Structure of Plasmodium falciparum Triose-phosphate Isomerase-2-Phosphoglycerate Complex at 1.1-Å Resolution

Abstract

Triose-phosphate isomerase, a key enzyme of the glycolytic pathway, catalyzes the isomerization of dihydroxy acetone phosphate and glyceraldehyde 3-phosphate. In this communication we report the crystal structure of Plasmodium falciparum triose-phosphate isomerase complexed to the inhibitor 2-phosphoglycerate at 1.1-Å resolution. The crystallographic asymmetric unit contains a dimeric molecule. The inhibitor bound to one of the subunits in which the flexible catalytic loop 6 is in the open conformation has been cleaved into two fragments presumably due to radiation damage. The cleavage products have been tentatively identified as 2-oxoglycerate and meta-phosphate. The intact 2-phosphoglycerate bound to the active site of the other subunit has been observed in two different orientations. The active site loop in this subunit is in both open and "closed" conformations, although the open form is predominant. Concomitant with the loop closure, Phe-96, Leu-167, and residues 208 -211 (YGGS) are also observed in dual conformations in the B-subunit. Detailed comparison of the active-site geometry in the present case to the Saccharomyces cerevisiae triose-phosphate isomerase-dihydroxy acetone phosphate and Leishmania mexicana triose-phosphate isomerase-phosphoglycolate complexes, which have also been determined at atomic resolution, shows that certain interactions are common to the three structures, although 2-phosphoglycerate is neither a substrate nor a transition state analogue. Triose-phosphate isomerase (TIM)1 is a ubiquitous glycolytic enzyme that catalyzes the isomerization of dihydroxy acetone phosphate (DHAP) and glyceraldehyde 3-phosphate through the intermediate formation of cis-enediol(ate(s)). Commenting on the catalytic efficiency of TIM, Knowles (1) states "This enzyme (TIM) appears to have arrived at the end of its evolutionary development as a catalyst." It has been argued that the evolutionary pressure for TIM to be a perfect catalyst has been intense, since for "flight or fight" there is an instant requirement for muscle ATP. The catalytic reaction of TIM is chemically simple and involves intermolecular protonation and deprotonation between the enzyme and substrate. The enzyme achieves the proton transfers with the help of certain elements as catalytic tools, a 10-residue loop that closes over the active site and stabilizes the reaction intermediate and a catalytic base and an acid to perform the enolization steps (1). It is believed that catalysis is a result of stronger binding of the enzyme to its transition state than to the initial enzyme-substrate complex (2). Although various schemes for this reaction have been proposed (for a review of the schemes, see Cui and Karplus (3)), the most frequently discussed mechanism is the one that involves Glu-165 as the catalytic base in the first proton transfer and His-95 as the catalytic acid for the rest of the reaction (3) (Fig. 1a). Despite numerous experimental (4 -9) and theoretical studies (10, 11), the precise mechanism of the multi-step reaction cataly...

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

“…For seven of these, the high deviation from planarity is maintained despite mutation of the residue. For one of the 16 cases [PDB code 1o5x:Phe150 (26)(27)(28)], the local backbone conformation in the homolog changed, and the nonplanarity was not conserved.…”

Structure of triosephosphate isomerase fromCryptosporidium parvum

“…The open conformation is typically found in apo structures. However, in P. falciparum TIM both open and closed conformations can be observed in a high-resolution (1.1 Å ) ligand-bound structure (Parthasarathy et al, 2003).…”

“…The open form has been observed for apo TIM, while ligand binding induces the closure of a loop. However, one ligand-bound structure of TIM from Plasmodium falciparum has been described with both an open and a closed conformation of the loop (Parthasarathy et al, 2003).…”

Structures of Unliganded and Inhibitor Complexes of W168F, a Loop6 Hinge Mutant of Plasmodium falciparum Triosephosphate Isomerase: Observation of an Intermediate Position of Loop6

“…Earlier studies of PfTIM [12][13][14] have shown that the loop6 predominantly occurs in the open conformation, in contrast to other TIMs where it closes on ligand binding when bound to ligands such as glycerol-3-phosphate (G3P), 15 3-phosphoglycerate (3PG), 15 2-phosphoglycolate (PGA) [16][17][18][19][20] and 2-phosphoglycerate (2PG). 21 Loop6 is also in an open conformation in the Trypanosoma brucei enzyme, where the active site has a bound N-hydroxy-4-phosphono-butanamide, 9 which has an additional methylene unit compared to the substrate.…”