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Proton transfer dynamics of GART: The pH-dependent catalytic mechanism examined by electrostatic calculations

¹ Department of Chemical and Environmental Engineering, University of California at Riverside, Riverside, California 92521-0444, USA
² Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242-1109, USA
³ Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, USA
⁴ Department of Pharmacology and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365, USA

Reprint requests to: Dimitrios Morikis, Department of Chemical and Environmental Engineering, University of California at Riverside, Riverside, CA 92521-0444, USA; e-mail: dmorikis{at}engr.ucr.edu; fax: (909) 787-2425.

The enzyme glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (fTHF) to glycinamide ribonucleotide (GAR), a process that is pH-dependent with pK_a of 8. Experimental studies of pH-rate profiles of wild-type and site-directed mutants of GART have led to the proposal that His108, Asp144, and GAR are involved in catalysis, with His108 being an acid catalyst, while forming a salt bridge with Asp144, and GAR being a nucleophile to attack the formyl group of fTHF. This model implied a protonated histidine with pK_a of 9.7 and a neutral GAR with pK_a of 6.8. These proposed unusual pK_as have led us to investigate the electrostatic environment of the active site of GART. We have used Poisson-Boltzmann-based electrostatic methods to calculate the pK_as of all ionizable groups, using the crystallographic structure of a ternary complex of GART involving the pseudosubstrate 5-deaza-5,6,7,8-THF (5dTHF) and substrate GAR. Theoretical mutation and deletion analogs have been constructed to elucidate pairwise electrostatic interactions between key ionizable sites within the catalytic site. Also, a construct of a more realistic catalytic site including a reconstructed pseudocofactor with an attached formyl group, in an environment with optimal local van der Waals interactions (locally minimized) that imitates closely the catalytic reactants, has been used for pK_a calculations. Strong electrostatic coupling among catalytic residues His108, Asp144, and substrate GAR was observed, which is extremely sensitive to the initial protonation and imidazole ring flip state of His108 and small structural changes. We show that a proton can be exchanged between GAR and His108, depending on their relative geometry and their distance to Asp144, and when the proton is attached on His108, catalysis could be possible. Using the formylated locally minimized construct of GART, a high pK_a for His108 was calculated, indicating a protonated histidine, and a low pK_a for GAR(NH₂) was calculated, indicating that GAR is in neutral form. Our results are in qualitative agreement with the current mechanistic picture of the catalytic process of GART deduced from the experimental data, but they do not reproduce the absolute magnitude of the pK_as extracted from fits of k_cat-pH profiles, possibly because the static time-averaged crystallographic structure does not describe adequately the dynamic nature of the catalytic site during binding and catalysis. In addition, a strong effect on the pK_a of GAR(NH₂) is produced by the theoretical mutations of His108Ala and Asp144Ala, which is not in agreement with the observed insensitivity of the pK_a of GAR(NH₂) modeled from the experimental data using similar mutations. Finally, we show that important three-way electrostatic interactions between highly conserved His137, with His108 and Asp144, are responsible for stabilizing the electrostatic microenvironment of the catalytic site. In conclusion, our data suggest that further detailed computational and experimental work is necessary.

Abbreviations: GAR, glycinamide ribonucleotide • GART, GAR transformylase • fGAR, formyl-GAR • THF, tetrahydrofolate • fTHF, N¹⁰-formyl-THF • 5dTHF, 5-deaza-5,6,7,8-THF • 5dfTHF, formylated 5dTHF • fDDF, N¹⁰-formyl-5,8-dideazafolate • PDB, Protein Data Bank

Keywords: GART; glycinamide ribonucleotide transformylase; electrostatic calculations; Poisson-Boltzmann; pKa; catalysis

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