1
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Russell PPS, Maytin AK, Rickard MM, Russell MC, Pogorelov TV, Gruebele M. Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation. J Phys Chem Lett 2024; 15:940-946. [PMID: 38252018 PMCID: PMC11180962 DOI: 10.1021/acs.jpclett.3c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Many enzymes undergo major conformational changes to function in cells, particularly when they bind to more than one substrate. We quantify the large-amplitude hinge-bending landscape of human phosphoglycerate kinase (PGK) in a human cytoplasm. Approximately 70 μs of all-atom simulations, upon coarse graining, reveal three metastable states of PGK with different hinge angle distributions and additional substates. The "open" state was more populated than the "semi-open" or "closed" states. In addition to free energies and barriers within the landscape, we characterized the average transition state passage time of ≈0.3 μs and reversible substrate and product binding. Human PGK in a dilute solution simulation shows a transition directly from the open to closed states, in agreement with previous SAXS experiments, suggesting that the cell-like model environment promotes stability of the human PGK semi-open state. Yeast PGK also sampled three metastable states within the cytoplasm model, with the closed state favored in our simulation.
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Affiliation(s)
| | - Andrew K. Maytin
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Meredith M. Rickard
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Matthew C. Russell
- Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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2
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 2020; 184:545-559.e22. [PMID: 33357446 PMCID: PMC7836100 DOI: 10.1016/j.cell.2020.12.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/21/2020] [Accepted: 12/11/2020] [Indexed: 02/02/2023]
Abstract
Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology. Dynamic structural proteomic screens detect functional changes at high resolution Detect enzyme activity, phosphorylation, and molecular interactions in situ Generate new molecular hypotheses and increase functional proteomics coverage Enabled discovery of a regulatory mechanism of glucose uptake in E. coli
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3
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Cerminara M, Schöne A, Ritter I, Gabba M, Fitter J. Mapping Multiple Distances in a Multidomain Protein for the Identification of Folding Intermediates. Biophys J 2020; 118:688-697. [PMID: 31916943 PMCID: PMC7002912 DOI: 10.1016/j.bpj.2019.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/13/2019] [Accepted: 12/10/2019] [Indexed: 10/27/2022] Open
Abstract
The investigation and understanding of the folding mechanism of multidomain proteins is still a challenge in structural biology. The use of single-molecule Förster resonance energy transfer offers a unique tool to map conformational changes within the protein structure. Here, we present a study following denaturant-induced unfolding transitions of yeast phosphoglycerate kinase by mapping several inter- and intradomain distances of this two-domain protein, exhibiting a quite heterogeneous behavior. On the one hand, the development of the interdomain distance during the unfolding transition suggests a classical two-state unfolding behavior. On the other hand, the behavior of some intradomain distances indicates the formation of a compact and transient molten globule intermediate state. Furthermore, different intradomain distances measured within the same domain show pronounced differences in their unfolding behavior, underlining the fact that the choice of dye attachment positions within the polypeptide chain has a substantial impact on which unfolding properties are observed by single-molecule Förster resonance energy transfer measurements. Our results suggest that, to fully characterize the complex folding and unfolding mechanism of multidomain proteins, it is necessary to monitor multiple intra- and interdomain distances because a single reporter can lead to a misleading, partial, or oversimplified interpretation.
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Affiliation(s)
- Michele Cerminara
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany.
| | - Antonie Schöne
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Ilona Ritter
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Matteo Gabba
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Jörg Fitter
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany; RWTH Aachen University, I. Physikalisches Institut (IA), Aachen, Germany.
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4
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Gabba M, Poblete S, Rosenkranz T, Katranidis A, Kempe D, Züchner T, Winkler RG, Gompper G, Fitter J. Conformational state distributions and catalytically relevant dynamics of a hinge-bending enzyme studied by single-molecule FRET and a coarse-grained simulation. Biophys J 2014; 107:1913-1923. [PMID: 25418172 PMCID: PMC4213667 DOI: 10.1016/j.bpj.2014.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 11/20/2022] Open
Abstract
Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions.
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Affiliation(s)
- Matteo Gabba
- Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany.
| | - Simón Poblete
- Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Tobias Rosenkranz
- Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Alexandros Katranidis
- Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Daryan Kempe
- I. Physikalisches Institut (IA), Arbeitsgruppe Biophysik, Rheinisch-Westfaelische Technische Hochschule, Aachen, Germany
| | - Tina Züchner
- Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Roland G Winkler
- Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Gerhard Gompper
- Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany
| | - Jörg Fitter
- Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany; I. Physikalisches Institut (IA), Arbeitsgruppe Biophysik, Rheinisch-Westfaelische Technische Hochschule, Aachen, Germany.
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5
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Large domain fluctuations on 50-ns timescale enable catalytic activity in phosphoglycerate kinase. Biophys J 2011; 99:2309-17. [PMID: 20923666 DOI: 10.1016/j.bpj.2010.08.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 08/05/2010] [Accepted: 08/10/2010] [Indexed: 11/23/2022] Open
Abstract
Large-scale domain motions of enzymes are often essential for their biological function. Phosphoglycerate kinase has a wide open domain structure with a hinge near the active center between the two domains. Applying neutron spin echo spectroscopy and small-angle neutron scattering we have investigated the internal domain dynamics. Structural analysis reveals that the holoprotein in solution seems to be more compact compared to the crystal structure but would not allow the functionally important phosphoryl transfer between the substrates if the protein were static. Brownian large-scale domain fluctuation dynamics on a timescale of 50 ns was revealed by neutron spin echo spectroscopy. The dynamics observed was compared to the displacement patterns of low-frequency normal modes. The displacements along the normal-mode coordinates describe our experimental results reasonably well. In particular, the domain movements facilitate a close encounter of the key residues in the active center to build the active configuration. The observed dynamics shows that the protein has the flexibility to allow fluctuations and displacements that seem to enable the function of the protein. Moreover, the presence of the substrates increases the rigidity, which is deduced from a faster dynamics with smaller amplitude.
