3NV9 | pdb_00003nv9

Crystal structure of Entamoeba histolytica Malic Enzyme

• PDB DOI: https://doi.org/10.2210/pdb3NV9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-08 Released: 2011-07-20 
• Deposition Author(s): Dutta, D., Chakrabarty, A., Ghosh, S.K., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Metronidazole Activation by a Deeply Entangled Dimeric Malic Enzyme in Entamoeba histolytica.

Chakrabarty, A., Dutta, D., Baidya, M., Dutta, A., Das, A.K., Ghosh, S.K.

(2025) Pathogens 14

• PubMed: 40137762 
• DOI: https://doi.org/10.3390/pathogens14030277
• Primary Citation of Related Structures:  
  3NV9


• PubMed Abstract: 
  

  Metronidazole is the preferred drug for treating amoebiasis caused by Entamoeba histolytica . Its antiamoebic activity is primarily attributed to activation by various reductases. This study reports an alternative activation pathway in E. histolytica mediated by the decarboxylating malic enzyme. Functional characterization of this NADPH-dependent enzyme reveals that it is secreted into the extracellular milieu and may play a role in E. histolytica adhesion to human enteric cells. Structural analysis of the E. histolytica malic enzyme (EhME) demonstrates that the protein forms a strict dimer, with the protomers interlocked by a unique knot structure formed by two polypeptide chains. This distinctive structural feature closely aligns EhME with its prokaryotic counterparts. In conclusion, our findings reveal that E. histolytica harbors a deeply entangled dimeric malic enzyme that contributes to metronidazole susceptibility, sharing structural similarities with bacterial malic enzymes.

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Organizational Affiliation: 
• Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, India.
Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu and Kashmir 181221, India.
Department of Biological Sciences, Adamas University, Kolkata 700126, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 109.17 kDa 
• Atom Count: 8,185 
• Modeled Residue Count: 972 
• Deposited Residue Count: 974 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malic enzyme	A, B	487	Entamoeba histolytica	Mutation(s): 0  Gene Names: EHI_044970, EhME EC: 1.1.1.40
UniProt
Find proteins for Q9NH04 (Entamoeba histolytica) Explore Q9NH04  Go to UniProtKB:  Q9NH04

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth B], DA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	BA [auth B], CA [auth B], O [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	J [auth A], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.731	α = 90
b = 117.731	β = 90
c = 157.615	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Dutta, D., Chakrabarty, A., Ghosh, S.K., Das, A.K.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2025-06-25
  Changes: Database references, Structure summary