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Bexkens ML, Martin OMF, van den Heuvel JM, Schmitz MGJ, Teusink B, Bakker BM, van Hellemond JJ, Haanstra JR, Walkinshaw MD, Tielens AGM. The unusual kinetics of lactate dehydrogenase of Schistosoma mansoni and their role in the rapid metabolic switch after penetration of the mammalian host. Int J Parasitol 2024; 54:367-378. [PMID: 38492780 DOI: 10.1016/j.ijpara.2024.03.005] [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: 06/01/2023] [Revised: 01/24/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Lactate dehydrogenase (LDH) from Schistosoma mansoni has peculiar properties for a eukaryotic LDH. Schistosomal LDH (SmLDH) isolated from schistosomes, and the recombinantly expressed protein, are strongly inhibited by ATP, which is neutralized by fructose-1,6-bisphosphate (FBP). In the conserved FBP/anion binding site we identified two residues in SmLDH (Val187 and Tyr190) that differ from the conserved residues in LDHs of other eukaryotes, but are identical to conserved residues in FBP-sensitive prokaryotic LDHs. Three-dimensional (3D) models were generated to compare the structure of SmLDH with other LDHs. These models indicated that residues Val187, and especially Tyr190, play a crucial role in the interaction of FBP with the anion pocket of SmLDH. These 3D models of SmLDH are also consistent with a competitive model of SmLDH inhibition in which ATP (inhibitor) and FBP (activator) compete for binding in a well-defined anion pocket. The model of bound ATP predicts a distortion of the nearby key catalytic residue His195, resulting in enzyme inhibition. To investigate a possible physiological role of this allosteric regulation of LDH in schistosomes we made a kinetic model in which the allosteric regulation of the glycolytic enzymes can be varied. The model showed that inhibition of LDH by ATP prevents fermentation to lactate in the free-living stages in water and ensures complete oxidation via the Krebs cycle of the endogenous glycogen reserves. This mechanism of allosteric inhibition by ATP prevents the untimely depletion of these glycogen reserves, the only fuel of the free-living cercariae. Neutralization by FBP of this ATP inhibition of LDH prevents accumulation of glycolytic intermediates when S. mansoni schistosomula are confronted with the sudden large increase in glucose availability upon penetration of the final host. It appears that the LDH of S. mansoni is special and well suited to deal with the variations in glucose availability the parasite encounters during its life cycle.
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Affiliation(s)
- Michiel L Bexkens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Olivier M F Martin
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jos M van den Heuvel
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marion G J Schmitz
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Barbara M Bakker
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jurgen R Haanstra
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Malcolm D Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Int J Mol Sci 2020; 21:ijms21186779. [PMID: 32947863 PMCID: PMC7554756 DOI: 10.3390/ijms21186779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/29/2022] Open
Abstract
Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Monomers are functionally independent from each other inside NDPK complexes and the nucleoside kinase catalytic mechanism involves transient phosphorylation of the conserved catalytic histidine. To be active, monomers must assemble into conserved head to tail dimers, which further assemble into hexamers or tetramers. The interfaces between these oligomeric states are very different but, surprisingly, the assembly structure barely affects the catalytic efficiency of the enzyme. While it has been shown that assembly into hexamers induces full formation of the catalytic site and stabilizes the complex, it is unclear why assembly into tetramers is required for function. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. However, we still lack the high resolution structural data of NDPK in complex with different partners, which is necessary for deciphering the mechanism of these diverse functions. In this review we discuss advances in the structure, folding and stability of NDPKs.
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Dautant A, Henri J, Wales TE, Meyer P, Engen JR, Georgescauld F. Remodeling of the Binding Site of Nucleoside Diphosphate Kinase Revealed by X-ray Structure and H/D Exchange. Biochemistry 2019; 58:1440-1449. [PMID: 30785730 DOI: 10.1021/acs.biochem.8b01308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To be fully active and participate in the metabolism of phosphorylated nucleotides, most nucleoside diphosphate kinases (NDPKs) have to assemble into stable hexamers. Here we studied the role played by six intersubunit salt bridges R80-D93 in the stability of NDPK from the pathogen Mycobacterium tuberculosis ( Mt). Mutating R80 into Ala or Asn abolished the salt bridges. Unexpectedly, compensatory stabilizing mechanisms appeared for R80A and R80N mutants and we studied them by biochemical and structural methods. The R80A mutant crystallized into space group I222 that is unusual for NDPK, and its hexameric structure revealed the occurrence at the trimer interface of a stabilizing hydrophobic patch around the mutation. Functionally relevant, a trimer of the R80A hexamer showed a remodeling of the binding site. In this conformation, the cleft of the active site is more open, and then active His117 is more accessible to substrates. H/D exchange mass spectrometry analysis of the wild type and the R80A and R80N mutants showed that the remodeled region of the protein is highly solvent accessible, indicating that equilibrium between open and closed conformations is possible. We propose that such equilibrium occurs in vivo and explains how bulky substrates access the catalytic His117.
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Affiliation(s)
- Alain Dautant
- Université de Bordeaux , CNRS, Institut de Biochimie et Génétique Cellulaires, UMR5095 , 146 rue Léo Saignat , 33077 Bordeaux , France
| | - Julien Henri
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Philippe Meyer
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - John R Engen
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Florian Georgescauld
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
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Dautant A, Meyer P, Georgescauld F. Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization. Biochemistry 2017; 56:2886-2896. [DOI: 10.1021/acs.biochem.7b00282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alain Dautant
- Université
de Bordeaux, CNRS, Institut de Biochimie et Génétique
Cellulaires, UMR 5095, Bordeaux, France
| | - Philippe Meyer
- Sorbonne Universités,
UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire
et Cellulaire des Eucaryotes, UMR 8226, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Florian Georgescauld
- Sorbonne Universités,
UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire
et Cellulaire des Eucaryotes, UMR 8226, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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Chandran AV, Prabu JR, Nautiyal A, Patil KN, Muniyappa K, Vijayan M. Structural studies on Mycobacterium tuberculosis RecA: molecular plasticity and interspecies variability. J Biosci 2015; 40:13-30. [PMID: 25740138 DOI: 10.1007/s12038-014-9497-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the 'switch' residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.
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Affiliation(s)
- Anu V Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012
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Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M. Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications. ACTA ACUST UNITED AC 2015; 71:1514-27. [DOI: 10.1107/s1399004715009311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
17 independent crystal structures of family I uracil-DNA glycosylase fromMycobacterium tuberculosis(MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5′ position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.
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