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6
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Gloor GB, Tyagi G, Abrassart DM, Kingston AJ, Fernandes AD, Dunn SD, Brandl CJ. Functionally compensating coevolving positions are neither homoplasic nor conserved in clades. Mol Biol Evol 2010; 27:1181-91. [PMID: 20065119 DOI: 10.1093/molbev/msq004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We demonstrated that a pair of positions in phosphoglycerate kinase that score highly by three nonparametric covariation measures are important for function even though the positions can be occupied by aliphatic, aromatic, or charged residues. Examination of these pairs suggested that the majority of the covariation scores could be explained by within-clade conservation. However, an analysis of diversity showed that the conservation within clades of covarying pairs was indistinguishable from pairs of positions that do not covary, thus ruling out both clade conservation and extensive homoplasy as means to identify covarying positions. Mutagenesis showed that the residues in the covarying pair were epistatic, with the type of epistasis being dependent on the initial pair. The results show that nonconserved covarying positions that affect protein function can be identified with high precision.
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Affiliation(s)
- Gregory B Gloor
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.
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7
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Varga A, Lionne C, Lallemand P, Szabó J, Adamek N, Valentin C, Vas M, Barman T, Chaloin L. Direct Kinetic Evidence That Lysine 215 Is Involved in the Phospho-Transfer Step of Human 3-Phosphoglycerate Kinase. Biochemistry 2009; 48:6998-7008. [DOI: 10.1021/bi900396h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Corinne Lionne
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Perrine Lallemand
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Judit Szabó
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Nancy Adamek
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Christian Valentin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Mária Vas
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Tom Barman
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
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8
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Thermodynamic analysis of the nondenaturational conformational change of baker's yeast phosphoglycerate kinase at 24 degrees C. Arch Biochem Biophys 2008; 478:206-11. [PMID: 18656441 DOI: 10.1016/j.abb.2008.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 07/04/2008] [Accepted: 07/08/2008] [Indexed: 11/22/2022]
Abstract
A plot of the Gibbs free energy of unfolding vs. temperature is calculated for baker's yeast phosphoglycerate kinase in 150 mM sodium phosphate (pH=7.0) from a combination of reversible differential scanning calorimetry measurements and isothermal guanidine hydrochloride titrations. The stability curve reveals the existence of two stable, folded conformers with an abrupt conformational transition occurring at 24 degrees C. The transition state thermodynamics for the low- to high-temperature conformational change are calculated from slow-scan-rate differential scanning calorimetry measurements where it is found that the free energy barrier for the conversion is 90 kJ/mol and the transition state possesses a significant unfolding quality. This analysis also confirms a nondenaturational conformational transition at 24 degrees C. The data therefore suggest that X-ray structures obtained from crystals grown below this temperature may differ considerably from the physiological structure and that the two conformers are not readily interconverted.
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9
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Young TA, Skordalakes E, Marqusee S. Comparison of Proteolytic Susceptibility in Phosphoglycerate Kinases from Yeast and E. coli: Modulation of Conformational Ensembles Without Altering Structure or Stability. J Mol Biol 2007; 368:1438-47. [PMID: 17397866 DOI: 10.1016/j.jmb.2007.02.077] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 02/15/2007] [Accepted: 02/22/2007] [Indexed: 11/21/2022]
Abstract
Escherichia coli phosphoglycerate kinase (PGK) is resistant to proteolytic cleavage while the yeast homolog from Saccharomyces cerevisiae is not. We have explored the biophysical basis of this surprising difference. The sequences of these homologs are 39% identical and 56% similar. Determination of the crystal structure for the E. coli protein and comparison to the previously solved yeast structure reveals that the two proteins have extremely similar tertiary structures, and their global stabilities determined by equilibrium denaturation are also very similar. The extrapolated unfolding rate of E. coli PGK is, however, 10(5) slower than that of the yeast homolog. This surprisingly large difference in unfolding rates appears to arise from a divergence in the extent of cooperativity between the two structural domains (the N and C-domains) that make up these kinases. This is supported by: (1) the C-domain of E. coli PGK cannot be expressed or fold independently of the N-domain, while both domains of the yeast protein fold in isolation into stable structures and (2) the energetics and kinetics of the proteolytically sensitive state of E. coli PGK match those for global unfolding. This suggests that proteolysis occurs from the globally unfolded state of E. coli PGK, while the characteristics defining the yeast homolog suggest that proteolysis occurs upon unfolding of only the C-domain, with the N-domain remaining folded and consequently resistant to cleavage.
