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. 2023 Jan 25:11:1077188.
doi: 10.3389/fchem.2023.1077188. eCollection 2023.

Catalytic deAMPylation in AMPylation-inhibitory/assistant forms of FICD protein

Meili Liu  1   2 , Li Li  1 , Zhiqin Wang  1 , Shuang Wang  1   3 , Xiaowen Tang  1
Affiliations

Catalytic deAMPylation in AMPylation-inhibitory/assistant forms of FICD protein

Meili Liu et al. Front Chem. .

Abstract

DeAMPylation, as a reversible reaction of AMPylation and mediated by the endoplasmic reticulum-localized enzyme FICD (filamentation induced by cAMP domain protein, also known as HYPE), is an important process in protein posttranslational modifications (PTMs). Elucidating the function and catalytic details of FICD is of vital importance to provide a comprehensive understanding of protein folding homeostasis. However, the detailed deAMPylation mechanism is still unclear. Furthermore, the role of a conserved glutamine (Glu234), that plays an inhibitory role in the AMPylation response, is still an open question in the deAMPylation process. In the present work, the elaborated deAMPylation mechanisms with AMPylation-inhibitory/assistant forms of FICD (wild type and Glu234Ala mutant) were investigated based on the QM(DFT)/MM MD approach. The results revealed that deAMPylation was triggered by proton transfer from protonated histidine (His363) to AMPylated threonine, instead of a nucleophilic attack of water molecules adding to the phosphorus of AMP. The free energy barrier of deAMPylation in the wild type (∼17.3 kcal/mol) is consistent with that in the Glu234Ala mutant of FICD (∼17.1 kcal/mol), suggesting that the alteration of the Glu234 residue does not affect the deAMPylation reaction and indirectly verifying the inducement of deAMPylation in FICD. In the wild type, the proton in the nucleophilic water molecule is transferred to Glu234, whereas it is delivered to Asp367 through the hydrogen-bond network of coordinated water molecules in the Glu234Ala mutant. The present findings were inspirational for understanding the catalytic and inhibitory mechanisms of FICD-mediated AMP transfer, paving the way for further studies on the physiological role of FICD protein.

Keywords: FICD protein; QM/MM MD; catalytic mechanism; deAMPylation; inhibitory helix.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

SCHEME 1
SCHEME 1
FICD-catalyzed AMPylation and deAMPylation processes. Some crucial atoms/groups are labeled by color.
FIGURE 1
FIGURE 1
Schematic research model and defined reaction coordinates for the deAMPylation process in the FICD wild type (A) and Glu234Ala mutant (B). Electron transfer path of deAMPylation is labeled in blue arrows, and atoms involved directly in this process are colored in red.
FIGURE 2
FIGURE 2
Free energy profiles (A, B) and pivotal distance changes (C, D) along the reaction coordinate (RC) of the deAMPylation process in the wild type and Glu234Ala mutant system.
FIGURE 3
FIGURE 3
Representative structures of reactants (R), transition states (TS), and products (P) identified according to the free energy profile of Figure 2. Structures in the wild type and Glu234Ala mutant system are distinguished by the subscript (Glu and Ala). Atoms are colored for clarity, C (yellow for residues and green for AMP), P (orange), O (red), N (blue), and H (white). Distances are given in angstrom.
FIGURE 4
FIGURE 4
Overall deAMPylation mechanism with FICD in the wild type (A) and Glu234Ala mutants (B).
See this image and copyright information in PMC

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