2OMA

Crystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA)

• PDB DOI: https://doi.org/10.2210/pdb2OMA/pdb

• Classification: ISOMERASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-21 Released: 2007-11-20 
• Deposition Author(s): Rodriguez-Romero, A., Gomez-Puyou, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.250 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi.

Olivares-Illana, V., Rodriguez-Romero, A., Becker, I., Berzunza, M., Garcia, J., Perez-Montfort, R., Cabrera, N., Lopez-Calahorra, F., de Gomez-Puyou, M.T., Gomez-Puyou, A.

(2007) PLoS Negl Trop Dis 1: e1-e1

• PubMed: 17989778 
• DOI: https://doi.org/10.1371/journal.pntd.0000001
• Primary Citation of Related Structures:  
  2OMA


• PubMed Abstract: 
  

  Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM), and tested if they kill the parasite.

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Organizational Affiliation: 

Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 56.04 kDa 
• Atom Count: 4,210 
• Modelled Residue Count: 500 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	250	Trypanosoma cruzi	Mutation(s): 1  EC: 5.3.1.1
UniProt
Find proteins for P52270 (Trypanosoma cruzi) Explore P52270  Go to UniProtKB:  P52270

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	N [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth A], I [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CS1	A, B	L-PEPTIDE LINKING	C9 H12 N2 O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.250 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.206	α = 90
b = 75.337	β = 90
c = 146.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Rodriguez-Romero, A., Gomez-Puyou, A.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description