Structures ofPlasmodium vivaxserine hydroxymethyltransferase: implications for ligand-binding specificity and functional control

Abstract

Plasmodiumparasites, the causative agent of malaria, rely heavily onde novofolate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) fromPlasmodiumspp., an enzyme involved in folate recycling and dTMP synthesis, has been shown to catalyze the conversion of L- and D-serine to glycine (Gly) in a THF-dependent reaction, the mechanism of which is not yet fully understood. Here, the crystal structures ofP. vivaxSHMT (PvSHMT) in a binary complex with L-serine and in a ternary complex with D-serine (D-Ser) and (6R)-5-formyltetrahydrofolate (5FTHF) provide clues to the mechanism underlying the control of enzyme activity. 5FTHF in the ternary-complex structure was found in the 6Rform, thus differing from the previously reported structures of SHMT–Gly–(6S)-5FTHF from other organisms. This suggested that the presence of D-Ser in the active site can alter the folate-binding specificity. Investigation of binding in the presence of D-Ser and the (6R)- or (6S)-5FTHF enantiomers indicated that both forms of 5FTHF can bind to the enzyme but that only (6S)-5FTHF gives rise to a quinonoid intermediate. Likewise, a large surface area with a highly positively charged electrostatic potential surrounding thePvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs. Furthermore, as inP. falciparumSHMT, a redox switch created from a cysteine pair (Cys125–Cys364) was observed. Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity ofPvSHMT.

Kinetic Mechanism and the Rate-limiting Step of Plasmodium vivax Serine Hydroxymethyltransferase

“…Currently, there are seven x-ray structures of SHMT ternary complexes with amino acid and folate analogues (PDB code number 1EQB (32), PDB code number 1DFO (33), PDB code number 1KL2 (34), PDB code number 2VGW (35), PDB code numbers 2W7H and 2W7M (36), and PDB code number and 2W7M (37)) including the recently published structure of PvSHMT in complex with D-serine and H 4 folate analogue (6R-5-CHO-H 4 folate) at 2.4-Å resolution (PDB code 4OYT) (38) (Fig. 9).…”

Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold

“…Molecular modeling with MOLOC, by using previously obtained co‐crystal structures with pyrazolopyran‐based inhibitors, was used to guide the structural modifications of the ligands. As shown in the schematic representation of the binding mode of carboxylate (+)‐ 18 at the active site of Pv SHMT (PDB ID: https://www.rcsb.org/structure/5GVN, 2.3 Å resolution) (Figure ), two sub‐pockets are distinguishable: the pyrazolopyran core binds into the pterin binding pocket, which normally hosts the pterin core of H 4 F (PDB ID: https://www.rcsb.org/structure/4OYT, 2.4 Å), whereas the bicyclic scaffold occupies the para ‐aminobenzoate ( p ABA) channel. The ligands reported herein feature a spirocyclic motif on the 4‐position of the pyran ring to address a small lipophilic pocket within the pterin binding site (see below).…”

“…The co‐crystals diffracted to 2.4, 2.3, 2.2, and 2.2 Å resolution, respectively, and belonged to the C 2 space group. The structures were solved by molecular replacement by using the coordinates of a chain A protomer of Pv SHMT (PDB ID: https://www.rcsb.org/structure/4OYT) as the template . Importantly, both active sites of Pv SHMT homodimer were populated with a ligand in each complex and the conformations of the ligands occupying the binding sites were very similar (Supporting Information, Section S5.1, Figures S13 and S14).…”

“…X‐ray diffraction data and refinement statistics are listed in the Supporting Information, Section S5.1, Table S3. The structure of Pv SHMT was determined by molecular replacement by using Phaser in the CCP4 suite with a chain A protomer of Pv SHMT coordinate (PDB ID: https://www.rcsb.org/structure/4OYT) as the template. Model building and structure refinement were performed by using Coot and Refmac5 .…”

“…Surprisingly, little attention has been paid to the inhibition of serine hydroxymethyltransferase (SHMT) for developing antimalarials. SHMT is involved in the folate biosynthesis cycle and is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (H 4 F) that leads to the formation of the one‐carbon carrier 5,10‐methylenetetrahydrofolate (5,10‐CH 2 ‐H 4 F) . To date, only a limited number of active substances have been tested against Plasmodium falciparum ( Pf ) and Plasmodium vivax ( Pv ) SHMT .…”