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Affiliation(s)
- Tracy A Young
- Department of Molecular and Cell Biology and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-3206, USA
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10
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Renzone G, Salzano AM, Arena S, D'Ambrosio C, Scaloni A. Selective ion tracing and MSn analysis of peptide digests from FSBA-treated kinases for the analysis of protein ATP-binding sites. J Proteome Res 2007; 5:2019-24. [PMID: 16889425 DOI: 10.1021/pr0601234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinases play a key role in many cellular processes by catalyzing the transfer of phosphoryl groups from ATP to a broad number of substrates, including amino acids on target proteins. The reagent 5'-fluorosulfonylbenzoyl-5'-adenosine (FSBA) has been widely used to identify ATP-binding sites in kinases since it reacts with nucleophilic amino acids occurring within these motifs, determining a mass increase of 433 Da. In this study, we present a versatile MS approach that has been developed to recognize labeled peptides generated after enzymatic digestion of FSBA-treated kinases. Using selective ion tracing and MS(2)/MS(3) experiments, we were able to easily identify peptides occurring at protein ATP-binding sites, also affording a complete characterization of the modified amino acids. This methodology may be used in the development of future parent ion scanning-based applications directed to large scale analysis of kinases within complex protein mixtures.
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Affiliation(s)
- Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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11
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Zecchinon L, Oriol A, Netzel U, Svennberg J, Gerardin-Otthiers N, Feller G. Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychrophilic phosphoglycerate kinase. A microcalorimetric study. J Biol Chem 2005; 280:41307-14. [PMID: 16227206 DOI: 10.1074/jbc.m506464200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cold-active phosphoglycerate kinase from the Antarctic bacterium Pseudomonas sp. TACII18 exhibits two distinct stability domains in the free, open conformation. It is shown that these stability domains do not match the structural N- and C-domains as the heat-stable domain corresponds to about 80 residues of the C-domain, including the nucleotide binding site, whereas the remaining of the protein contributes to the main heat-labile domain. This was demonstrated by spectroscopic and microcalorimetric analyses of the native enzyme, of its mutants, and of the isolated recombinant structural domains. It is proposed that the heat-stable domain provides a compact structure improving the binding affinity of the nucleotide, therefore increasing the catalytic efficiency at low temperatures. Upon substrate binding, the enzyme adopts a uniformly more stable closed conformation. Substrate-induced stability changes suggest that the free energy of ligand binding is converted into an increased conformational stability used to drive the hinge-bending motions and domain closure.
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Affiliation(s)
- Laurent Zecchinon
- Laboratory of Biochemistry, University of Liège, Institute of Chemistry B6a, B-4000 Liège-Sart Tilman, Belgium
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12
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de Almeida JRM, de Moraes LMP, Torres FAG. Molecular characterization of the 3-phosphoglycerate kinase gene (PGK1) from the methylotrophic yeast Pichia pastoris. Yeast 2005; 22:725-37. [PMID: 16034819 DOI: 10.1002/yea.1243] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We report the cloning of the 3-phosphoglycerate kinase gene (PGK1) from the methylotrophic yeast Pichia pastoris by a PCR approach. The coding sequence of the PGK1 gene comprises 1251 bp with the potential to encode a polypeptide of 416 amino acid residues, which shows high identity to homologous proteins from other yeasts. The promoter region of this gene (P(PGK1)) contains regulatory cis-elements found in other PGK1 genes, such as TATA box, CT-rich block and a heat shock element. In the 3' downstream region we identified a tripartite element 5'-TAG-TAGT-TTT-3', which is supposed to be important for transcription termination. As in other yeasts, the PGK1 gene from P. pastoris is present as a single-copy gene. Northern blot analysis revealed that the gene is transcribed as a 1.5 kb mRNA; when cells are grown on glucose the levels of this mRNA are increased two-fold in comparison to cells grown on glycerol. The transcriptional regulation of this gene by the carbon source was further confirmed when the alpha-amylase gene from Bacillus subtilis was placed under the control of P(PGK1): higher levels of expression were obtained when cells were grown on glucose as compared to glycerol and methanol. Preliminary results related to the strength of P(PGK1) show that it represents a potential alternative to constitutive heterologous expression in P. pastoris.
