Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 56445.66 
• Atom Count: 4073 
• Residue Count: 496 
• Unique protein chains: 1

2VFH

Crystal structure of the F96W mutant of Plasmodium falciparum triosephosphate isomerase complexed with 3-phosphoglycerate

• DOI: 10.2210/pdb2VFH/pdb

• Classification: ISOMERASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2007-11-04 Released: 2008-12-09 
• Deposition Author(s): Gayathri, P., Banerjee, M., Vijayalakshmi, A., Balaram, H., Balaram, P., Murthy, M.R.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.245 
• R-Value Work: 0.193 

Literature

Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer-Interface Ligand-Binding Site.

Gayathri, P., Banerjee, M., Vijayalakshmi, A., Balaram, H., Balaram, P., Murthy, M.R.N.

(2009) Acta Crystallogr.,Sect.D 65: 847

• PubMed: 19622869 
• DOI: 10.1107/S0907444909018666
• Primary Citation of Related Structures:  
  2VFI, 2VFG, 2VFF, 2VFE, 2VFD


• PubMed Abstract: 
  

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K(m) values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant; (1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

---

Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRIOSEPHOSPHATE ISOMERASE	A, B	248	Plasmodium falciparum	Mutation(s): 2  Gene Names: TPI EC: 5.3.1.1
Find proteins for Q07412 (Plasmodium falciparum) Go to UniProtKB:  Q07412

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3PG	A, B	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.245 
• R-Value Work: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.543	α = 90.00
b = 51.182	β = 92.40
c = 86.568	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	phasing
SCALEPACK	data scaling
REFMAC	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-04 
• Released Date: 2008-12-09 
• Deposition Author(s): Gayathri, P., Banerjee, M., Vijayalakshmi, A., Balaram, H., Balaram, P., Murthy, M.R.N.

Revision History 

• Version 1.0: 2008-12-09
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance