title: Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.
abstract: This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies.
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
authors.forename: Cátia
authors.identifier: http://orcid.org/0000-0002-6904-2511
authors.initials: C
authors.lastname: Moreira
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
authors.forename: Maria J
authors.identifier: http://orcid.org/0000-0002-7554-8324
authors.initials: MJ
authors.lastname: Ramos
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal. pafernan@fc.up.pt.
authors.forename: Pedro Alexandrino
authors.identifier: http://orcid.org/0000-0003-2748-4722
authors.initials: PA
authors.lastname: Fernandes
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D005974:Glutamate-Ammonia Ligase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D010710:Phosphates; D005974:Glutamate-Ammonia Ligase
keywords: computer chemistry; density functional calculations; metalloenzymes; quantum chemistry; reaction mechanisms