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Abdoul-Zabar J, Sorel I, Hélaine V, Charmantray F, Devamani T, Yi D, de Berardinis V, Louis D, Marlière P, Fessner WD, Hecquet L. Thermostable Transketolase fromGeobacillus stearothermophilus:Characterization and Catalytic Properties. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200590] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pastré D, Hamon L, Sorel I, Le Cam E, Curmi PA, Piétrement O. Specific DNA-protein interactions on mica investigated by atomic force microscopy. Langmuir 2010; 26:2618-2623. [PMID: 19791748 DOI: 10.1021/la902727b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA processing by site-specific proteins on surface remains a challenging issue for nanobioscience applications and, in particular, for high-resolution imaging by atomic force microscopy (AFM). To obtain high-resolution conditions, mica, an atomically flat and negatively charged surface, is generally used. However, even though many specific DNA/protein interactions have already been observed by AFM, little is known about DNA accessibility to specific enzymes on mica. Here we measured the accessibility of adsorbed DNA to restriction endonucleases (EcoRI and EcoRV) using AFM. By increasing the concentration of divalent or multivalent salts, DNA adsorption on mica switches from weak to strong binding. Interestingly, while the accessibility of strongly bound DNA was inhibited, loosely adsorbed DNA was efficiently cleaved on mica. This result opens new perspective to study DNA/protein interaction by AFM or to modify specifically DNA on surface.
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Affiliation(s)
- David Pastré
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM/UEVE U829, Université d'Evry val d'Essonne, Evry F-91025, France.
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Pastré D, Hamon L, Mechulam A, Sorel I, Baconnais S, Curmi PA, Le Cam E, Piétrement O. Atomic Force Microscopy Imaging of DNA under Macromolecular Crowding Conditions. Biomacromolecules 2007; 8:3712-7. [DOI: 10.1021/bm700856u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Pastré
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Loïc Hamon
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Alain Mechulam
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Isabelle Sorel
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Sonia Baconnais
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Patrick A. Curmi
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Eric Le Cam
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Olivier Piétrement
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
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Sorel I, Piétrement O, Hamon L, Baconnais S, Cam EL, Pastré D. The EcoRI-DNA complex as a model for investigating protein-DNA interactions by atomic force microscopy. Biochemistry 2007; 45:14675-82. [PMID: 17144660 DOI: 10.1021/bi060293u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy (AFM) is a technique widely used to image protein-DNA complexes, and its application has now been extended to the measurements of protein-DNA binding constants and specificities. However, the spreading of the protein-DNA complexes on a flat substrate, generally mica, is required prior to AFM imaging. The influence of the surface on protein-DNA interactions is therefore an issue which needs to be addressed. For that purpose, the extensively studied EcoRI-DNA complex was investigated with the aim of providing quantitative information about the surface influence. The equilibrium binding constant of the complex was determined by AFM at both low and high ionic strengths and compared to electrophoretic mobility shift assay measurements (EMSA). In addition, the effect of the DNA length on dissociation of the protein from its specific site was analyzed. It turned out that the AFM measurements are similar to those obtained by EMSA at high ionic strengths. We then advance the idea that this effect is due to the high counterion concentration near the highly negatively charged mica surface. In addition, a dissociation of the complexes once they are adsorbed onto the surface was observed, which is weakly dependent on the ionic strength contrary to what occurs in solution. Finally, a two-step mechanism, which describes the adsorption of the EcoRI-DNA complexes on the surface, is proposed. This model could also be extended to other protein-DNA complexes.