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Affiliation(s)
- João Ricardo Moreira de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF 70910-900, Brazil
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13
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Varga A, Flachner B, Gráczer E, Osváth S, Szilágyi AN, Vas M. Correlation between conformational stability of the ternary enzyme-substrate complex and domain closure of 3-phosphoglycerate kinase. FEBS J 2005; 272:1867-85. [PMID: 15819882 DOI: 10.1111/j.1742-4658.2005.04618.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
3-phosphoglycerate kinase (PGK) is a typical two-domain hinge-bending enzyme with a well-structured interdomain region. The mechanism of domain-domain interaction and its regulation by substrate binding is not yet fully understood. Here the existence of strong cooperativity between the two domains was demonstrated by following heat transitions of pig muscle and yeast PGKs using differential scanning microcalorimetry and fluorimetry. Two mutants of yeast PGK containing a single tryptophan fluorophore either in the N- or in the C-terminal domain were also studied. The coincidence of the calorimetric and fluorimetric heat transitions in all cases indicated simultaneous, highly cooperative unfolding of the two domains. This cooperativity is preserved in the presence of substrates: 3-phosphoglycerate bound to the N domain or the nucleotide (MgADP, MgATP) bound to the C domain increased the structural stability of the whole molecule. A structural explanation of domain-domain interaction is suggested by analysis of the atomic contacts in 12 different PGK crystal structures. Well-defined backbone and side-chain H bonds, and hydrophobic and electrostatic interactions between side chains of conserved residues are proposed to be responsible for domain-domain communication. Upon binding of each substrate newly formed molecular contacts are identified that firstly explain the order of the increased heat stability in the various binary complexes, and secondly describe the possible route of transmission of the substrate-induced conformational effects from one domain to the other. The largest stability is characteristic of the native ternary complex and is abolished in the case of a chemically modified inactive form of PGK, the domain closure of which was previously shown to be prevented [Sinev MA, Razgulyaev OI, Vas M, Timchenko AA & Ptitsyn OB (1989) Eur J Biochem180, 61-66]. Thus, conformational stability correlates with domain closure that requires simultaneous binding of both substrates.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
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14
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Jakeman DL, Ivory AJ, Blackburn GM, Williamson MP. Orientation of 1,3-bisphosphoglycerate analogs bound to phosphoglycerate kinase. J Biol Chem 2003; 278:10957-62. [PMID: 12509431 DOI: 10.1074/jbc.m211769200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have previously reported dissociation constants for a range of bisphosphonate analogs of 1,3-bisphospho-D-glyceric acid binding to yeast phosphoglycerate kinase. Data for the unsymmetrical analogs were difficult to interpret because it was not clear in which of the two possible orientations these ligands bound. Here we report a novel NMR method for quantifying orientation preference based on relaxation effects induced by titration with CrADP, which is applied to these ligands. It is shown that all ligands can bind in both orientations but that the driving force for the orientational preference is to put the alpha,alpha-difluoromethanephosphonate group in the "basic patch" (nontransferable phosphate) position. The relevance to the design of phosphoglycerate kinase inhibitors is discussed.
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Affiliation(s)
- David L Jakeman
- Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S10 2TN, United Kingdom
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15
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Marina A, Mott C, Auyzenberg A, Hendrickson WA, Waldburger CD. Structural and mutational analysis of the PhoQ histidine kinase catalytic domain. Insight into the reaction mechanism. J Biol Chem 2001; 276:41182-90. [PMID: 11493605 DOI: 10.1074/jbc.m106080200] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PhoQ is a transmembrane histidine kinase belonging to the family of two-component signal transducing systems common in prokaryotes and lower eukaryotes. In response to changes in environmental Mg(2+) concentration, PhoQ regulates the level of phosphorylated PhoP, its cognate transcriptional response-regulator. The PhoQ cytoplasmic region comprises two independently folding domains: the histidine-containing phosphotransfer domain and the ATP-binding kinase domain. We have determined the structure of the kinase domain of Escherichia coli PhoQ complexed with the non-hydrolyzable ATP analog adenosine 5'-(beta,gamma-imino)triphosphate and Mg(2+). Nucleotide binding appears to be accompanied by conformational changes in the loop that surrounds the ATP analog (ATP-lid) and has implications for interactions with the substrate phosphotransfer domain. The high resolution (1.6 A) structure reveals a detailed view of the nucleotide-binding site, allowing us to identify potential catalytic residues. Mutagenic analyses of these residues provide new insights into the catalytic mechanism of histidine phosphorylation in the histidine kinase family. Comparison with the active site of the related GHL ATPase family reveals differences that are proposed to account for the distinct functions of these proteins.
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Affiliation(s)
- A Marina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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16
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Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Erlandsen H, Abola EE, Stevens RC. Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. Curr Opin Struct Biol 2000; 10:719-30. [PMID: 11114510 DOI: 10.1016/s0959-440x(00)00154-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An important goal of structural genomics is to complete the structural analysis of all the enzymes in metabolic pathways and to understand the structural similarities and differences. A preliminary glimpse of this type of analysis was achieved before structural genomics efforts with the glycolytic pathway and efforts are underway for many other pathways, including that of catecholamine metabolism. Structural enzymology necessitates a complete structural characterization, even for highly homologous proteins (greater than 80% sequence homology), as every active site has distinct structural features and it is these active site differences that distinguish one enzyme from another. Short cuts with homology modeling cannot be taken with our current knowledge base. Each enzyme structure in a pathway needs to be determined, including structures containing bound substrates, cofactors, products and transition state analogs, in order to obtain a complete structural and functional understanding of pathway-related enzymes.
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Affiliation(s)
- H Erlandsen
- The Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA
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18
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Abstract
Two hemoglobins with cysteine residues highly reactive toward electrophiles have been identified and characterized. Cys-125beta of guinea pig hemoglobin has a low pK(a) and forms conjugates with electrophiles more quickly than glutathione and several orders of magnitude more quickly than other protein thiols. This cysteine is capable of intercepting benzoquinone, a known carcinogenic metabolite, before other protein nucleophiles can be modified. Cys-13beta of mouse hemoglobin was observed to conjugate with electrophiles as quickly as glutathione. The structural basis of reactivity is different in the two hemoglobins and is analyzed in terms of hydrogen-bonding, solvent accessibility, and helix-dipole contributions. Complementing a previously characterized highly reactive cysteine in rat hemoglobin, identification of these cysteines suggests that the reactivity of these hemoglobins could represent a common function as a detoxification sink against carcinogens.
