On the chemical mechanism of succinic semialdehyde dehydrogenase (GabD1) from Mycobacterium tuberculosis |
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Authors: | de Carvalho Luiz Pedro S Ling Yan Shen Chun Warren J David Rhee Kyu Y |
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Institution: | aDepartment of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Ave. New York, NY 10065, USA;bDepartment of Biochemistry and Milstein Chemistry Core Facility, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10065, USA;cDivision of Infectious Diseases, Department of Medicine, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10065, USA |
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Abstract: | Succinic semialdehyde dehydrogenases (SSADHs) are ubiquitous enzymes that catalyze the NAD(P)+-coupled oxidation of succinic semialdehyde (SSA) to succinate, the last step of the γ-aminobutyrate shunt. Mycobacterium tuberculosis encodes two paralogous SSADHs (gabD1 and gabD2). Here, we describe the first mechanistic characterization of GabD1, using steady-state kinetics, pH-rate profiles, 1H NMR, and kinetic isotope effects. Our results confirmed SSA and NADP+ as substrates and demonstrated that a divalent metal, such as Mg2+, linearizes the time course. pH-rate studies failed to identify any ionizable groups with pKa between 5.5 and 10 involved in substrate binding or rate-limiting chemistry. Primary deuterium, solvent and multiple kinetic isotope effects revealed that nucleophilic addition to SSA is very fast, followed by a modestly rate-limiting hydride transfer and fast thioester hydrolysis. Proton inventory studies revealed that a single proton is associated with the solvent-sensitive rate-limiting step. Together, these results suggest that product dissociation and/or conformational changes linked to it are rate-limiting. Using structural information for the human homolog enzyme and 1H NMR, we further established that nucleophilic attack takes place at the Si face of SSA, generating a thiohemiacetal with S stereochemistry. Deuteride transfer to the Pro-R position in NADP+ generates the thioester intermediate and 4A-2H, 4B-1H] NADPH. A chemical mechanism based on these data and the structural information available is proposed. |
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Keywords: | Succinic semialdehyde dehydrogenase Aldehyde dehydrogenase Chemical mechanism Stereochemistry Hydride transfer Isotope effects |
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