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Affiliation(s)
- Isabelle Sorel
- Laboratoire Structures et Reconnaissance des Biomolécules, EA 3637, Université d'Evry, Rue du Père Jarlan, 91025 Evry Cedex, France
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Pastré D, Hamon L, Landousy F, Sorel I, David MO, Zozime A, Le Cam E, Piétrement O. Anionic polyelectrolyte adsorption on mica mediated by multivalent cations: a solution to DNA imaging by atomic force microscopy under high ionic strengths. Langmuir 2006; 22:6651-60. [PMID: 16831009 DOI: 10.1021/la053387y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Adsorption of DNA molecules on mica, a highly negatively charged surface, mediated by divalent or trivalent cations is considered. By analyzing atomic force microscope (AFM) images of DNA molecules adsorbed on mica, phase diagrams of DNA molecules interacting with a mica surface are established in terms of concentrations of monovalent salt (NaCl) and divalent (MgCl2) or multivalent (spermidine, cobalt hexamine) salts. These diagrams show two transitions between nonadsorption and adsorption. The first one arises when the concentration of multivalent counterions is larger than a limit value, which is not sensitive to the monovalent salt concentration. The second transition is due to the binding competition between monovalent and multivalent counterions. In addition, we develop a model of polyelectrolyte adsorption on like-charged surfaces with multivalent counterions. This model shows that the correlations of the multivalent counterions at the interface between DNA and mica play a critical role. Furthermore, it appears that DNA adsorption takes place when the energy gain in counterion correlations overcomes an energy barrier. This barrier is induced by the entropy loss in confining DNA in a thin adsorbed layer, the entropy loss in the interpenetration of the clouds of mica and DNA counterions, and the electrostatic repulsion between DNA and mica. The analysis of the experimental results provides an estimation of this energy barrier. We then discuss some important issues, including DNA adsorption under physiological conditions.
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Affiliation(s)
- David Pastré
- Laboratoire Structure et Reconnaissance des Biomolécules, EA 3637, Université d'Evry, Rue du Père Jarlan, 91025 Evry Cedex, France.
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Drevelle A, Graille M, Heyd B, Sorel I, Ulryck N, Pecorari F, Desmadril M, van Tilbeurgh H, Minard P. Structures of in Vitro Evolved Binding Sites on Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways. J Mol Biol 2006; 358:455-71. [PMID: 16529771 DOI: 10.1016/j.jmb.2006.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 01/24/2006] [Accepted: 02/02/2006] [Indexed: 11/15/2022]
Abstract
We have recently applied in vitro evolution methods to create in Neocarzinostatin a new binding site for a target molecule unrelated to its natural ligand. The main objective of this work was to solve the structure of some of the selected binders in complex with the target molecule: testosterone. Three proteins (1a.15, 3.24 and 4.1) were chosen as representative members of sequence families that came out of the selection process within different randomization schemes. In order to evaluate ligand-induced conformational adaptation, we also determined the structure of one of the proteins (3.24) in the free and complexed forms. Surprisingly, all these mutants bind not one but two molecules of testosterone in two very different ways. The 3.24 structure revealed that the protein spontaneously evolved in the system to bind two ligand molecules in one single binding crevice. These two binding sites are formed by substituted as well as by non-variable side-chains. The comparison with the free structure shows that only limited structural changes are observed upon ligand binding. The X-ray structures of the complex formed by 1a.15 and 4.1 Neocarzinostatin mutants revealed that the two variants form very similar dimers. These dimers were observed neither for the uncomplexed variants nor for wild-type Neocarzinostatin but were shown here to be induced by ligand binding. Comparison of the three complexed forms clearly suggests that these unanticipated structural responses resulted from the molecular arrangement used for the selection experiments.
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Affiliation(s)
- Antoine Drevelle
- Equipe de Modélisation et Ingénierie des Protéines, IBBMC, CNRS, UMR8619, Université Paris XI, Bât. 430, 91405 Orsay, France
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7
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Liger D, Quevillon-Cheruel S, Sorel I, Bremang M, Blondeau K, Aboulfath I, Janin J, van Tilbeurgh H, Leulliot N. Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily. Proteins 2006; 60:778-86. [PMID: 16021630 DOI: 10.1002/prot.20548] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 A resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the "hot dog" fold, identifies the protein as a "kinked double hot dog" fold.
