Title | On the chemical mechanism of succinic semialdehyde dehydrogenase (GabD1) from Mycobacterium tuberculosis. |
Publication Type | Journal Article |
Year of Publication | 2011 |
Authors | de Carvalho LPedro S, Ling Y, Shen C, J Warren D, Rhee KY |
Journal | Arch Biochem Biophys |
Volume | 509 |
Issue | 1 |
Pagination | 90-9 |
Date Published | 2011 May 01 |
ISSN | 1096-0384 |
Keywords | Amino Acid Sequence, gamma-Aminobutyric Acid, Humans, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Mycobacterium tuberculosis, NADP, Nuclear Magnetic Resonance, Biomolecular, Sequence Alignment, Stereoisomerism, Substrate Specificity, Succinate-Semialdehyde Dehydrogenase |
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 pK(a) 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. |
DOI | 10.1016/j.abb.2011.01.023 |
Alternate Journal | Arch Biochem Biophys |
PubMed ID | 21303655 |
PubMed Central ID | PMC3094805 |
Grant List | R01 AI064768-01 / AI / NIAID NIH HHS / United States R01 AI064768-03 / AI / NIAID NIH HHS / United States R01AI64768 / AI / NIAID NIH HHS / United States R01 AI064768 / AI / NIAID NIH HHS / United States R01 AI064768-02 / AI / NIAID NIH HHS / United States R01 AI064768-04 / AI / NIAID NIH HHS / United States R01 AI064768-05 / AI / NIAID NIH HHS / United States |