2VFH

Crystal structure of the F96W mutant of Plasmodium falciparum triosephosphate isomerase complexed with 3-phosphoglycerate

Summary for 2VFH

• Entry DOI: 10.2210/pdb2vfh/pdb
• Related: 1LYX 1LZO 1M7O 1M7P 1O5X 1VGA 1WOA 1WOB 1YDV 2VFD 2VFE 2VFF 2VFG 2VFI
• Descriptor: TRIOSEPHOSPHATE ISOMERASE, 3-PHOSPHOGLYCERIC ACID (3 entities in total)
• Functional Keywords: plasmodium falciparum, fatty acid biosynthesis, triosephosphate isomerase, pentose shunt, gluconeogenesis, lipid synthesis, tim, mutant, loop open, isomerase, glycolysis
• Biological source: PLASMODIUM FALCIPARUM (MALARIAL PARASITE)
• Total number of polymer chains: 2
• Total formula weight: 56445.66

Authors

Gayathri, P.,Banerjee, M.,Vijayalakshmi, A.,Balaram, H.,Balaram, P.,Murthy, M.R.N. (deposition date: 2007-11-04, release date: 2008-12-09, Last modification date: 2023-12-13)

Primary citation

Gayathri, P.,Banerjee, M.,Vijayalakshmi, A.,Balaram, H.,Balaram, P.,Murthy, M.R.N.
Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer-Interface Ligand-Binding Site.
Acta Crystallogr.,Sect.D, 65:847-, 2009

PubMed Abstract: Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K(m) values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant; (1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

PubMed: 19622869
DOI: 10.1107/S0907444909018666

Experimental method

X-RAY DIFFRACTION (2 Å)