Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei

Abstract

Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7 Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.

Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic Bacteria Synechocystis

“…The topology of this tree also suggests that TPIs from green algae, like C. reinhardtii , have followed a distinct evolutionary trajectory in comparison to plastidic TPI form land plants (Figure 2B ). A superimposition of the crystal structure of SyTPI with TPIs crystalized in the absence of ligand (AtcTPI and AtpdTPI) (Figure 2C ) illustrates that SyTPI exhibits a closed loop 6 conformation (Mande et al, 1994 ; Lopez-Zavala et al, 2016 ). This superposition also indicates that the secondary structural elements of SyTPI are virtually identical between photosynthetic TPIs.…”

A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease

“…through unfolding experiments concluded that this residue 45 in TvTIMs controls the dimer‐monomer equilibrium . In whiteleg shrimp ( Litopenaeus vannamei ) residue 47 ( 45 ) is a C, involved in intersubunit contact, the mutation C47A ( 45 ) has a very similar catalytic efficiency but is less stable in experiments of thermal denaturation . See also 17 . Residue 47 ( 46 ) is a H in TbTIM.…”

Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites

“…A single dataset was integrated and scaled using XDS and XSCALE respectively [30]. Phases were solved by molecular replacement using the program PHASER [31] and the crystal structure of TPI from Litopenaeus vannamei [49] as a search model. Initial model and refinement were executed using COOT and PHENIX.…”