9FEE

Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase

Summary for 9FEE

• Entry DOI: 10.2210/pdb9fee/pdb
• Related: 8GGD 8GGH 8GH2 8GH3 8GI0
• EMDB information: 50339
• Descriptor: malate dehydrogenase (1 entity in total)
• Functional Keywords: oxidoreductase, tetramer, metabolic enzyme
• Biological source: Trypanosoma cruzi strain CL Brener
• Total number of polymer chains: 4
• Total formula weight: 140551.92

Authors

Lipinski, O.,Sonani, R.R.,Blat, A.,Jemiola-Rzeminska, M.,Patel, S.N.,Sood, T.,Dubin, G. (deposition date: 2024-05-19, release date: 2024-05-29, Last modification date: 2026-01-14)

Primary citation

Sonani, R.R.,Blat, A.,Jemiola-Rzeminska, M.,Lipinski, O.,Patel, S.N.,Sood, T.,Dubin, G.
Structure of Trypanosoma peroxisomal import complex unveils conformational heterogeneity.
Nat Commun, 16:11398-11398, 2025

PubMed Abstract: Peroxisomes are membrane enclosed organelles hosting diverse metabolic processes in eukaryotic cells. Having no protein synthetic abilities, peroxisomes import all required enzymes from the cytosol through a peroxin (Pex) import system. Peroxisome targeting sequence 1 (PTS1)-tagged cargo is recognized by cytosolic receptor, Pex5. The cargo-Pex5 complex docks at the peroxisomal membrane translocon, composed of Pex14 and Pex13, facilitating translocation into the peroxisomal lumen. Despite its significance, the structural basis of the process is only partially understood. Here, we characterize the cargo-Pex5-Pex14 ternary complex from Trypanosoma cruzi. Cryo-electron microscopy maps enabled model building for Pex5 (residues 327-462 and 487-653) bound to malate dehydrogenase (MDH; residues 1-323) cargo tetramer and Pex14 (residues 21-85). The model provides insight into conformational heterogeneity and identifies secondary interfaces. Specifically, we observe that orientations of Pex5 relative to MDH span a 17° angle. Additionally, PTS1- and Wxxx(F/Y)-independent contact surfaces are observed at MDH-Pex5 and Pex5-Pex14 interfaces, respectively. Mutational analysis indicates that the non-PTS1 MDH-Pex5 interface does not significantly contribute to the affinity, but limits the conformational heterogeneity of MDH-Pex5 interface. The Pex5-Pex14 interface constitutes an extended binding site of Pex14 over Pex5. We discuss the implications of these findings for understanding peroxisomal import mechanism.

PubMed: 41381475
DOI: 10.1038/s41467-025-66207-8

Experimental method

ELECTRON MICROSCOPY (3.03 Å)