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Affiliation(s)
- Dominique Liger
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Orsay, France
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Pastré D, Piétrement O, Landousy F, Hamon L, Sorel I, David MO, Delain E, Zozime A, Le Cam E. A new approach to DNA bending by polyamines and its implication in DNA condensation. Eur Biophys J 2005; 35:214-23. [PMID: 16247626 DOI: 10.1007/s00249-005-0025-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 07/28/2005] [Accepted: 08/02/2005] [Indexed: 11/30/2022]
Abstract
Polyamines are known to induce dynamical bending of DNA molecules. This mechanism is very important since many DNA binding proteins (DNAse, transcription factor, etc.) exert their action by their ability to bend DNA. We propose an analytical model which describes the dynamical bending of DNA by polyamine ions in highly diluted DNA solutions. The bending probability depends on the entropy loss of polyamines due to their localization. This localization is facilitated by the electrostatic repulsion between multivalent counterions condensed on DNA, which reduces the entropy loss in counterion localization. Therefore DNA bending by polyamines depends on the competition between monovalent counterions and polyamines. We find that the bending probability is weak for a low binding ratio of polyamines (i.e. number of bound polyamines per base pair), whereas a high bending probability can be reached at large polyamine binding ratio. In addition, we describe a new mechanism of DNA bending. It occurs with the help of thermal agitation, which initiates the bending and favours the polyamine localization. This model provides further insights into DNA bending by polyamines and its implication in DNA condensation. A qualitative estimation of the DNA bending probability is obtained by measuring the cleavage efficiency of DNA by bleomycin versus spermidine concentration. Indeed, a local helix distortion by polyamines results in an amplification of the double-strand cleavage by bleomycin. The measurement of the bleomycin amplification is performed by analysing images of DNA molecules with atomic force microscope. Some features of the dynamical bending indicate that condensation and bending are interrelated.
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Affiliation(s)
- David Pastré
- Laboratoire d'Etude des Milieux Nanométriques, Université d'Evry, Rue du Père Jarlan, 91025 Evry Cedex, France.
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Leulliot N, Trésaugues L, Bremang M, Sorel I, Ulryck N, Graille M, Aboulfath I, Poupon A, Liger D, Quevillon-Cheruel S, Janin J, van Tilbeurgh H. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all? Acta Crystallogr D Biol Crystallogr 2005; 61:664-70. [PMID: 15930617 DOI: 10.1107/s0907444905000028] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Accepted: 01/13/2005] [Indexed: 11/11/2022]
Abstract
Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France.
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10
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Zhou CZ, Meyer P, Quevillon-Cheruel S, Li De La Sierra-Gallay I, Collinet B, Graille M, Blondeau K, François JM, Leulliot N, Sorel I, Poupon A, Janin J, Van Tilbeurgh H. Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold. Protein Sci 2005; 14:209-15. [PMID: 15608122 PMCID: PMC2253319 DOI: 10.1110/ps.041121305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 A. The protein has no close homologs and its molecular and cellular functions are unknown. The structure of the protein is a jelly-roll fold consisting of ten beta-strands organized in two parallel packed beta-sheets. The protein has strong structural resemblance to the plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) but also to some plant and bacterial enzymes (epimerase, germin). The protein forms homodimers in the crystal, confirming measurements of its molecular mass in solution. Two monomers have their beta-sheet packed together to form the dimer. The presence of a hydrophobic ligand in a well conserved pocket inside the barrel and local sequence similarity with bacterial epimerases may suggest a biochemical function for this protein.
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Affiliation(s)
- Cong-Zhao Zhou
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8619, Université Paris-Sud, 91405 Orsay, France
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11
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Graille M, Meyer P, Leulliot N, Sorel I, Janin J, Van Tilbeurgh H, Quevillon-Cheruel S. Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes. Biochimie 2005; 87:763-9. [PMID: 16054529 DOI: 10.1016/j.biochi.2005.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Revised: 02/04/2005] [Accepted: 03/08/2005] [Indexed: 10/25/2022]
Abstract
Ribose-5-phosphate isomerase A has an important role in sugar metabolism by interconverting ribose-5-phosphate and ribulose-5-phosphate. This enzyme is ubiquitous and highly conserved among the three kingdoms of life. We have solved the 2.1 A resolution crystal structure of the Saccharomyces cerevisiae enzyme by molecular replacement. This protein adopts the same fold as its archaeal and bacterial orthologs with two alpha/beta domains tightly packed together. Mapping of conserved residues at the surface of the protein reveals strong invariability of the active site pocket, suggesting a common ligand binding mode and a similar catalytic mechanism. The yeast enzyme associates as a homotetramer similarly to the archaeal protein. The effect of an inactivating mutation (Arg189 to Lys) is discussed in view of the information brought by this structure.
