A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release

Abstract

Edited by Ruma BanerjeeHuman cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/⌬flap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/⌬flap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of ␤-hydroxyamino acid. hcSHMT/⌬flap was less sensitive to THF inhibition than the WT (K i of 0.65 and 0.27 mM THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/⌬flap, indicating that the flap is important for THF binding. hcSHMT/ ⌬flap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.Serine hydroxymethyltransferase (SHMT 2 ; EC 2.1.2.1.) is a pyridoxal 5Ј-phosphate (PLP)-dependent enzyme in which the PLP cofactor facilitates the reversible transfer of a hydroxymethyl group from L-serine to (6S)-tetrahydrofolate (THF) to yield glycine and 5,10-methylenetetrahydrofolate (5,10-CH 2 -THF) as products (1-3). SHMT is one of the enzymes in the deoxythymidylate (dTMP) synthesis cycle in which the other two enzymes, thymidylate synthase (TS) and dihydrofolate reductase (DHFR), also take part in the recycling of folate compounds and production of 5,10-CH 2 -THF via the SHMT reaction. 5,10-CH 2 -THF serves as a methyl donor for the TS reaction to convert dUMP to dTMP, which is a requisite precursor for DNA biosynthesis (4). Due to its important role in DNA biosynthesis, cell proliferation, and cell survival, SHMT is one of the attractive targets for antimalarial (5-12) and anticancer chemotherapy (10,(13)(14)(15)(16).

Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode

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“…Fitting of the initial velocity data to the Michaelis-Menten model returned a K m,L-Ser of 240 Ϯ 30 M (Table 1). These kinetic parameters are also similar to those of the human enzyme using the same assay (35).…”

Shmt2: A Stat3 Signaling New Player in Prostate Cancer Energy Metabolism

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Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii

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