Abstract
The production of gamma-aminobutyric acid (GABA) is catalyzed by two isoforms of glutamic acid decarboxylase (GAD), using pyridoxal 5′-phosphate (PLP) as the cofactor. Between the two enzymes, GAD67 accounts for normal GABA requirement, while GAD65 stays inactive until emergent demand for GABA. Recent crystal structure findings revealed that the distinct conformation of a common catalytic loop of the enzymes may account for their different functions (Fenalti et al Nat Struct Mol Biol, 14:280-286, 2007). Enlightened by their inferences, we studied the underlying reaction mechanism of the two GAD isoforms using density functional theory (DFT). A rather complete reaction pathway is identified, including nine transition state (TS) structures and 14 intermediate (IM) structures. The rate limiting step occurs early during the reaction and involves a proton transfer. In the late stage, there are two pathways that involve C4’ and Cα protonation by Tyr or Lys. Our calculations show that the reaction barriers corroborate the conjecture made by Fenalti et al.
The production of gamma-aminobutyric acid (GABA) is catalyzed by two isoforms of glutamic acid decarboxylase (GAD), using pyridoxal 5′-phosphate (PLP) as the cofactor. Between the two enzymes, GAD67 accounts for normal GABA requirement, while GAD65 stays inactive until emergent demand for GABA. Recent crystal structure findings revealed that the distinct conformation of a common catalytic loop of the enzymes may account for their different functions. In this paper, we studied the underlying reaction mechanism of the two GAD isoforms using density functional theory (DFT), aiming to provide more quantitative support. A rather complete reaction pathway with two branches in the late stage is identified for a fairly large reaction model, including nine transition state (TS) structures and 14 intermediate (IM) structures. The different transition barriers of two late reaction pathways may explain the distinct functions of the two GAD isoforms. The results not only corroborate the experimental conjectures, but also help to enrich our understanding of the working principles of the two GAD isoforms
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Acknowledgments
We would like to thank the support from National Natural Science Foundation of China (Grant No. 21073108), Ministry of Education of China (Grant No. 20090131120020) and Independent Innovation Foundation of Shandong University (Grant No. 2012TS006).
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Wang, C., Zhu, R., Sun, H. et al. Quantum chemistry studies of the catalysis mechanism differences between the two isoforms of glutamic acid decarboxylase. J Mol Model 19, 705–714 (2013). https://doi.org/10.1007/s00894-012-1594-x
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DOI: https://doi.org/10.1007/s00894-012-1594-x