Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site

Autor: Bernard Badet, Philippe Durand, Bernard Maigret, Nicolas Floquet, David Perahia, Marie-Ange Badet-Denisot
Přispěvatelé: Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), laboratoire de chimie théorique, Laboratoire de Physico-Chimie Théorique (LPCT), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université de Reims Champagne-Ardenne (URCA), Laboratoire de Physique Quantique (LPQ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Natural Language Processing & Knowledge Discovery (LORIA - NLPKD), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2009
Předmět:
Models
Molecular
MESH: Fructosephosphates
Stereochemistry
MESH: Motion
[SDV.BC]Life Sciences [q-bio]/Cellular Biology
Glutamine binding
Crystallography
X-Ray
Ligands
01 natural sciences
Motion
03 medical and health sciences
Ammonia
chemistry.chemical_compound
MESH: Protein Structure
Tertiary
Structural Biology
Normal mode
0103 physical sciences
Atom
MESH: Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)
MESH: Ligands
MESH: Ammonia
Molecular Biology
ComputingMilieux_MISCELLANEOUS
Fructose-6-phosphate binding
030304 developmental biology
Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)
chemistry.chemical_classification
0303 health sciences
Binding Sites
010304 chemical physics
ATP synthase
biology
Fructosephosphates
MESH: Crystallography
X-Ray
Protein Structure
Tertiary
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biophysics
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
Enzyme
chemistry
Catalytic cycle
MESH: Binding Sites
biology.protein
MESH: Models
Molecular
Zdroj: Journal of Molecular Biology
Journal of Molecular Biology, Elsevier, 2009, 385 (2), pp.653-664. ⟨10.1016/j.jmb.2008.10.032⟩
Journal of Molecular Biology, 2009, 385 (2), pp.653-664. ⟨10.1016/j.jmb.2008.10.032⟩
ISSN: 0022-2836
1089-8638
DOI: 10.1016/j.jmb.2008.10.032⟩
Popis: International audience; The large protein motions of the bacterial enzyme glucosamine-6-phosphate synthase have been addressed using full atom normal modes analysis for the empty, the glucose-6-phosphate and the glucose-6-phosphate+glutamate bound proteins. The approach that was used involving energy minimizations along the normal modes coordinates identified functional motions of the protein, some of which were characterized earlier by X-ray diffraction studies. This method made it possible for the first time to highlight significant energy differences according to whether none, only one or both of the active sites of the protein were occupied. Our data favoured a specific motion of the glutamine binding domain following the fixation of fructose-6-phosphate and suggested a rigidified structure with both sites occupied. Here, we show that most of the collective large amplitude motions of glucosamine-6-phosphate synthase that are modulated by ligand binding are crucial for the enzyme catalytic cycle, as they strongly modify the geometry of both the ammonia channel and the C-tail, demonstrating their role in ammonia transfer and ligand binding.
Databáze: OpenAIRE
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