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Affiliation(s)
- J J Miranda
- Department of Chemistry, Reed College, Portland, Oregon 97202, USA
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19
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Valentin C, Birgens H, Craescu CT, Brødum-Nielsen K, Cohen-Solal M. A phosphoglycerate kinase mutant (PGK Herlev; D285V) in a Danish patient with isolated chronic hemolytic anemia: mechanism of mutation and structure-function relationships. Hum Mutat 2000; 12:280-7. [PMID: 9744480 DOI: 10.1002/(sici)1098-1004(1998)12:4<280::aid-humu10>3.0.co;2-v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phosphoglycerate kinase (PGK) is a X-linked enzyme that plays a key role in the glycolytic pathway. Twelve different variants have already been reported. We describe a new PGK variant, PGK Herlev (Asp 285-->Val), in a 69-year-old Danish patient with isolated chronic hemolysis but who had no neurological or muscular disorders. The description of the mutation is based upon PCR amplification of specific regions of the PGK gene, followed by direct sequencing. Although observed in a male patient, this mutated X-linked gene is expressed partially, i.e., both normal and substituted nucleotides are present at the same position in a ratio of approximately 1:9. The most likely explanation for this observation is based on the occurrence of a somatic mutation of the PGK gene. The relationship of structure to function in PGK Herlev, as well as in all known variants, was examined by the use of a computer model based on the known spatial structure of the yeast and horse enzymes. Such an approach can be generalized to any other protein that has been crystallized and for which x-ray diffraction data are available in a species closely related to man.
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Affiliation(s)
- C Valentin
- Unité INSERM U.474, Hôpital Henri Mondor, Créteil, France
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20
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Vaidehi N, Goddard WA. Domain Motions in Phosphoglycerate Kinase using Hierarchical NEIMO Molecular Dynamics Simulations. J Phys Chem A 2000. [DOI: 10.1021/jp991985d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nagarajan Vaidehi
- Materials and Process Simulation Center, Beckman Institute (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William A. Goddard
- Materials and Process Simulation Center, Beckman Institute (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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21
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Abstract
The metabolic myopathies are distinguished by extensive clinical and genetic heterogeneity within and between individual disorders. There are a number of explanations for the variability observed that go beyond single gene mutations or degrees of heteroplasmy in the case of mitochondrial DNA mutations. Some of the contributing factors include protein subunit interactions, tissue-specificity, modifying genetic factors, and environmental triggers. Advances in the molecular analysis of metabolic myopathies during the last decade have not only improved the diagnosis of individual disorders but also helped to characterize the contributing factors that make these disorders so complex.
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Affiliation(s)
- G D Vladutiu
- Associate Professor, Departments of Pediatrics, Neurology, and Pathology, Division of Genetics, School of Medicine and Biomedical Studies, State University of New York at Buffalo, 14209, USA.
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22
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Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R. Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys 1999; 31:141-64. [PMID: 10593256 DOI: 10.1007/bf02738169] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of "induced fit" binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels, a priori contain both the "open" and the "closed" conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes. This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield "domain swapping;" the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac repressor. Nonallosteric subunit transitions are also addressed, with some examples (aspartate receptor and BamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations.
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Affiliation(s)
- S Kumar
- Intramural Research Support Program-SAIC, Laboratory of Experimental and Computational Biology, NCI-FCRDC, Frederick, MD, 21702, USA
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23
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Valentin C, Birgens H, Craescu CT, Brødum-Nielsen K, Cohen-Solal M. A phosphoglycerate kinase mutant (PGK Herlev; D285V) in a Danish patient with isolated chronic hemolytic anemia: mechanism of mutation and structure-function relationships. Hum Mutat 1998. [PMID: 9744480 DOI: 10.1002/(sici)1098-1004(1998)12:4%3c280::aid-humu10%3e3.0.co;2-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Phosphoglycerate kinase (PGK) is a X-linked enzyme that plays a key role in the glycolytic pathway. Twelve different variants have already been reported. We describe a new PGK variant, PGK Herlev (Asp 285-->Val), in a 69-year-old Danish patient with isolated chronic hemolysis but who had no neurological or muscular disorders. The description of the mutation is based upon PCR amplification of specific regions of the PGK gene, followed by direct sequencing. Although observed in a male patient, this mutated X-linked gene is expressed partially, i.e., both normal and substituted nucleotides are present at the same position in a ratio of approximately 1:9. The most likely explanation for this observation is based on the occurrence of a somatic mutation of the PGK gene. The relationship of structure to function in PGK Herlev, as well as in all known variants, was examined by the use of a computer model based on the known spatial structure of the yeast and horse enzymes. Such an approach can be generalized to any other protein that has been crystallized and for which x-ray diffraction data are available in a species closely related to man.
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Affiliation(s)
- C Valentin
- Unité INSERM U.474, Hôpital Henri Mondor, Créteil, France
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24
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Jakeman DL, Ivory AJ, Williamson MP, Blackburn GM. Highly potent bisphosphonate ligands for phosphoglycerate kinase. J Med Chem 1998; 41:4439-52. [PMID: 9804684 DOI: 10.1021/jm970839y] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have synthesized a series of novel analogs of 1, 3-bisphospho-D-glyceric acid, 1,3-BPG,3 and evaluated their binding to phosphoglycerate kinase, PGK (EC 2.7.2.3). Nonscissile methanephosphonic acids replace the two phosphate monoesters of 1, 3-BPG and lead to several stable, tight-binding mimics of this intermediate species in glycolysis. Multiple fluorine substitution for hydrogen in the alpha-methylene groups of the phosphonic acid 1, 3-BPG analogs markedly improves their binding to PGK as determined by NMR analysis. The best ligands bind some 50-100 times more strongly than does the substrate 3-phospho-D-glyceric acid and show a requirement for pKa3 to be generally below 6.0, while the presence of a beta-carbonyl group seems to be of secondary importance.
