8J7C

Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57

Replaces:  5CG7

Summary for 8J7C

• Entry DOI: 10.2210/pdb8j7c/pdb
• Descriptor: Triosephosphate isomerase, ARSENIC (3 entities in total)
• Functional Keywords: triosephosphate isomerase, tim-barrel, dimer, an arsenic atom bound at cys57, isomerase
• Biological source: Leishmania orientalis
• Total number of polymer chains: 2
• Total formula weight: 58638.81

Authors

Kuaprasert, B.,Attarataya, J.,Riangrungroj, P.,Pornthanakasem, W.,Suginta, W.,Mungthin, M.,Leelayoova, S.,Choowongkomon, K.,Leartsakulpanich, U. (deposition date: 2023-04-27, release date: 2024-05-01, Last modification date: 2026-01-21)

Primary citation

Kuaprasert, B.,Leartsakulpanich, U.,Riangrungroj, P.,Pornthanakasem, W.,Suginta, W.,Mungthin, M.,Leelayoova, S.,Kiriwan, D.,Choowongkomon, K.
Crystal structure of Leishmania orientalis triosephosphate isomerase at 1.88 angstrom resolution and its specific inhibitors.
Biochimie, 233:27-35, 2025

PubMed Abstract: Leishmania orientalis, previously called L. siamensis, is a new species characterized as causing cutaneous leishmaniasis in Thailand. This study solves the crystal structure of the L. orientalis triosephosphate isomerase (LoTIM) in apo form at 1.88 Å resolution by using molecular replacement method. Tyrosine118 presents in the LoTIM protein sequence, whereas L. mexicana and Trypanosoma cruzi TIMs have a relative Cys118, which plays a major role in their specific ligand binding. Sulfur atom of the Cys57 thiol group is covalently bound to an arsenic (As) atom present in the precipitating solution. Although the electron density of loop-6 (Gly174-Tyr175-Gly176-Lys177-Val178) is missing in the structure due to this region lacking rigidity, the biological assembly of the two monomers of the LoTIM crystal structures are like that of L. mexicana and T. cruzi. 3D molecular protein-ligand docking was performed using the dimeric interfacial pocket of the enzyme as a ligand-binding receptor to identify its specific inhibitors. Five potential inhibiting compounds, including NSC639174, NSC606498, NSC110039, NSC58446, and NSC345647, were obtained with their IC 2.79 ± 0.10, 3.28 ± 0.80, 3.67 ± 0.11, 4.59 ± 0.87 and 15.44 ± 0.14 μM, respectively. However, specific inhibition assays against TIMs from L. orientalis and rabbit muscle indicate that NSC639174 and NSC110039 are the most potent inhibitors for LoTIM, whereas NSC58446 inhibits well both the parasitic and rabbit enzymes.

PubMed: 39984112
DOI: 10.1016/j.biochi.2025.02.004

Experimental method

X-RAY DIFFRACTION (1.88 Å)