4YWI

F96S/L167V Double mutant of Plasmodium Falciparum Triosephosphate Isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme

Pareek, V.Samanta, M.Joshi, N.V.Balaram, H.Murthy, M.R.N.Balaram, P.

(2016) Chembiochem 17: 620-629

  • DOI: 10.1002/cbic.201500532
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon subs ...

    Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position 96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residue--phenylalanine--at this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue 96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Triosephosphate isomerase
A, B
248Plasmodium falciparumMutation(s): 3 
Gene Names: TPI
EC: 5.3.1.1
Find proteins for Q07412 (Plasmodium falciparum)
Go to UniProtKB:  Q07412
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.933α = 90.00
b = 53.809β = 90.00
c = 174.495γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of BiotechnologyIndia--

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references