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Affiliation(s)
- D L Jakeman
- Krebs Institute, Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
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25
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Bernstein BE, Williams DM, Bressi JC, Kuhn P, Gelb MH, Blackburn GM, Hol WG. A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei. J Mol Biol 1998; 279:1137-48. [PMID: 9642090 DOI: 10.1006/jmbi.1998.1835] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The glycolytic enzyme phosphoglycerate kinase (PGK) catalyzes phosphoryl transfer between 1,3-bis-phosphoglycerate and ADP to form 3-phosphoglycerate and ATP. During catalysis, a major hinge bending motion occurs which brings the N and C-terminal enzyme domains and their bound substrates together and in-line for phosphoryl transfer. We have crystallized Trypanosoma brucei PGK in the presence of the bisubstrate analog, adenylyl 1,1,5,5-tetrafluoropentane-1, 5-bisphosphonate, and solved the structure of this complex in two different crystal forms at 1.6 and 2.0 A resolution, obtained from PEG 8000 and ammonium phosphate solutions, respectively. These high resolution structures of PGK:inhibitor complexes are of particular interest for drug design since Trypanosoma brucei, the causative agent of African sleeping sickness, relies on glycolysis as its sole energy source. In both structures, the inhibitor is bound in a fully extended conformation with its adenosine moiety assuming exactly the same position as in ADP:PGK complexes and with its 5' phosphonate group occupying part of the 1,3-bis-phosphoglycerate binding site. The bisubstrate analog forces PGK to assume a novel, "inhibited" conformation, intermediate in hinge angle between the native structures of open and closed form PGK. These structures of enzyme-inhibitor complexes demonstrate that PGK has two distinct hinge points that can each be independently activated. In the "PEG" structure, the C-terminal hinge is partially activated while the N-terminal hinge point remains in an open state. In the "phosphate" structure, closure of the N-terminal hinge point is also evident. Finally and most unexpectedly, both complex structures also contain a 3 A shift of a helix that lies outside the flexible hinge region. We propose that a transient shift of this helix is a required element of PGK hinge closure during catalysis.
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Affiliation(s)
- B E Bernstein
- Departments of Biological Structure and Biochemistry Howard Hughes Medical Institute and Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA
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26
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Bernstein BE, Michels PA, Kim H, Petra PH, Hol WG. The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK. Protein Sci 1998; 7:504-7. [PMID: 9521128 PMCID: PMC2143923 DOI: 10.1002/pro.5560070232] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Phosphoglycerate kinase (PGK) catalyzes the phosphoryl transfer between 1,3 bis-phosphoglycerate and ADP to form 3-phosphoglycerate and ATP, undergoing significant conformational changes during catalysis. To more precisely document this reaction and the corresponding conformational changes, we have crystallized Trypanosoma brucei PGK in several crystal forms: (1) in the presence of 3-phosphoglycerate and MgADP, PGK crystallizes with four molecules in the asymmetric unit; (2) in the presence of the ATP analog, AMP-PNP, PGK crystallizes in a similar form; (3) in the presence of the bisubstrate analog, adenylyl 1,1,5,5-tetrafluoropentane-1,5-bisphosphonate, PGK crystals grow with one molecule in the asymmetric unit. Large scale expression and purification of T. brucei PGK from an E. coli overexpression system was required to obtain sufficient enzyme yields. Results from dynamic light scattering experiments allowed us to identify substrates and analogs which were amenable for crystallization. Ease of crystal growth and diffraction quality for a particular PGK-ligand complex is highly consistent with the apparent monodispersity of the complex in solution as judged by dynamic light scattering. The three-dimensional structures of the various enzyme-ligand complexes are currently being exploited to obtain a better understanding of PGK catalysis, as well as for structure based design of enzyme inhibitors to be used in the development of anti-trypanosomal agents.
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Affiliation(s)
- B E Bernstein
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle 98195, USA
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27
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Abstract
Conformational flexibility and structural fluctuations play an important role in enzyme activity. A great variety of internal motions ranging over different time scales and of different amplitudes are involved in the catalytic cycle. These different types of motions and their functional consequences are considered in the light of experimental data and theoretical analyses. The conformational changes upon substrate binding, and particularly the hinge-bending motion which occurs in enzymes made of two domains, are analyzed from several well documented examples. The conformational events accompanying the different steps of the catalytic cycle are discussed. The last section concerns the motions involved in the allosteric transition which regulates the enzyme activity.
