Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition

Abstract

The folate and methionine cycles are crucial for biosynthesis of lipids, nucleotides and proteins, and production of the methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain. The latter domain of novel fold provides the predominant interface for MTHFR homo-dimerization, positioning the N-terminal serine-rich phosphorylation region near the C-terminal SAM-binding domain. This explains how MTHFR phosphorylation, identified on 11 N-terminal residues (16 in total), increases sensitivity to SAM binding and inhibition. Finally, we demonstrate that the 25-amino-acid inter-domain linker enables conformational plasticity and propose it to be a key mediator of SAM regulation. Together, these results provide insight into the molecular regulation of MTHFR.

Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism

“…The modeled yeast MTHFR structure aligns well with human MTHFR protein with rmsd value of 0.48 Å ( Figure S2), which exists as a homodimer with each monomer consisting of a catalytic domain and a regulatory domain ( Figure S3). The two monomers are held together by interactions of the regulatory domain, as has been reported for the human MTHFR (10).…”

“…We initially built a homology model of the yeast MTHFR, Met13p, based on the crystal structure of human MTHFR, which has been recently solved (10). The modeled yeast MTHFR structure aligns well with human MTHFR protein with rmsd value of 0.48 Å ( Figure S2), which exists as a homodimer with each monomer consisting of a catalytic domain and a regulatory domain ( Figure S3).…”

“…Among the probable SAM binding residues, two residues-E422 and Y404, appeared critical ( Figure 2B). E422 is the equivalent of the mammalian E463 that is predicted to be involved in binding to SAM (10). In the yeast MTHFR, Y404 also appeared to be critical since its benzyl ring can putatively interact with the aromatic ring of SAM around the hydrophobic region within the SAM binding pocket.…”

Vitamin B12, folate, and the methionine remethylation cycle—biochemistry, pathways, and regulation

“…SHMT1 protein levels, by contrast, are elevated during the S phase of HeLa cells, but without changes in mRNA levels. 115,116 Meanwhile, we found that phosphorylation of MTHFR leads to an increased sensitivity to AdoMet inhibition, 117 and the kinase responsible for this phosphorylation has been suggested to be the cyclin dependent kinase 1 (CDK1) in association with cyclin B1. 118 Together, these data provide a link between the cellcycle state and regulation of proteins involved in methionine cycle or the one-carbon metabolic pathway.…”

Click chemistry‐inspired design, synthesis, and molecular docking studies of biscoumarin derivatives using carbon‐based acid catalyst

“…The inhibition of this enzyme is helpful in the treatment of HIV infection 50 . Moreover, MTHFR having PDB ID 6FCX is concerned with the irreversible reduction of 5,10‐methylenetetrahydrofolate to 5‐methyl‐tetrahydrofolate that is indirectly involved in the biosynthesis of monophosphates and purines 51 . This target is believed to be essential for the investigation of anticancer drugs 52 …”