6TIM

THE ADAPTABILITY OF THE ACTIVE SITE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE AS OBSERVED IN THE CRYSTAL STRUCTURES OF THREE DIFFERENT COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes.

Noble, M.E.Wierenga, R.K.Lambeir, A.M.Opperdoes, F.R.Thunnissen, A.M.Kalk, K.H.Groendijk, H.Hol, W.G.

(1991) Proteins 10: 50-69

  • DOI: 10.1002/prot.340100106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystals of triosephosphate isomerase from Trypanosoma brucei brucei have been used in binding studies with three competitive inhibitors of the enzyme's activity. Highly refined structures have been deduced for the complexes between trypanosomal trio ...

    Crystals of triosephosphate isomerase from Trypanosoma brucei brucei have been used in binding studies with three competitive inhibitors of the enzyme's activity. Highly refined structures have been deduced for the complexes between trypanosomal triosephosphate isomerase and a substrate analogue (glycerol-3-phosphate to 2.2 A), a transition state analogue (3-phosphonopropionic acid to 2.6 A), and a compound structurally related to both (3-phosphoglycerate to 2.2 A). The active site structures of these complexes were compared with each other, and with two previously determined structures of triosephosphate isomerase either free from inhibitor or complexed with sulfate. The comparison reveals three conformations available to the "flexible loop" near the active site of triosephosphate isomerase: open (no ligand), almost closed (sulfate), and fully closed (phosphate/phosphonate complexes). Also seen to be sensitive to the nature of the active site ligand is the catalytic residue Glu-167. The side chain of this residue occupies one of two discrete conformations in each of the structures so far observed. A "swung out" conformation unsuitable for catalysis is observed when sulfate, 3-phosphoglycerate, or no ligand is bound, while a "swung in" conformation ideal for catalysis is observed in the complexes with glycerol-3-phosphate or 3-phosphonopropionate. The water structure of the active site is different in all five structures. The results are discussed with respect to the triosephosphate isomerase structure function relationship, and with respect to an on-going drug design project aimed at the selective inhibition of glycolytic enzymes of T. brucei.


    Related Citations: 
    • Structure Determination of the Glycosomal Triosephosphate Isomerase from Trypanosoma Brucei Brucei at 2.4 Angstroms Resolution
      Wierenga, R.K.,Kalk, K.H.,Hol, W.G.J.
      (1987) J.Mol.Biol. 198: 109
    • The Crystal Structure of the "Open" and the "Closed" Conformation of the Flexible Loop of Trypanosomal Triosephosphate Isomerase
      Wierenga, R.K.,Noble, M.E.M.,Postma, J.P.M.,Groendijk, H.,Kalk, K.H.,Hol, W.G.J.,Opperdoes, F.R.
      (1991) Proteins 10: 33
    • Preliminary Crystallographic Studies of Triosephosphate Isomerase from the Blood Parasite Trypanosoma Brucei Brucei
      Wierenga, R.K.,Hol, W.G.J.,Misset, O.,Opperdoes, F.R.
      (1984) J.Mol.Biol. 178: 487
    • Crystallographic and Molecular Modeling Studies on Trypanosomal Triosephosphate Isomerase: A Critical Assessment of the Predicted and Observed Structures of the Complex with 2-Phosphoglycerate
      Noble, M.E.M.,Verlinde, C.L.M.J.,Groendijk, H.,Kalk, K.H.,Wierenga, R.K.,Hol, W.G.J.
      (1991) J.Med.Chem. 34: 2709
    • Refined 1.83 Angstroms Structure of Trypanosomal Triosephosphate Isomerase Crystallized in the Presence of 2.4 M-Ammonium Sulphate. A Comparison with the Structure of the Trypanosomal Triosephosphate Isomerase-Glycerol-3-Phosphate Complex
      Wierenga, R.K.,Noble, M.E.M.,Vriend, G.,Nauche, S.,Hol, W.G.J.
      (1991) J.Mol.Biol. 220: 995


    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A, B
250Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.3.1.1
Find proteins for P04789 (Trypanosoma brucei brucei)
Go to UniProtKB:  P04789
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3P
Query on G3P

Download SDF File 
Download CCD File 
B
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G3PKi: 610000 nM BINDINGMOAD
G3PKi: 610000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 112.360α = 90.00
b = 97.590β = 90.00
c = 46.650γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance