Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 53.90 kDa 
• Atom Count: 3867 
• Modelled Residue Count: 498 
• Deposited Residue Count: 500 
• Unique protein chains: 1

6TIM

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

• PDB DOI: 10.2210/pdb6TIM/pdb

• Classification: ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
• Organism(s): Trypanosoma brucei brucei
• Mutation(s): No 


• Deposited: 1991-04-23 Released: 1992-10-15 
• Deposition Author(s): Noble, M.E.M., Wierenga, R.K., Hol, W.G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.370 

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

• PubMed: 2062828 
• DOI: 10.1002/prot.340100106
• Primary Citation of Related Structures:  
  1IIG, 1IIH, 6TIM


• 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 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: 

• 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

• 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

• 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

• 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

• 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

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIOSEPHOSPHATE ISOMERASE	A, B	250	Trypanosoma brucei brucei	Mutation(s): 0  EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei) Explore P04789  Go to UniProtKB:  P04789

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3P	C [auth B]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G3P	PDBBind:  6TIM	Ki: 6.10e+5 (nM) from 1 assay(s)
	Binding MOAD:  6TIM	Ki: 6.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Observed: 0.370 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.36	α = 90
b = 97.59	β = 90
c = 46.65	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1991-04-23 
• Released Date: 1992-10-15 
Deposition Author(s): Noble, M.E.M., Wierenga, R.K., Hol, W.G.J.

Revision History  

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