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Affiliation(s)
- J M Yon
- Laboratoire de Modélisation et d'Ingénérie des Protéines, Unité Associée du CNRS, Université de Paris-Sud, Orsay, France
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28
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Auerbach G, Huber R, Grättinger M, Zaiss K, Schurig H, Jaenicke R, Jacob U. Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability. Structure 1997; 5:1475-83. [PMID: 9384563 DOI: 10.1016/s0969-2126(97)00297-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Phosphoglycerate kinase (PGK) is essential in most living cells both for ATP generation in the glycolytic pathway of aerobes and for fermentation in anaerobes. In addition, in many plants the enzyme is involved in carbon fixation. Like other kinases, PGK folds into two distinct domains, which undergo a large hinge-bending motion upon catalysis. The monomeric 45 kDa enzyme catalyzes the transfer of the C1-phosphoryl group from 1, 3-bisphosphoglycerate to ADP to form 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP. For decades, the conformation of the enzyme during catalysis has been enigmatic. The crystal structure of PGK from the hyperthermophilic organism Thermotoga maritima (TmPGK) represents the first structure of an extremely thermostable PGK. It adds to a series of four known crystal structures of PGKs from mesophilic via moderately thermophilic to a hyperthermophilic organism, allowing a detailed analysis of possible structural determinants of thermostability. RESULTS The crystal structure of TmPGK was determined to 2.0 A resolution, as a ternary complex with the product 3-phosphoglycerate and the product analogue AMP-PNP (adenylyl-imido diphosphate). The complex crystallizes in a closed conformation with a drastically reduced inter-domain angle and a distance between the two bound ligands of 4.4 A, presumably representing the active conformation of the enzyme. The structure provides new details of the catalytic mechanism. An inter-domain salt bridge between residues Arg62 and Asp200 forms a strap to hold the two domains in the closed state. We identify Lys197 as a residue involved in stabilization of the transition state phosphoryl group, and so term it the 'phosphoryl gripper'. CONCLUSIONS The hinge-bending motion of the two domains upon closure of the structure, as seen in the Trypanosoma PGK structure, is confirmed. This closed conformation obviously occurs after binding of both substrates and is locked by the Arg62-Asp200 salt bridge. Re-orientations in the conserved active-site loop region around Thr374 also bring both domains into direct contact in the core region of the former inter-domain cleft, to form the complete catalytic site. Comparison of extremely thermostable TmPGK with less thermostable homologues reveals that its increased rigidity is achieved by a raised number of intramolecular interactions, such as an increased number of ion pairs and additional stabilization of alpha helix and loop regions. The covalent fusion with triosephosphate isomerase might represent an additional stabilization strategy.
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Affiliation(s)
- G Auerbach
- Max-Planck-Institut für Biochemie, Abt. Strukturforschung, 82152, Martinsried, Germany.
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29
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Murali N, Lin Y, Mechulam Y, Plateau P, Rao BD. Adenosine conformations of nucleotides bound to methionyl tRNA synthetase by transferred nuclear Overhauser effect spectroscopy. Biophys J 1997; 72:2275-84. [PMID: 9129831 PMCID: PMC1184423 DOI: 10.1016/s0006-3495(97)78872-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The conformations of MgATP and AMP bound to a monomeric tryptic fragment of methionyl tRNA synthetase have been investigated by two-dimensional proton transferred nuclear Overhauser effect spectroscopy (TRNOESY). The sample protocol was chosen to minimize contributions from adventitious binding of the nucleotides to the observed NOE. The experiments were performed at 500 MHz on three different complexes, E.MgATP, E.MgATP.L-methioninol, and E.AMP.L-methioninol. A starter set of distances obtained by fitting NOE build-up curves (not involving H5' and H5") were used to determine a CHARMm energy-minimized structure. The positioning of the H5' and H5" protons was determined on the basis of a conformational search of the torsion angle to obtain the best fit with the observed NOEs for their superposed resonance. Using this structure, a relaxation matrix was set up to calculate theoretical build-up curves for all of the NOEs and compare them with the observed curves. The final structures deduced for the adenosine moieties in the three complexes are very similar, and are described by a glycosidic torsion angle (chi) of 56 degrees +/- 5 degrees and a phase angle of pseudorotation (P) in the range of 47 degrees to 52 degrees, describing a 3(4)T-4E sugar pucker. The glycosidic torsion angle, chi, deduced here for this adenylyl transfer enzyme and those determined previously for three phosphoryl transfer enzymes (creatine kinase, arginine kinase, and pyruvate kinase), and one pyrophosphoryl enzyme (PRibPP synthetase), are all in the range 52 degrees +/- 8 degrees. The narrow range of values suggests a possible common motif for the recognition and binding of the adenosine moiety at the active sites of ATP-utilizing enzymes, irrespective of the point of cleavage on the phosphate chain.
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Affiliation(s)
- N Murali
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis 46202-3273, USA
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30
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Sherman MA, Chen Y, Mas MT. An engineered amino-terminal domain of yeast phosphoglycerate kinase with native-like structure. Protein Sci 1997; 6:882-91. [PMID: 9098898 PMCID: PMC2144753 DOI: 10.1002/pro.5560060415] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Previous studies have suggested that the carboxy-terminal peptide (residues 401-415) and interdomain helix (residues 185-199) of yeast phosphoglycerate kinase, a two-domain enzyme, play a role in the folding and stability of the amino-terminal domain (residues 1-184). A deletion mutant has been created in which the carboxy-terminal peptide is attached to the amino-terminal domain (residues 1-184) plus interdomain helix (residues 185-199) through a flexible peptide linker, thus eliminating the carboxy-terminal domain entirely. CD, fluorescence, gel filtration, and NMR experiments indicated that, unlike versions described previously, this isolated N-domain is soluble, monomeric, compactly folded, native-like in structure, and capable of binding the substrate 3-phosphoglycerate with high affinity in a saturable manner. The midpoint of the guanidine-induced unfolding transition was the same as that of the native two-domain protein (Cm approximately 0.8 M). The free energy change associated with guanidine-induced unfolding was one-third that of the native enzyme, in agreement with previous studies that evaluated the intrinsic stability of the N-domain and the contribution of domain-domain interactions to the stability of PGK. These observations suggest that the C-terminal peptide and interdomain helix are sufficient for maintaining a native-like fold of the N-domain in the absence of the C-domain.
