammonia to diverse metabolites. The two catalytic activities, glutaminolysis and the subsequent amination of the acceptor substrate, happen in two distinct catalytic pockets connected by a channel that facilitates the movement of ammonia. The de novo pathway for the synthesis of guanosine monophosphate (GMP) from xanthosine monophosphate (XMP) is enabled by the GAT GMP synthetase (GMPS). In most available crystal structures of GATs, the ammonia channel is evident in their native state or upon ligand binding, providing molecular details of the conduit. In addition, conformational changes that enable the coordination of the two catalytic chemistries are also informed by the available structures. In contrast, despite the first structure of a GMPS being published in 1996, the understanding of catalysis in the acceptor domain and inter-domain crosstalk became possible only after the structure of a glutamine-bound mutant of Plasmodium falciparum GMPS was determined. In this review, we present the current status of our understanding of the molecular basis of catalysis in GMPS, becoming the first comprehensive assessment of the biochemical function of this intriguing enzyme.
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Affiliation(s)
- Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sanjeev Kumar
- Trivedi School of Biosciences, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India;
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur 560064, Bangalore, India
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Shivakumaraswamy S, Kumar S, Bellur A, Polisetty SD, Balaram H. Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme. Biochemistry 2022; 61:1988-2006. [PMID: 36040251 DOI: 10.1021/acs.biochem.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine 5'-monophosphate (GMP) synthetases, enzymes that catalyze the conversion of xanthosine 5'-monophosphate (XMP) to GMP, are composed of two different catalytic units, which are either two domains of a polypeptide chain or two subunits that associate to form a complex. The glutamine amidotransferase (GATase) unit hydrolyzes glutamine generating ammonia, and the ATP pyrophosphatase (ATPPase) unit catalyzes the formation of an AMP-XMP intermediate. The substrate-bound ATPPase allosterically activates GATase, and the ammonia thus generated is tunneled to the ATPPase active site where it reacts with AMP-XMP generating GMP. In ammonia channeling enzymes reported thus far, a tight complex of the two subunits is observed, while the interaction of the two subunits of Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is transient with the underlying mechanism of allostery and substrate channeling largely unclear. Here, we present a mechanistic model encompassing the various steps in the catalytic cycle of MjGMPS based on biochemical experiments, crystal structure, and cross-linking mass spectrometry guided integrative modeling. pH dependence of enzyme kinetics establishes that ammonia is tunneled across the subunits with the lifetime of the complex being ≤0.5 s. The crystal structure of the XMP-bound ATPPase subunit reported herein highlights the role of conformationally dynamic loops in enabling catalysis. The structure of MjGMPS derived using restraints obtained from cross-linking mass spectrometry has enabled the visualization of subunit interactions that enable allostery under catalytic conditions. We integrate the results and propose a functional mechanism for MjGMPS detailing the various steps involved in catalysis.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Satya Dev Polisetty
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
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Shivakumaraswamy S, Pandey N, Ballut L, Violot S, Aghajari N, Balaram H. Helices on Interdomain Interface Couple Catalysis in the ATPPase Domain with Allostery in Plasmodium falciparum GMP Synthetase. Chembiochem 2020; 21:2805-2817. [PMID: 32358899 DOI: 10.1002/cbic.202000158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/30/2020] [Indexed: 11/07/2022]
Abstract
GMP synthetase catalyses the conversion of XMP to GMP through a series of reactions that include hydrolysis of Gln to generate ammonia in the glutamine amidotransferase (GATase) domain, activation of XMP to adenyl-XMP intermediate in the ATP pyrophosphatase (ATPPase) domain and reaction of ammonia with the intermediate to generate GMP. The functioning of GMP synthetases entails bidirectional domain crosstalk, which leads to allosteric activation of the GATase domain, synchronization of catalytic events and tunnelling of ammonia. Herein, we have taken recourse to the analysis of structures of GMP synthetases, site-directed mutagenesis and steady-state and transient kinetics on the Plasmodium falciparum enzyme to decipher the molecular basis of catalysis in the ATPPase domain and domain crosstalk. Our results suggest an arrangement at the interdomain interface, of helices with residues that play roles in ATPPase catalysis as well as domain crosstalk enabling the coupling of ATPPase catalysis with GATase activation. Overall, the study enhances our understanding of GMP synthetases, which are drug targets in many infectious pathogens.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Nivedita Pandey
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Lionel Ballut
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Sébastien Violot
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Nushin Aghajari
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
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Kumar S, Prakash S, Gupta K, Dongre A, Balaram P, Balaram H. Unexpected functional implication of a stable succinimide in the structural stability of Methanocaldococcus jannaschii glutaminase. Nat Commun 2016; 7:12798. [PMID: 27677693 PMCID: PMC5052720 DOI: 10.1038/ncomms12798] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Protein ageing is often mediated by the formation of succinimide intermediates. These short-lived intermediates derive from asparaginyl deamidation and aspartyl dehydration and are rapidly converted into β-aspartyl or D-aspartyl residues. Here we report the presence of a highly stable succinimide intermediate in the glutaminase subunit of GMP synthetase from the hyperthermophile Methanocaldoccocus jannaschii. By comparing the biophysical properties of the wild-type protein and of several mutants, we show that the presence of succinimide increases the structural stability of the glutaminase subunit. The protein bearing this modification in fact remains folded at 100 °C and in 8 M guanidinium chloride. Mutation of the residue following the reactive asparagine provides insight into the factors that contribute to the hydrolytic stability of the succinimide. Our findings suggest that sequences that stabilize succinimides from hydrolysis may be evolutionarily selected to confer extreme thermal stability. Succinimide is a post-translational modification susceptible to rapid hydrolysis and generally associated with protein destabilisation. Here, the authors use mass spectroscopy to identify a stable succinimide intermediate that is responsible for the high thermostability of a thermophilic enzyme.
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Affiliation(s)
- Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Dongre
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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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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Oliver JC, Gudihal R, Burgner JW, Pedley AM, Zwierko AT, Davisson VJ, Linger RS. Conformational changes involving ammonia tunnel formation and allosteric control in GMP synthetase. Arch Biochem Biophys 2014; 545:22-32. [PMID: 24434004 DOI: 10.1016/j.abb.2014.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/27/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022]
Abstract
GMP synthetase is the glutamine amidotransferase that catalyzes the final step in the guanylate branch of de novo purine biosynthesis. Conformational changes are required to efficiently couple distal active sites in the protein; however, the nature of these changes has remained elusive. Structural information derived from both limited proteolysis and sedimentation velocity experiments support the hypothesis of nucleotide-induced loop- and domain-closure in the protein. These results were combined with information from sequence conservation and precedents from other glutamine amidotransferases to develop the first structural model of GMPS in a closed, active state. In analyzing this Catalytic model, an interdomain salt bridge was identified residing in the same location as seen in other triad glutamine amidotransferases. Using mutagenesis and kinetic analysis, the salt bridge between H186 and E383 was shown to function as a connection between the two active sites. Mutations at these residues uncoupled the two half-reactions of the enzyme. The chemical events of nucleotide binding initiate a series of conformational changes that culminate in the establishment of a tunnel for ammonia as well as an activated glutaminase catalytic site. The results of this study provide a clearer understanding of the allostery of GMPS, where, for the first time, key substrate binding and interdomain contacts are modeled and analyzed.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Ravidra Gudihal
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - John W Burgner
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, United States
| | - Anthony M Pedley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Alexander T Zwierko
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Rebecca S Linger
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States.
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