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Affiliation(s)
- M Graille
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS-UMR 8619, Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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Tran TT, Sorel I, Lewit-Bentley A. Statistical experimental design of protein crystallization screening revisited. Acta Crystallogr D Biol Crystallogr 2004; 60:1562-8. [PMID: 15333926 DOI: 10.1107/s0907444904015732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 06/28/2004] [Indexed: 11/11/2022]
Abstract
A statistical experimental design approach was used to prepare a set of solutions for the screening of protein crystallization conditions. This approach is shown to be amenable to quantitative evaluation and therefore to the rational optimization of the screening results. All solutions contain a cryoprotectant, thus eliminating the need for subsequent optimization of crystal freezing conditions.
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Affiliation(s)
- Thanh Tam Tran
- LURE, CNRS, CEA, Ministère de la Recherche, BP 34, 91898 Orsay CEDEX, France
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Leulliot N, Quevillon-Cheruel S, Sorel I, Graille M, Meyer P, Liger D, Blondeau K, Janin J, van Tilbeurgh H. Crystal Structure of Yeast Allantoicase Reveals a Repeated Jelly Roll Motif. J Biol Chem 2004; 279:23447-52. [PMID: 15020593 DOI: 10.1074/jbc.m401336200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-Unité Mixte de Recherche 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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14
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Li de La Sierra-Gallay I, Collinet B, Graille M, Quevillon-Cheruel S, Liger D, Minard P, Blondeau K, Henckes G, Aufrère R, Leulliot N, Zhou CZ, Sorel I, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase. Proteins 2004; 54:776-83. [PMID: 14997573 DOI: 10.1002/prot.10596] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined.
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Affiliation(s)
- Ines Li de La Sierra-Gallay
- Laboratoire d'Enzymologie et Biochimie Structurales (CNRS-UPR 9063), Bât. 34, 1 Av. de la Terrasse, 91198 Gif sur Yvette, France
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15
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Leulliot N, Quevillon-Cheruel S, Sorel I, Li de La Sierra-Gallay I, Collinet B, Graille M, Blondeau K, Bettache N, Poupon A, Janin J, van Tilbeurgh H. Structure of protein phosphatase methyltransferase 1 (PPM1), a leucine carboxyl methyltransferase involved in the regulation of protein phosphatase 2A activity. J Biol Chem 2003; 279:8351-8. [PMID: 14660564 DOI: 10.1074/jbc.m311484200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The important role of the serine/threonine protein phosphatase 2A (PP2A) in various cellular processes requires a precise and dynamic regulation of PP2A activity, localization, and substrate specificity. The regulation of the function of PP2A involves the reversible methylation of the COOH group of the C-terminal leucine of the catalytic subunit, which, in turn, controls the enzyme's heteromultimeric composition and confers different protein recognition and substrate specificity. We have determined the structure of PPM1, the yeast methyltransferase responsible for methylation of PP2A. The structure of PPM1 reveals a common S-adenosyl-l-methionine-dependent methyltransferase fold, with several insertions conferring the specific function and substrate recognition. The complexes with the S-adenosyl-l-methionine methyl donor and the S-adenosyl-l-homocysteine product and inhibitor unambiguously revealed the co-substrate binding site and provided a convincing hypothesis for the PP2A C-terminal peptide binding site. The structure of PPM1 in a second crystal form provides clues to the dynamic nature of the PPM1/PP2A interaction.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bât. 430, 91405 Orsay, France