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Affiliation(s)
- M A Sherman
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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31
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Prade L, Hof P, Bieseler B. Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification. Biol Chem 1997; 378:317-20. [PMID: 9165087 DOI: 10.1515/bchm.1997.378.3-4.317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana has been solved at 2.2 A resolution (Reinemer et al., 1996). The enzyme forms a dimer of two identical subunits. The structure shows a new G-site architecture and a novel and unique dimer interface. Each monomer of the protein forms a separate G-site. Therefore, the requirements on the dimer interface are reduced. As a consequence, the interactions between the monomers are weaker and residues at the dimer interface are more variable. Thus, the dimer interface looses its relevance for a classification of plant glutathione S-transferases and the formation of heterodimers becomes even more difficult to predict.
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Affiliation(s)
- L Prade
- Max-Planck-Institut für Biochemie, Abt. Strukturforschung, Martinsried, Germany
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32
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Pappu KM, Kunnumal B, Serpersu EH. A new metal-binding site for yeast phosphoglycerate kinase as determined by the use of a metal-ATP analog. Biophys J 1997; 72:928-35. [PMID: 9017217 PMCID: PMC1185615 DOI: 10.1016/s0006-3495(97)78726-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Suicide substrate beta, gamma-bidentate Rh(III)ATP (RhATP) was used to map the metal ion-binding site in yeast phosphoglycerate kinase (PGK). Cleavage of the RhATP-inactivated enzyme with pepsin and subsequent separation of peptides by reverse-phase high-performance liquid chromatography gave two Rh-nucleotide bound peptides. One of the peptides corresponded to the C-terminal residues of PGK, and the other to a part of helix V. Of the four glutamates present in the C-terminal peptide, Glu 398 may be a likely metal coordination site. Therefore, importance of the C-terminal residues in PGK catalysis may be attributed, in part to the coordination of metal ion of the metal-ATP substrate. Metal coordination may then align the C-terminal peptide to extend toward the N-terminal domain and form the "closed" active site. Results presented in this paper suggest that one or more side chains of the enzyme may be coordinated to the metal ion in the PGK.3-phospho-D-glycerate-RhATP complex, and that exchange-inert metal-ATP analogs could be used to determine metal coordination sites on kinases and other metal-ATP-utilizing enzymes.
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Affiliation(s)
- K M Pappu
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville 37996-0840, USA
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Bernstein BE, Michels PA, Hol WG. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature 1997; 385:275-8. [PMID: 9000079 DOI: 10.1038/385275a0] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Phosphoglycerate kinase (PGK), a key enzyme in glycolysis, catalyses the transfer of a phosphoryl-group from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP. Despite extensive kinetic and structural investigations over more than two decades, the conformation assumed by this enzyme during catalysis remained unknown. Here we present the 2.8 A crystal structure of a ternary complex of PGK from Trypanosoma brucei, the causative agent of sleeping sickness. This structure determination relied on a procedure in which fragments containing less than 10% of the scattering mass were successively positioned in the unit cell to obtain phases. The PGK ternary complex exhibits a dramatic closing of the large cleft between the two domains seen in all previous studies, thereby bringing the two ligands, 3-phosphoglycerate and ADP into close proximity. Our results demonstrate that PGK is a hinge-bending enzyme, reveal a novel mechanism in which substrate-induced effects combine synergistically to induce major conformational changes and, to our knowledge, afford the first observation of the PGK active site in a catalytic conformation.
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Affiliation(s)
- B E Bernstein
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle 98195, USA
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Cheung CW, Mas MT. Substrate-induced conformational changes in yeast 3-phosphoglycerate kinase monitored by fluorescence of single tryptophan probes. Protein Sci 1996; 5:1144-9. [PMID: 8762145 PMCID: PMC2143445 DOI: 10.1002/pro.5560050616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
3-Phosphoglycerate kinase (PGK) catalyzes the reversible conversion of 3-phosphoglycerate (3-PG) and ATP to 1,3-diphosphoglycerate (1,3-diPG) and ADP in the presence of magnesium ions. PGK is a single polypeptide chain arranged in two domains, with an active site located in the interdomain cleft. The large distance between the binding sites for 3-PG and ATP, deduced from the crystallographic structures of the binary complexes, gave rise to the hypothesis that this enzyme undergoes a hinge-bending domain motion from open to closed conformation during catalysis. However, no direct experimental evidence exists for the "closed" conformation in the presence of both substrates. In this study, several PGK mutants with single tryptophans placed in various location were used as intrinsic fluorescent probes to examine the extent and delocalization of conformational changes induced by the binding of 3-PG, 1,3-diPG, ADP, ATP, and PNP-AMP (nonhydrolyzable analogue of ATP), and by 3-PG and PNP-AMP together. The results showed that only the probes situated in the hinge and in parts of each domain close to the hinge reflect substrate-induced conformational changes. Binding of substrates to one domain was found to induce spectral perturbation of the probes in the opposite domain, indicating a transmission of conformational changes between the domains. A combination of both substrates generated much larger fluorescence changes than the individual substrates. The binding constants were determined for each substrate using probes situated in different locations.
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Affiliation(s)
- C W Cheung
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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