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- PDB-9fee: Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9fee
TitleCryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase
Componentsmalate dehydrogenase
KeywordsOXIDOREDUCTASE / Tetramer / Metabolic enzyme
Function / homology
Function and homology information


intracellular organelle lumen / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
malate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLipinski, O. / Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Patel, S.N. / Sood, T. / Dubin, G.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
Polish National Science Centre2020/39/B/NZ1/01551 Poland
Citation
Journal: Nat Commun / Year: 2025
Title: Structure of Trypanosoma peroxisomal import complex unveils conformational heterogeneity.
Authors: Ravi R Sonani / Artur Blat / Malgorzata Jemiola-Rzeminska / Oskar Lipinski / Stuti N Patel / Tabassum Sood / Grzegorz Dubin /
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 ...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.
#1: Journal: Biorxiv / Year: 2024
Title: Structure of Trypanosoma peroxisomal import complex unveils conformational dynamics
Authors: Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Lipinski, O. / Patel, S.N. / Sood, T. / Dubin, G.
History
DepositionMay 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: malate dehydrogenase
B: malate dehydrogenase
C: malate dehydrogenase
D: malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)140,5524
Polymers140,5524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
malate dehydrogenase


Mass: 35137.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Gene: Tc00.1047053506503.69 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4DRD8, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric complex of glycosomal malate dehydrogenase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 42.25 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312103 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049269
ELECTRON MICROSCOPYf_angle_d0.56512630
ELECTRON MICROSCOPYf_dihedral_angle_d4.41307
ELECTRON MICROSCOPYf_chiral_restr0.0461559
ELECTRON MICROSCOPYf_plane_restr0.0051621

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