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Zhou CZ, Li de La Sierra-Gallay I, Quevillon-Cheruel S, Collinet B, Minard P, Blondeau K, Henckes G, Aufrère R, Leulliot N, Graille M, Sorel I, Savarin P, de la Torre F, Poupon A, Janin J, van Tilbeurgh H. Crystal Structure of the Yeast Phox Homology (PX) Domain Protein Grd19p Complexed to Phosphatidylinositol-3-phosphate. J Biol Chem 2003; 278:50371-6. [PMID: 14514667 DOI: 10.1074/jbc.m304392200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phox homology (PX) domains have been recently identified in a number of different proteins and are involved in various cellular functions such as vacuolar targeting and membrane protein trafficking. It was shown that these modules of about 130 amino acids specifically binding to phosphoinositides and that this interaction is crucial for their cellular function. The yeast genome contains 17 PX domain proteins. One of these, Grd19p, is involved in the localization of the late Golgi membrane proteins DPAP A and Kex2p. Grd19p consists of the PX domain with 30 extra residues at the N-terminal and is homologous to the functionally characterized human sorting nexin protein SNX3. We determined the 2.0 A crystal structure of Grd19p in the free form and in complex with d-myo-phosphatidylinositol 3-phosphate (diC4PtdIns(3)P), representing the first case of both free and ligand-bound conformations of the same PX module. The ligand occupies a well defined positively charged binding pocket at the interface between the beta-sheet and alpha-helical parts of the molecule. The structure of the free and bound protein are globally similar but show some significant differences in a region containing a polyproline peptide and a putative membrane attachment site.
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Affiliation(s)
- Cong-Zhao Zhou
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-Unité Mixte de Recherche 8619), Université Paris-Sud, Bât. 430, 91405 Orsay, France
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Quevillon-Cheruel S, Leulliot N, Meyer P, Graille M, Bremang M, Blondeau K, Sorel I, Poupon A, Janin J, van Tilbeurgh H. Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae. J Biol Chem 2003; 279:619-25. [PMID: 14573601 DOI: 10.1074/jbc.m310380200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chorismate synthase (EC 4.2.3.5), the seventh enzyme in the shikimate pathway, catalyzes the transformation of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate, which is the last common precursor in the biosynthesis of numerous aromatic compounds in bacteria, fungi, and plants. The chorismate synthase reaction involves a 1,4-trans-elimination of phosphoric acid from EPSP and has an absolute requirement for reduced FMN as a cofactor. We have determined the three-dimensional x-ray structure of the yeast chorismate synthase from selenomethionine-labeled crystals at 2.2-A resolution. The structure shows a novel betaalphabetaalpha fold consisting of an alternate tight packing of two alpha-helical and two beta-sheet layers, showing no resemblance to any documented protein structure. The molecule is arranged as a tight tetramer with D2 symmetry, in accordance with its quaternary structure in solution. Electron density is missing for 23% of the amino acids, spread over sequence regions that in the three-dimensional structure converge on the surface of the protein. Many totally conserved residues are contained within these regions, and they probably form a structured but mobile domain that closes over a cleft upon substrate binding and catalysis. This hypothesis is supported by previously published spectroscopic measurements implying that the enzyme undergoes considerable structural changes upon binding of both FMN and EPSP.
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Affiliation(s)
- Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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Quevillon-Cheruel S, Collinet B, Zhou CZ, Minard P, Blondeau K, Henkes G, Aufrère R, Coutant J, Guittet E, Lewit-Bentley A, Leulliot N, Ascone I, Sorel I, Savarin P, Li de La Sierra Gallay I, de la Torre F, Poupon A, Fourme R, Janin J, van Tilbeurgh H. A structural genomics initiative on yeast proteins. J Synchrotron Radiat 2003; 10:4-8. [PMID: 12511784 DOI: 10.1107/s0909049502017284] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2002] [Accepted: 08/29/2002] [Indexed: 05/24/2023]
Abstract
A canonical structural genomics programme is being conducted at the Paris-Sud campus area on baker's yeast proteins. Experimental strategies, first results and identified bottlenecks are presented. The actual or potential contributions to the structural genomics of several experimental structure-determination methods are discussed.
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Affiliation(s)
- Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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