1QDS

SUPERSTABLE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE (TIM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.

Lambeir, A.M.Backmann, J.Ruiz-Sanz, J.Filimonov, V.Nielsen, J.E.Kursula, I.Norledge, B.V.Wierenga, R.K.

(2000) Eur.J.Biochem. 267: 2516-2524


  • PubMed Abstract: 
  • The amino acid sequence of Leishmania mexicana triose phosphate isomerase is unique in having at position 65 a glutamic acid instead of a glutamine. The stability properties of LmTIM and the E65Q mutant were investigated by pH and guanidinium chlorid ...

    The amino acid sequence of Leishmania mexicana triose phosphate isomerase is unique in having at position 65 a glutamic acid instead of a glutamine. The stability properties of LmTIM and the E65Q mutant were investigated by pH and guanidinium chloride-induced unfolding. The crystal structure of E65Q was determined. Three important observations were made: (a) there are no structural rearrangements as the result of the substitution; (b) the mutant is more stable than the wild-type; and (c) the stability of the wild-type enzyme shows strong pH dependence, which can be attributed to the ionization of Glu65. Burying of the Glu65 side chain in the uncharged environment of the dimer interface results in a shift in pKa of more than 3 units. The pH-dependent decrease in overall stability is due to weakening of the monomer-monomer interactions (in the dimer). The E65Q substitution causes an increase in stability as the result of the formation of an additional hydrogen bond in each subunit (DeltaDeltaG degrees of 2 kcal.mol-1 per monomer) and the elimination of a charged group in the dimer interface (DeltaDeltaG degrees of at least 9 kcal.mol-1 per dimer). The computated shift in pKa and the stability of the dimer calculated from the charge distribution in the protein structure agree closely with the experimental results. The guanidinium chloride dependence of the unfolding constant was smaller than expected from studies involving monomeric model proteins. No intermediates could be identified in the unfolding equilibrium by combining fluorescence and CD measurements. Study of a stable monomeric triose phosphate isomerase variant confirmed that the phenomenon persists in the monomer.


    Related Citations: 
    • Structural and Mutagenesis Studies of Leishmania Triosephosphate Isomerase: a Point Mutation Can Convert a Mesophilic Enzyme into a Superstable Enzyme without Losing Catalytic Power
      Williams, J.C.,Zeelen, J.P.,Neubauer, G.,Vriend, G.,Backmann, J.,Michels, P.A.M.,Lambeir, A.-M.,Wierenga, R.
      (1999) Protein Eng. 12: 243


    Organizational Affiliation

    Laboratory for Medical Biochemistry, University of Antwerp (UIA), Wilrijk, Belgium. lambeir@uia.ua.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A
251Leishmania mexicanaMutation(s): 1 
EC: 5.3.1.1
Find proteins for P48499 (Leishmania mexicana)
Go to UniProtKB:  P48499
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download SDF File 
Download CCD File 
A
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PGAKi: 48000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.260α = 90.00
b = 52.790β = 118.09
c = 58.880γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Database references, Experimental preparation