Abstract
The active form of vitamin B6, pyridoxal 5’-phosphate (PLP), plays an essential role in the catalytic mechanism of various proteins, including human glutamate-oxaloacetate transaminase (hGOT1), an important enzyme in amino acid metabolism. A recent molecular and genetic study showed that the E266K, R267H, and P300L substitutions in aspartate aminotransferase, the Arabidopsis analog of hGOT1, genetically suppress a developmentally arrested Arabidopsis RUS mutant. Furthermore, CD analyses suggested that the variants exist as apo proteins and implicated a possible role of PLP in the regulation of PLP homeostasis and metabolic pathways. In this work, we assessed the stability of PLP bound to hGOT1 for the three variant and wildtype (WT) proteins using a combined 6 μs of molecular dynamics (MD) simulation. For the variants and WT in the holo form, the MD simulations reproduced the “closed-open” transition needed for substrate binding. This conformational transition was associated with the rearrangement of the P15-R32 small domain loop providing substrate access to the R387/R293 binding motif. We also showed that formation of the dimer interface is essential for PLP affinity to the active site. The position of PLP in the WT binding site was stabilized by a unique hydrogen bond network of the phosphate binding cup, which placed the cofactor for formation of the covalent Schiff base linkage with K259 for catalysis. The amino acid substitutions at positions 266, 267, and 300 reduced the structural correlation between PLP and the protein active site and/or integrity of the dimer interface. Principal component analysis and energy decomposition clearly suggested dimer misalignment and dissociation for the three variants tested in our work. The low affinity of PLP in the hGOT1 variants observed in our computational work provided structural rationale for the possible role of vitamin B6 in regulating metabolic pathways.
Highlights
Vitamin B6 is essential to all living organisms
The open and closed conformations of the hGOT1 active site produced by molecular dynamics (MD) simulations are shown in Fig 2A and 2B
We showed that the removal of the inhibitor or substrate from the crystal structure produced an open conformation of the P15-R32 loop, which reestablished access to the active site
Summary
Vitamin B6 is essential to all living organisms. It serves as a cofactor in metabolic pathways and is a potent antioxidant against stress [1,2,3]. Pyridoxal 5’-phosphate (PLP), an active form of vitamin B6, is a ubiquitous cofactor for numerous enzymes in various catalytic mechanisms such as decarboxylation, racemization, transamination, α/β elimination, and retro-aldol cleavage [4, 5]. This versatile cofactor forms a covalent bond with a catalytic lysine in all PLPdependent enzymes forming an internal aldimine, commonly known as a Schiff base. The mechanism of the external aldimine formation from a Schiff base is a conserved mechanistic feature in all PLPcatalyzed reactions Once this common central intermediate is formed, the reaction proceeds depending on the enzyme’s function [8]
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