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

Protein Science : a Publication of the Protein Society
D MorikisJ Andrew McCammon

Abstract

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 approximately 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(a)s 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(a)s 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 recon...Continue Reading

References

Mar 20, 1992·Journal of Molecular Biology·D Bashford, K Gerwert
Jul 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R J AlmassyZ Hostomska
Mar 1, 1990·Journal of Molecular Graphics·G Vriend
Mar 1, 1993·Proteins·A S YangB Honig
May 26, 1995·Science·B Honig, A Nicholls
May 6, 1994·Journal of Molecular Biology·J AntosiewiczM K Gilson
May 20, 1993·Journal of Molecular Biology·A S Yang, B Honig
Jun 18, 1996·Biochemistry·J AntosiewiczM K Gilson
Feb 1, 1996·Journal of Molecular Graphics·R KoradiK Wüthrich
Oct 11, 1996·Journal of Molecular Biology·C A Mullen, P A Jennings
Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·G J Kleywegt, T A Jones
Sep 2, 1999·Protein Engineering·J E NielsenR C Wade
Dec 14, 1999·European Biophysics Journal : EBJ·G M Ullmann, E W Knapp
Oct 18, 2001·Protein Science : a Publication of the Protein Society·D MorikisJ A McCammon

❮ Previous
Next ❯

Citations

Sep 23, 2003·Biophysical Chemistry·Dimitrios MorikisJ Andrew McCammon
Jul 4, 2009·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Yu-He LiangLan-Fen Li
Oct 18, 2001·Protein Science : a Publication of the Protein Society·D MorikisJ A McCammon
Oct 19, 2006·Journal of Molecular Graphics & Modelling·Thanyada RungrotmongkolSupa Hannongbua
Jun 10, 2004·The Journal of Immunology : Official Journal of the American Association of Immunologists·Dimitrios Morikis, John D Lambris
Oct 19, 2004·The Journal of Biological Chemistry·Madan KatragaddaJohn D Lambris
Apr 13, 2011·Biotechnology Progress·Chris A KieslichDimitrios Gunopulos
Aug 6, 2021·The Journal of Physical Chemistry. B·Pancham Lal GuptaAdrian E Roitberg

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.